Mad1l1 (mitotic arrest deficient 1 like 1)

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Gene: Mad1l1 (mitotic arrest deficient 1 like 1) Rattus norvegicus

Analyze

Symbol:

Mad1l1

Name:

mitotic arrest deficient 1 like 1

RGD ID:

1596881

Description:

Predicted to enable identical protein binding activity and kinetochore binding activity. Predicted to be involved in several processes, including attachment of mitotic spindle microtubules to kinetochore; cytoplasmic sequestering of protein; and regulation of mitotic metaphase/anaphase transition. Predicted to act upstream of or within negative regulation of T cell proliferation; regulation of mitotic cell cycle phase transition; and thymus development. Predicted to be located in cytoplasm; nucleus; and spindle pole. Predicted to be part of nuclear pore nuclear basket. Predicted to be active in kinetochore; mitotic spindle; and nuclear envelope. Predicted to colocalize with mitotic spindle pole. Human ortholog(s) of this gene implicated in lymphoma and prostate cancer. Orthologous to human MAD1L1 (mitotic arrest deficient 1 like 1); PARTICIPATES IN cell cycle pathway, mitotic; INTERACTS WITH (+)-schisandrin B; acrylamide; bisphenol A.

Type:

protein-coding

RefSeq Status:

PROVISIONAL

Also known as:

LOC680006; MAD1 mitotic arrest deficient like 1; MAD1 mitotic arrest deficient-like 1; MAD1 mitotic arrest deficient-like 1 (yeast); mitotic arrest deficient 1-like 1; mitotic spindle assembly checkpoint protein MAD1; similar to Mitotic spindle assembly checkpoint protein MAD1 (Mitotic arrest deficient-like protein 1) (MAD1-like 1)

RGD Orthologs

Human

Mouse

Chinchilla

Bonobo

Dog

Squirrel

Pig

Green Monkey

Naked Mole-Rat

Alliance Genes

More Info

more info ...

More Info

Species	Gene symbol and name	Data Source	Assertion derived from	less info ...
Orthologs ¹				less info ...
Homo sapiens (human):	MAD1L1 (mitotic arrest deficient 1 like 1)	HGNC	EggNOG, Ensembl, HomoloGene, Inparanoid, NCBI, OMA, OrthoDB, OrthoMCL, Panther, PhylomeDB, Treefam
Mus musculus (house mouse):	Mad1l1 (MAD1 mitotic arrest deficient 1-like 1)	HGNC	Treefam, EggNOG, OrthoMCL, NCBI, OMA, HomoloGene, Inparanoid, Panther, PhylomeDB, OrthoDB, Ensembl
Chinchilla lanigera (long-tailed chinchilla):	Mad1l1 (mitotic arrest deficient 1 like 1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Pan paniscus (bonobo/pygmy chimpanzee):	MAD1L1 (mitotic arrest deficient 1 like 1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Canis lupus familiaris (dog):	MAD1L1 (mitotic arrest deficient 1 like 1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Ictidomys tridecemlineatus (thirteen-lined ground squirrel):	Mad1l1 (mitotic arrest deficient 1 like 1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Sus scrofa (pig):	MAD1L1 (mitotic arrest deficient 1 like 1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chlorocebus sabaeus (green monkey):	MAD1L1 (mitotic arrest deficient 1 like 1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Heterocephalus glaber (naked mole-rat):	Mad1l1 (mitotic arrest deficient 1 like 1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Alliance orthologs ³
Homo sapiens (human):	MAD1L1 (mitotic arrest deficient 1 like 1)	Alliance	DIOPT (Ensembl Compara\|HGNC\|Hieranoid\|InParanoid\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|TreeFam)
Mus musculus (house mouse):	Mad1l1 (MAD1 mitotic arrest deficient 1-like 1)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|TreeFam)
Danio rerio (zebrafish):	mad1l1 (mitotic arrest deficient 1 like 1)	Alliance	DIOPT (PhylomeDB\|TreeFam)
Saccharomyces cerevisiae (baker's yeast):	MAD1	Alliance	DIOPT (Hieranoid\|OrthoFinder\|PANTHER)
Drosophila melanogaster (fruit fly):	Mad1	Alliance	DIOPT (Hieranoid\|InParanoid\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB)
Caenorhabditis elegans (roundworm):	mdf-1	Alliance	DIOPT (Ensembl Compara\|InParanoid\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB)

Latest Assembly:

mRatBN7.2 - mRatBN7.2 Assembly

Position:

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
mRatBN7.2	12	14,320,892 - 14,630,750 (+)	NCBI	mRatBN7.2
mRatBN7.2 Ensembl	12	14,320,892 - 14,630,703 (+)	Ensembl
Rnor_6.0	12	16,410,083 - 16,721,232 (+)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	12	16,410,083 - 16,719,824 (+)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	12	18,402,692 - 18,711,591 (+)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	12	14,793,899 - 15,107,476 (+)	NCBI	RGSC3.4		rn4	RGSC3.4
Celera	12	16,079,638 - 16,388,296 (+)	NCBI		Celera
Cytogenetic Map	12	q11	NCBI

JBrowse:

View Region in Genome Browser (JBrowse)

Model

Annotation Click to see Annotation Detail View

Disease Annotations Click to see Annotation Detail View

Breast Neoplasms (ISO)

Familial Prostate Cancer (ISO)

juvenile rheumatoid arthritis (ISO)

lymphoma (ISO)

prostate cancer (ISO)

Prostate Cancer, Somatic (ISO)

Prostatic Neoplasms (ISO)

Testicular Germ Cell Tumor (ISO)

Gene-Chemical Interaction Annotations Click to see Annotation Detail View

(+)-schisandrin B (EXP)

1,2-dimethylhydrazine (ISO)

17alpha-ethynylestradiol (ISO)

17beta-estradiol (ISO)

17beta-hydroxy-17-methylestra-4,9,11-trien-3-one (ISO)

2,2',4,4',5,5'-hexachlorobiphenyl (ISO)

2,3,7,8-tetrachlorodibenzodioxine (ISO)

3-methylcholanthrene (ISO)

4-hydroxyphenyl retinamide (ISO)

5-azacytidine (ISO)

acrolein (ISO)

acrylamide (EXP)

aflatoxin B1 (ISO)

Aflatoxin B2 alpha (ISO)

all-trans-retinoic acid (ISO)

alpha-pinene (ISO)

arsane (ISO)

arsenic atom (ISO)

benzo[a]pyrene (ISO)

benzo[a]pyrene diol epoxide I (ISO)

benzo[e]pyrene (ISO)

bisphenol A (EXP,ISO)

carbon nanotube (ISO)

carmustine (ISO)

cisplatin (ISO)

copper(II) sulfate (ISO)

crocidolite asbestos (ISO)

Cuprizon (EXP)

cyclosporin A (ISO)

dibutyl phthalate (EXP)

doxorubicin (ISO)

endosulfan (EXP)

ethyl methanesulfonate (ISO)

formaldehyde (ISO)

genistein (ISO)

ivermectin (ISO)

methapyrilene (ISO)

methyl methanesulfonate (ISO)

N,N-diethyl-m-toluamide (EXP)

Nor-9-carboxy-delta9-THC (ISO)

O-methyleugenol (EXP,ISO)

oxaliplatin (EXP)

ozone (ISO)

permethrin (EXP)

phenobarbital (ISO)

phorbol 13-acetate 12-myristate (ISO)

pirinixic acid (ISO)

pregnenolone 16alpha-carbonitrile (ISO)

promethazine (EXP)

quercetin (ISO)

sodium arsenite (ISO)

tetrachloromethane (EXP)

thioacetamide (EXP)

topotecan (EXP)

triptonide (ISO)

tungsten (ISO)

valproic acid (ISO)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

attachment of mitotic spindle microtubules to kinetochore (IBA)

cytoplasmic sequestering of protein (ISO)

deactivation of mitotic spindle assembly checkpoint (ISO)

mitotic spindle assembly checkpoint signaling (IBA,ISO)

negative regulation of T cell proliferation (ISO)

positive regulation of mitotic cell cycle spindle assembly checkpoint (ISO)

regulation of metaphase plate congression (ISO)

regulation of mitotic cell cycle phase transition (ISO)

thymus development (ISO)

Cellular Component

cytoplasm (ISO)

kinetochore (IBA,ISO)

MAD1 complex (ISO)

mitotic spindle (IBA,ISO)

mitotic spindle assembly checkpoint MAD1-MAD2 complex (ISO)

mitotic spindle pole (ISO)

nuclear envelope (IBA,ISO)

nuclear pore nuclear basket (ISO)

nucleus (ISO)

spindle pole (ISO)

Molecular Function

identical protein binding (ISO)

kinetochore binding (ISO)

protein binding (ISO)

Molecular Pathway Annotations Click to see Annotation Detail View

cell cycle pathway, mitotic (IEA)

References

References - curated


1.	Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
2.	OMIM Disease Annotation Pipeline
3.	Pipeline to import KEGG annotations from KEGG into RGD
4.	RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
5.	RGD automated import pipeline for gene-chemical interactions

Additional References at PubMed

PMID:9130602	PMID:11313860	PMID:16189514	PMID:17363900	PMID:17504913	PMID:17938250	PMID:18981471	PMID:20133940	PMID:21558374	PMID:22351768	PMID:22493223	PMID:27107012

Genomics

Comparative Map Data

Mad1l1
(Rattus norvegicus - Norway rat)

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
mRatBN7.2	12	14,320,892 - 14,630,750 (+)	NCBI	mRatBN7.2
mRatBN7.2 Ensembl	12	14,320,892 - 14,630,703 (+)	Ensembl
Rnor_6.0	12	16,410,083 - 16,721,232 (+)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	12	16,410,083 - 16,719,824 (+)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	12	18,402,692 - 18,711,591 (+)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	12	14,793,899 - 15,107,476 (+)	NCBI	RGSC3.4		rn4	RGSC3.4
Celera	12	16,079,638 - 16,388,296 (+)	NCBI		Celera
Cytogenetic Map	12	q11	NCBI

MAD1L1
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38.p13 Ensembl	7	1,815,793 - 2,233,243 (-)	Ensembl	GRCh38		hg38	GRCh38
GRCh38	7	1,815,795 - 2,232,945 (-)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh37	7	1,855,431 - 2,272,580 (-)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	7	1,821,954 - 2,239,109 (-)	NCBI	NCBI36		hg18	NCBI36
Build 34	7	1,628,673 - 2,043,593	NCBI
Celera	7	1,824,029 - 2,242,272 (-)	NCBI
Cytogenetic Map	7	p22.3	NCBI
HuRef	7	1,775,090 - 2,191,874 (-)	NCBI		HuRef
CHM1_1	7	1,855,013 - 2,272,150 (-)	NCBI		CHM1_1
CRA_TCAGchr7v2	7	1,908,333 - 2,321,257 (-)	NCBI

Mad1l1
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	5	139,994,444 - 140,307,346 (-)	NCBI	GRCm39		mm39
GRCm39 Ensembl	5	139,994,444 - 140,307,307 (-)	Ensembl
GRCm38	5	140,008,689 - 140,321,608 (-)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	5	140,008,689 - 140,321,552 (-)	Ensembl	GRCm38		mm10	GRCm38
MGSCv37	5	140,484,643 - 140,797,506 (-)	NCBI	GRCm37		mm9	NCBIm37
MGSCv36	5	140,261,163 - 140,574,024 (-)	NCBI			mm8
Celera	5	137,065,976 - 137,380,304 (-)	NCBI		Celera
Cytogenetic Map	5	G2	NCBI
cM Map	5	78.82	NCBI

Mad1l1
(Chinchilla lanigera - long-tailed chinchilla)

Chinchilla Assembly	Chr	Position (strand)	Source	Genome Browsers
Chinchilla Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
ChiLan1.0 Ensembl	NW_004955460	9,340,681 - 9,672,134 (-)	Ensembl	ChiLan1.0
ChiLan1.0	NW_004955460	9,340,728 - 9,672,478 (-)	NCBI	ChiLan1.0	ChiLan1.0

MAD1L1
(Pan paniscus - bonobo/pygmy chimpanzee)

Bonobo Assembly	Chr	Position (strand)	Source	Genome Browsers
Bonobo Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
PanPan1.1	7	2,187,104 - 2,604,168 (-)	NCBI	panpan1.1	PanPan1.1	panPan2
PanPan1.1 Ensembl	7	2,187,104 - 2,601,328 (-)	Ensembl	panpan1.1		panPan2
Mhudiblu_PPA_v0	7	2,070,299 - 2,502,471 (-)	NCBI	Mhudiblu_PPA_v0		panPan3

MAD1L1
(Canis lupus familiaris - dog)

Dog Assembly	Chr	Position (strand)	Source	Genome Browsers
Dog Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
CanFam3.1	6	14,889,126 - 15,236,194 (+)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1
CanFam3.1 Ensembl	6	14,882,875 - 15,236,192 (+)	Ensembl	CanFam3.1		canFam3	CanFam3.1
Dog10K_Boxer_Tasha	6	16,351,128 - 16,704,460 (+)	NCBI
ROS_Cfam_1.0	6	15,015,423 - 15,362,579 (+)	NCBI
UMICH_Zoey_3.1	6	14,818,674 - 15,165,656 (+)	NCBI
UNSW_CanFamBas_1.0	6	14,745,470 - 15,092,432 (+)	NCBI
UU_Cfam_GSD_1.0	6	15,033,169 - 15,380,211 (+)	NCBI

Mad1l1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)

Squirrel Assembly	Chr	Position (strand)	Source	Genome Browsers
Squirrel Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
HiC_Itri_2	NW_024409344	143,053,218 - 143,167,762 (+)	NCBI
SpeTri2.0	NW_004936754	1,842,588 - 1,957,116 (-)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

MAD1L1
(Sus scrofa - pig)

Pig Assembly	Chr	Position (strand)	Source	Genome Browsers
Pig Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Sscrofa11.1 Ensembl	3	1,236,066 - 1,559,041 (-)	Ensembl	Sscrofa11.1		susScr11	Sscrofa11.1
Sscrofa11.1	3	1,236,066 - 1,559,346 (-)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1
Sscrofa10.2	3	1,859,406 - 1,883,565 (-)	NCBI	Sscrofa10.2	Sscrofa10.2	susScr3

MAD1L1
(Chlorocebus sabaeus - green monkey)

Green Monkey Assembly	Chr	Position (strand)	Source	Genome Browsers
Green Monkey Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
ChlSab1.1	28	19,358,942 - 19,768,079 (+)	NCBI	ChlSab1.1		chlSab2
ChlSab1.1 Ensembl	28	19,359,233 - 19,768,078 (+)	Ensembl	ChlSab1.1		chlSab2
Vero_WHO_p1.0	NW_023666090	1,956,015 - 2,370,489 (-)	NCBI	Vero_WHO_p1.0

Mad1l1
(Heterocephalus glaber - naked mole-rat)

Naked Mole-rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Naked Mole-rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
HetGla 1.0	NW_004624740	27,174,450 - 27,523,366 (-)	NCBI	HetGla_female_1.0		hetGla2

Position Markers

D12Got30

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	12	14,463,967 - 14,464,125 (+)	MAPPER	mRatBN7.2
Rnor_6.0	12	16,553,097 - 16,553,251	NCBI	Rnor6.0
Rnor_5.0	12	18,544,968 - 18,545,122	UniSTS	Rnor5.0
RGSC_v3.4	12	14,940,432 - 14,940,590	RGD	RGSC3.4
RGSC_v3.4	12	14,940,433 - 14,940,590	UniSTS	RGSC3.4
RGSC_v3.1	12	14,970,361 - 14,970,518	RGD
Celera	12	16,222,308 - 16,222,465	UniSTS
RH 3.4 Map	12	224.9	UniSTS
RH 3.4 Map	12	224.9	RGD
RH 2.0 Map	12	168.7	RGD
Cytogenetic Map	12	q11	UniSTS

RH130878

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	12	14,630,527 - 14,630,680 (+)	MAPPER	mRatBN7.2
Rnor_6.0	12	16,719,649 - 16,719,801	NCBI	Rnor6.0
Rnor_5.0	12	18,711,416 - 18,711,568	UniSTS	Rnor5.0
RGSC_v3.4	12	15,107,301 - 15,107,453	UniSTS	RGSC3.4
Celera	12	16,388,121 - 16,388,273	UniSTS
RH 3.4 Map	12	239.1	UniSTS
Cytogenetic Map	12	q11	UniSTS

QTLs in Region (mRatBN7.2)

The following QTLs overlap with this region.

RGD ID	Symbol	Name	LOD	P Value	Trait	Sub Trait	Chr	Start	Stop	Species
2312418	Kidm41	Kidney mass QTL 41	3.7	0.0001	kidney mass (VT:0002707)	single kidney wet weight to body weight ratio (CMO:0000622)	12	1	19611090	Rat
10755457	Coatc14	Coat color QTL 14		0.01759	coat/hair pigmentation trait (VT:0010463)	pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)	12	1	22591684	Rat
6893681	Bw109	Body weight QTL 109	2.3	0.004	body mass (VT:0001259)	body weight (CMO:0000012)	12	1	23297788	Rat
1581516	Cm56	Cardiac mass QTL 56	4.2	0.05	heart left ventricle mass (VT:0007031)	heart left ventricle weight to body weight ratio (CMO:0000530)	12	1	29333307	Rat
1598855	Bp294	Blood pressure QTL 294	3.5		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	12	1	34851688	Rat
7411660	Foco28	Food consumption QTL 28	10.9	0.001	eating behavior trait (VT:0001431)	feed conversion ratio (CMO:0001312)	12	1	42110980	Rat
9590086	Insglur6	Insulin/glucose ratio QTL 6	18.97	0.001	blood insulin amount (VT:0001560)	calculated plasma insulin level (CMO:0002170)	12	1	42110980	Rat
8694179	Bw150	Body weight QTL 150	2.9	0.001	body mass (VT:0001259)	body weight gain (CMO:0000420)	12	1	42110980	Rat
7411586	Foco5	Food consumption QTL 5	5.4	0.001	eating behavior trait (VT:0001431)	feed conversion ratio (CMO:0001312)	12	1	42110980	Rat
7411595	Foco9	Food consumption QTL 9	4	0.001	eating behavior trait (VT:0001431)	feed conversion ratio (CMO:0001312)	12	1	42110980	Rat
7411545	Bw128	Body weight QTL 128	5.2	0.001	body mass (VT:0001259)	body weight gain (CMO:0000420)	12	1	42110980	Rat
9590147	Scort7	Serum corticosterone level QTL 7	13.61	0.001	blood corticosterone amount (VT:0005345)	plasma corticosterone level (CMO:0001173)	12	1	42110980	Rat
2303575	Insul14	Insulin level QTL 14	4		blood insulin amount (VT:0001560)	blood insulin level (CMO:0000349)	12	1	42450532	Rat
737979	Pia22	Pristane induced arthritis QTL 22	53.1		joint integrity trait (VT:0010548)	joint inflammation composite score (CMO:0000919)	12	1	44465750	Rat
634351	Apr5	Acute phase response QTL 5	6.7		blood interleukin-6 amount (VT:0008595)	plasma interleukin-6 level (CMO:0001927)	12	1	44503507	Rat
2302042	Pia38	Pristane induced arthritis QTL 38	3.5	0.001	blood immunoglobulin amount (VT:0002460)	serum immunoglobulin G1 level (CMO:0002115)	12	1	44503507	Rat
634350	Apr4	Acute phase response QTL 4	6		orosomucoid 1 amount (VT:0010541)	plasma orosomucoid 1 level (CMO:0001467)	12	1172005	46172005	Rat
8552918	Pigfal7	Plasma insulin-like growth factor 1 level QTL 7			blood insulin-like growth factor amount (VT:0010479)	plasma insulin-like growth factor 1 level (CMO:0001299)	12	5564495	46669029	Rat
7411547	Bw129	Body weight QTL 129		0.001	body mass (VT:0001259)	body weight gain (CMO:0000420)	6	5564495	46669029	Rat
7411597	Foco10	Food consumption QTL 10		0.001	eating behavior trait (VT:0001431)	feed conversion ratio (CMO:0001312)	12	5564495	46669029	Rat
7411641	Foco19	Food consumption QTL 19	27.7	0.001	eating behavior trait (VT:0001431)	feed conversion ratio (CMO:0001312)	12	5564495	46669029	Rat
8552964	Pigfal17	Plasma insulin-like growth factor 1 level QTL 17	3.5		blood insulin-like growth factor amount (VT:0010479)	plasma insulin-like growth factor 1 level (CMO:0001299)	12	5564495	46669029	Rat
7411588	Foco6	Food consumption QTL 6		0.001	eating behavior trait (VT:0001431)	feed conversion ratio (CMO:0001312)	12	5564495	46669029	Rat
8552912	Pigfal6	Plasma insulin-like growth factor 1 level QTL 6	5		blood insulin-like growth factor amount (VT:0010479)	plasma insulin-like growth factor 1 level (CMO:0001299)	12	5564498	46669029	Rat
10059594	Kidm46	Kidney mass QTL 46	3.79	0.025	kidney mass (VT:0002707)	both kidneys wet weight to body weight ratio (CMO:0000340)	12	6107579	46669029	Rat
1600391	Edcs2	Endometrial carcinoma susceptibility QTL2	3.5	0.01	uterus morphology trait (VT:0001120)	percentage of study population developing endometrioid carcinoma during a period of time (CMO:0001759)	12	6833190	17870186	Rat
1302792	Scl21	Serum cholesterol level QTL 21	3.8	0.0011	blood cholesterol amount (VT:0000180)	plasma total cholesterol level (CMO:0000585)	12	7196730	46669029	Rat
2293086	Iddm30	Insulin dependent diabetes mellitus QTL 30	3.82		blood glucose amount (VT:0000188)	blood glucose level (CMO:0000046)	12	8449490	28302290	Rat
61331	Eau2	Experimental allergic uveoretinitis QTL 2		0.0005	uvea integrity trait (VT:0010551)	experimental autoimmune uveitis score (CMO:0001504)	12	8525423	28064601	Rat
1300157	Rf21	Renal function QTL 21	4.4		renal blood flow trait (VT:2000006)	absolute change in renal blood flow rate (CMO:0001168)	12	9318216	32103380	Rat
1549829	Scl48	Serum cholesterol level QTL 48	5		blood cholesterol amount (VT:0000180)	serum total cholesterol level (CMO:0000363)	12	9603277	46669029	Rat
2293699	Bss49	Bone structure and strength QTL 49	5.61	0.0001	lumbar vertebra size trait (VT:0010518)	lumbar vertebra trabecular cross-sectional area (CMO:0001692)	12	10474137	46669029	Rat
2300186	Bmd59	Bone mineral density QTL 59	7.1	0.0001	lumbar vertebra mineral mass (VT:0010511)	volumetric bone mineral density (CMO:0001553)	12	10474137	46669029	Rat
1331786	Kidm11	Kidney mass QTL 11	3.571		kidney mass (VT:0002707)	right kidney wet weight (CMO:0000082)	12	11073825	24234895	Rat
1331755	Bp219	Blood pressure QTL 219	3.041		arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	12	11073825	28064557	Rat
1331761	Bp218	Blood pressure QTL 218	2.973		arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	12	11073825	45055165	Rat
61404	Bw120	Body weight QTL 120	5.1		body mass (VT:0001259)	body mass index (BMI) (CMO:0000105)	12	12351619	46669029	Rat
1641928	Alcrsp5	Alcohol response QTL 5			response to alcohol trait (VT:0010489)	duration of loss of righting reflex (CMO:0002289)	12	12812385	46669029	Rat
2303569	Gluco44	Glucose level QTL 44	2		blood glucose amount (VT:0000188)	blood glucose level (CMO:0000046)	12	12812385	46669029	Rat
7204484	Bp358	Blood pressure QTL 358		0.001	arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	12	13008296	19212979	Rat
1549902	Bp269	Blood pressure QTL 269			arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	12	13182736	46669029	Rat
1549912	Bp268	Blood pressure QTL 268			arterial blood pressure trait (VT:2000000)	diastolic blood pressure (CMO:0000005)	10	13182736	46669029	Rat
2302060	Pia37	Pristane induced arthritis QTL 37	6.1	0.001	blood immunoglobulin amount (VT:0002460)	serum immunoglobulin G1 level (CMO:0002115)	12	13198157	46669029	Rat
61416	Pia4	Pristane induced arthritis QTL 4	8.4		joint integrity trait (VT:0010548)	arthritic paw count (CMO:0001460)	12	13635523	30827399	Rat
61421	Cia12	Collagen induced arthritis QTL 12	4.6		joint integrity trait (VT:0010548)	joint inflammation composite score (CMO:0000919)	12	13635523	35682913	Rat

miRNA Target Status

Predicted Target Of

	Summary Value
Count of predictions:	130
Count of miRNA genes:	100
Interacting mature miRNAs:	111
Transcripts:	ENSRNOT00000001709
Prediction methods:	Microtar, Miranda, Rnahybrid, Targetscan
Result types:	miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.

Expression

RNA-SEQ Expression

High: > 1000 TPM value Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM Below Cutoff: < 0.5 TPM

	alimentary part of gastrointestinal system	circulatory system	endocrine system	exocrine system	hemolymphoid system	hepatobiliary system	integumental system	musculoskeletal system	nervous system	renal system	reproductive system	respiratory system	appendage
High
Medium	2	18	52	39	19	39			52	23	41	11
Low	1	25	5	2		2	8	11	22	12			8
Below cutoff

View RNA-SEQ Expression Data

Sequence

Nucleotide Sequences


RefSeq Transcripts	NM_001109387	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_017598453	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	AC117065	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	CH474012	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	JACYVU010000225	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

Reference Sequences

RefSeq Acc Id:

ENSRNOT00000001709 ⟹ ENSRNOP00000001709

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2 Ensembl	12	14,320,892 - 14,630,703 (+)	Ensembl
Rnor_6.0 Ensembl	12	16,410,083 - 16,719,824 (+)	Ensembl

RefSeq Acc Id:

ENSRNOT00000114435 ⟹ ENSRNOP00000087168

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2 Ensembl	12	14,321,013 - 14,630,703 (+)	Ensembl

RefSeq Acc Id:

NM_001109387 ⟹ NP_001102857

RefSeq Status:

PROVISIONAL

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	12	14,320,892 - 14,630,703 (+)	NCBI
Rnor_6.0	12	16,410,083 - 16,719,824 (+)	NCBI
Rnor_5.0	12	18,402,692 - 18,711,591 (+)	NCBI
RGSC_v3.4	12	14,793,899 - 15,107,476 (+)	RGD
Celera	12	16,079,638 - 16,388,296 (+)	RGD

Sequence:

show sequence

GGGAGATCTGAGCCGCTGCTGCAGCACTCGGCTCCTCAACTCGGGAGGGTGACCATGGAAGACC
TTGGGGAGAACACCACAGTCCTGTCCACCCTGAGATCTCTCAACAACTTCATTTCTCAGCGAAT
GGAGGGAGCATCAGGCTTGGATGTGTCCACATCTGCCTCAGGGTCCCTACAGAAGCAGTATGAA
CAGAACATGCAGCTGGAGGAGAGAGCAGAGCAGATCCGTTCAAAGTCCTACCTCATCCAGGTGG
AGCGGGAGAAGATGCAGATGGAGCTGAGCCACAAGAGGGCTCGGGTGGAGCTGGAGAGAGCGGC
CAGCACCAATGCCAGGAACTATGAGCGCGAGGTGGATCGCAACCAGGAACTCCTGGCACGCATT
CGGCAGCTCCAGGAGCGTGAGGCCGCAGCAGAAGAGAAGATGCGGGAGCAGCTGGAGCGCCACA
GGCTGTGCAAGCAGAGCCTGGACGCTGCCAGTCAGCAGCTGCGGGAACGAGAGGATGGCCTGGC
TGCAGCCAGGGAGACGATTAGTTCATTGAAGGGGCGAGTCTCCGAGCTGCAGTTGAGTGCGATG
GACCAGAAGGTACAGGTCAAGCGCCTGGAGTCTGAGAAGCAGGAGCTGAAGGAGCAGCTGGAAC
TGCAGCAGCGGAAATGGCAGGAGGCAAATCAGAAGATCCAGGAGCTACAGGCCAGTCAAGAAGA
GAGAACTGACCAGGAGCAGAAGATTAAGGACCTGGAGCAGAAGCTGTGTCTGCAAGAGCAGGAT
GCAGCTGTGGTGAAGAGCATGAAATCTGAGCTGTTGCGACTGCCTCGGATGGAGCGTGAGCTAA
AGAGGCTGCGTGAGGAGAACACTCATCTAAGGGAGATGAGGGAGACCAATGGGCTGCTCACAGA
GGAGCTGGAAGGTCTGCAGAGGAAGCTGGGCCGCCAGGAGAAGATGCAGGAAGCTCTGGTTGAT
CTGGAGTTGGAGAAGGAGAAGCTGCTTGCAAAGCTGCAGAGCTGGGAGAAACTGGACCAGACCA
TGGGCTTGAATCTCAGGACTCCAGAGGACCTTTCGAGGTTCGTGATTGAGCTGCAGCAGCGAGA
GCTGGCGCTGAAGGAGAAGAATAGCAGCATCACCAGCAGTGCCCGGGGTCTGGAGAAGGCCCAG
CAGCAGCTCCAGGATGAGGTCCGGCAGGTCAATGCACAGCTGCTGGAAGAGAGGAAGAAGAGGG
AGACACATGAGGCACTTGCCCGAAGGCTCCAGAAGCGCAATGCATTGCTGACCAAGGAGCGAGA
CGGCATGCGCGCCATCCTGGGATCCTACGACAGTGAGCTGACCCAAGCTGAGTACTCGCCCCAG
CTTACACAGCGCATGTGGGAGGCTGAGGACATGGTTCAGAAGGTGCATGCCCACAGCTCAGAGA
TGGAGGCTCAGCTGTCTCAGGCCCTGGAAGAGCTTGGGGTTCAGAAGCAGAGAGCTGACACGCT
GGAGATGGAGTTGAAGATGCTGAGGGCCCAGACAAGCTCAGCCGAAGCCAGCTTCCCATTCTGC
AAAGAGGAGGTGGATGCACTCAGGTTGAAGGTGGAGGAGCTGGAGGGTGAGCGGAGCCGTCTGG
AACAGGAAAAGCAGGCTCTGGAGATGCAGATGGAGAGACTAACCCTACAGGGTGACTACAACCA
GAGTCGAACCAAAGTGCTACACATGAGCCTGAACCCGGCTAGCATGGCCAGGCAGCGCCAGCGT
GAGGACCATGACCGGCTGCAGGAGGAATGCGAGCGCTTACGGGGACTTGTGCATGCCCTAGAGA
GAGGCGGTCCCATCCCTGCTGACCTGGAGGCTGCCTCCAGCCTGCCCTCATCCAAGGAGGTGGC
AGAGCTGCGGAAGCAGGTAGAAAGCGCTGAGCTGAAGAACCAGCGGCTCAAGGAGGTTTTCCAG
ACCAAGATCCAGGAGTTCCGCAAGGTTTGCTACACACTGACCGGCTACCAGATTGACGTGACCA
CTGAGAGCCAATACCGCCTCACCTCCCGATATGCTGAGCACCAGACTGACTGCCTCATCTTCAA
GGCCACAGGACCCTCGGGCTCCAAAATGCAGCTGCTGGAGACGGAGTTCTCCCGTTCAGTGCCT
GAGCTCATTGAGCTGCACCTGCTGCAGCAGGACAGCATCCCTGCCTTCCTCAGCGCGCTCACCA
TAGAGCTGTTCAGCCGCCAGACCTCTGTCTAGCCTCTTCCCATGAGCATCCACGCCTACAGCCA
CTGGACCTCGGCCTAGCCTATACCTGCAGCGTCTCACATGCAACCCTCAGACCTTGGCCTAGCT
CTTGGTCTTCCAGACAGTTACCCACATGTCCCCAAACCCCTTTGCTACCCATAGCTGCATCATG
TCACAAACACCATTCTTGTCCCTGGCCAGCAGGAGCAAGCTGCTGGGGATGACCAAGCCAGATC
ACACCCCACCATTCTCCTCTCCTCCCCACCCCATCGAGTTCTAGGGCTGTACTGTCCCAAGGTG
TGCCCGTACCGGCCCATGTGCTGGTTGCTTATGTCACTTTGGTGGCCAGACTGTGGCCTGCGTC
CACAGTCCCAGCCTGATGAAATAAAGTGCTACATTTATCTTCCCTCCCGGGA

hide sequence

RefSeq Acc Id:

XM_017598453 ⟹ XP_017453942

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	12	14,341,507 - 14,630,750 (+)	NCBI
Rnor_6.0	12	16,430,280 - 16,721,232 (+)	NCBI

Sequence:

show sequence

TCAGTCTGTGCAGCTTCCTATACTAAGCAGGGGTGGAGGCAGTCCTGTCACTCACAGACCTTCC
TGCCTAGAGGATGCATGCTGATTGTCTCGTGGATGCCAGGCCCTGTGCTGGCTCCTTGGGAGGC
CAAGTGAGTACTCAAGTGCTCAAGTGTCCCAGTGATGAAGACCCACAAGAAATCCACGGGAAAA
GGCTAACACAGAGGACTGCAATCTAGGGTTAGAGAGGTGTGCATAGGATACAACTGTGAGCCTA
GCCTGTTGAGGCTGAGATGAGAGGATCATGAGTTTGAGACCAGGTATTCCATGAAGTAGGTTTA
GAGGGGGTAGAGCATGGCTGAGCTAGGTCACCAGGCCAGGGCTGTTGATTTAAGTTCAGCCTCC
TTTATTACAGTGAATGTCGTTGGAGAGGTGGTGCCTTGAGCTTCCTTCCATGGTTTCCTGTTGT
CTTTAGTGTGATAACCAGTCCCAGGAAGGAGGACCTGGAGCAGAAGCTGTGTCTGCAAGAGCAG
GATGCAGCTGTGGTGAAGAGCATGAAATCTGAGCTGTTGCGACTGCCTCGGATGGAGCGTGAGC
TAAAGAGGCTGCGTGAGGAGAACACTCATCTAAGGGAGATGAGGGAGACCAATGGGCTGCTCAC
AGAGGAGCTGGAAGGTCTGCAGAGGAAGCTGGGCCGCCAGGAGAAGATGCAGGAAGCTCTGGTT
GATCTGGAGTTGGAGAAGGAGAAGCTGCTTGCAAAGCTGCAGAGCTGGGAGAAACTGGACCAGA
CCATGGGCTTGAATCTCAGGACTCCAGAGGACCTTTCGAGGTTCGTGATTGAGCTGCAGCAGCG
AGAGCTGGCGCTGAAGGAGAAGAATAGCAGCATCACCAGCAGTGCCCGGGGTCTGGAGAAGGCC
CAGCAGCAGCTCCAGGATGAGGTCCGGCAGGTCAATGCACAGCTGCTGGAAGAGAGGAAGAAGA
GGGAGACACATGAGGCACTTGCCCGAAGGCTCCAGAAGCGCAATGCATTGCTGACCAAGGAGCG
AGACGGCATGCGCGCCATCCTGGGATCCTACGACAGTGAGCTGACCCAAGCTGAGTACTCGCCC
CAGCTTACACAGCGCATGTGGGAGGCTGAGGACATGGTTCAGAAGGTGCATGCCCACAGCTCAG
AGATGGAGGCTCAGCTGTCTCAGGCCCTGGAAGAGCTTGGGGTTCAGAAGCAGAGAGCTGACAC
GCTGGAGATGGAGTTGAAGATGCTGAGGGCCCAGACAAGCTCAGCCGAAGCCAGCTTCCCATTC
TGCAAAGAGGAGGTGGATGCACTCAGGTTGAAGGTGGAGGAGCTGGAGGGTGAGCGGAGCCGTC
TGGAACAGGAAAAGCAGGCTCTGGAGATGCAGATGGAGAGACTAACCCTACAGGGTGACTACAA
CCAGAGTCGAACCAAAGTGCTACACATGAGCCTGAACCCGGCTAGCATGGCCAGGCAGCGCCAG
CGTGAGGACCATGACCGGCTGCAGGAGGAATGCGAGCGCTTACGGGGACTTGTGCATGCCCTAG
AGAGAGGCGGTCCCATCCCTGCTGACCTGGAGGCTGCCTCCAGCCTGCCCTCATCCAAGGAGGT
GGCAGAGCTGCGGAAGCAGGTAGAAAGCGCTGAGCTGAAGAACCAGCGGCTCAAGGAGGTTTTC
CAGACCAAGATCCAGGAGTTCCGCAAGGTTTGCTACACACTGACCGGCTACCAGATTGACGTGA
CCACTGAGAGCCAATACCGCCTCACCTCCCGATATGCTGAGCACCAGACTGACTGCCTCATCTT
CAAGGCCACAGGACCCTCGGGCTCCAAAATGCAGCTGCTGGAGACGGAGTTCTCCCGTTCAGTG
CCTGAGCTCATTGAGCTGCACCTGCTGCAGCAGGACAGCATCCCTGCCTTCCTCAGCGCGCTCA
CCATAGAGCTGTTCAGCCGCCAGACCTCTGTCTAGCCTCTTCCCATGAGCATCCACGCCTACAG
CCACTGGACCTCGGCCTAGCCTATACCTGCAGCGTCTCACATGCAACCCTCAGACCTTGGCCTA
GCTCTTGGTCTTCCAGACAGTTACCCACATGTCCCCAAACCCCTTTGCTACCCATAGCTGCATC
ATGTCACAAACACCATTCTTGTCCCTGGCCAGCAGGAGCAAGCTGCTGGGGATGACCAAGCCAG
ATCACACCCCACCATTCTCCTCTCCTCCCCACCCCATCGAGTTCTAGGGCTGTACTGTCCCAAG
GTGTGCCCGTACCGGCCCATGTGCTGGTTGCTTATGTCACTTTGGTGGCCAGACTGTGGCCTGC
GTCCACAGTCCCAGCCTGATGAAATAAAGTGCTACATTTATCTTCCCTCCCGGGACTGTGGCCA
AGGCTGTTCAGGCCTCACCACTGTGCTATGCTTCCCAACACCTGGCAGGTCTGTTCATACACGC
AGCCGAAAGGGACAGGCAGATGGGGTTGGAATGCTAGTGTCCCATCCCTCTGAGCCTGGGTGTC
TCATTCCCTGCCTTGGTTTCTTCCCTGCCTGCCCCTCCCCAAACCCCCGTGCGAGGCCTCTGAG
TCCAGTGGGTGAGCCTCCCTTGCTAGCTCCCCCTGCAAGGGGCCTCACCAAGCCCAGCCATCCA
TACCACTGCAAGTGTCCTGATTAACAGGTTTTCTTAGGCAGAGGTGGAGAGGTGAGGGCCTGAG
TTGGGGATGTATGTGTCTGGGCACCTGATCATGTGTCCCTCATGTGTTGATGACCTGTCACCTG
AGTGTATCATAGCCTCCTCACATGCCTTCAAGAAAATGGAAGTGAGACAGCCTGCTGGGAACGC
TCAGGCTTGGGCCAGAGAAAATTTTACTTGTGGCAGCCCCAGGCTTACACCAGCTCGTCACTGG
GCCCCCACTGATAAATGGGTCTTAAGCTGCTAATGACTCACTTTAAGGGATTAGTGGCATGGTG
ACAAGCGTCACAGCCAGGAGGTAACAGGATTTGCTATGTCCAGGCCTCCAGCTCCCCTACCAGG
GGACCCCTGCTGCCCCCACCTCCTCCCATCGAGCTCAGCTGGAGCAACTAGTTCTGCCATGACT
GAGTTCTTTATTGCCTTGTCCTTTGTTGCCTGGTGCAAGGCCCTCTGGGATATACAGATTGTGG
GTATTTCTCCAGCTCCTGGCCCATCCCAGGGACCTCCAGGCTGTTCCCAGGCAGGAATGAACAG
CCTCCCAGGGCACCCTCAGAATCCCCCAGCAGCCAGCGGGGACTGGTTGCACCCAGCTCTCTGC
TCGCTCTCTTCCATGTCAAGCTGGCCTTCCAGCTGGGTGGCATCAGGCTACAGGTTAGGGATGA
AGGGGTCCTGCTCCAGTCAGCTGTGGGTCTGGACTCAAACCCAGCTCTCCAAGCTACCTGGCTT
CAGAGTCATATGAATGGTCCTTCCTGCGGTGCTTATGTGTGCTTGCGATCTGAGTAGTACTTCT
GCCCAGAAAAGGATGTGCCCACCCAACACACACACACATACAGAGGGGTAGGGAGGAGACACCA
AGTGGGAGCAAGGAGCCCCGGCGAGGCCTATATTTATACCCGCTTTCTGGTTAACTGTACAACT
TGAATATCATTAAAGCAAAACGAATAAACCTCCAAAGAGACAGGAGGTGAGGGAAGGAGAGCCC
CTCCCCTGGCTCCCAGCCAGCCTCCAGCCTGGTGGGCGGACCTGCACACCTCGTGTGTGGATGG
GTGAGAGTGCCCAGGTTTGTTTCGTCAGATTCTGTACAGGAGTTTTTAATAACTG

hide sequence

Protein Sequences


Protein RefSeqs	NP_001102857	(Get FASTA)	NCBI Sequence Viewer
	XP_017453942	(Get FASTA)	NCBI Sequence Viewer
GenBank Protein	EDL89740	(Get FASTA)	NCBI Sequence Viewer

Reference Sequences

RefSeq Acc Id:

NP_001102857 ⟸ NM_001109387

- UniProtKB:

D3ZIV3 (UniProtKB/TrEMBL)

- Sequence:

show sequence

MEDLGENTTVLSTLRSLNNFISQRMEGASGLDVSTSASGSLQKQYEQNMQLEERAEQIRSKSYL
IQVEREKMQMELSHKRARVELERAASTNARNYEREVDRNQELLARIRQLQEREAAAEEKMREQL
ERHRLCKQSLDAASQQLREREDGLAAARETISSLKGRVSELQLSAMDQKVQVKRLESEKQELKE
QLELQQRKWQEANQKIQELQASQEERTDQEQKIKDLEQKLCLQEQDAAVVKSMKSELLRLPRME
RELKRLREENTHLREMRETNGLLTEELEGLQRKLGRQEKMQEALVDLELEKEKLLAKLQSWEKL
DQTMGLNLRTPEDLSRFVIELQQRELALKEKNSSITSSARGLEKAQQQLQDEVRQVNAQLLEER
KKRETHEALARRLQKRNALLTKERDGMRAILGSYDSELTQAEYSPQLTQRMWEAEDMVQKVHAH
SSEMEAQLSQALEELGVQKQRADTLEMELKMLRAQTSSAEASFPFCKEEVDALRLKVEELEGER
SRLEQEKQALEMQMERLTLQGDYNQSRTKVLHMSLNPASMARQRQREDHDRLQEECERLRGLVH
ALERGGPIPADLEAASSLPSSKEVAELRKQVESAELKNQRLKEVFQTKIQEFRKVCYTLTGYQI
DVTTESQYRLTSRYAEHQTDCLIFKATGPSGSKMQLLETEFSRSVPELIELHLLQQDSIPAFLS
ALTIELFSRQTSV

hide sequence

RefSeq Acc Id:

XP_017453942 ⟸ XM_017598453

- Peptide Label:

isoform X1

- Sequence:

show sequence

MKSELLRLPRMERELKRLREENTHLREMRETNGLLTEELEGLQRKLGRQEKMQEALVDLELEKE
KLLAKLQSWEKLDQTMGLNLRTPEDLSRFVIELQQRELALKEKNSSITSSARGLEKAQQQLQDE
VRQVNAQLLEERKKRETHEALARRLQKRNALLTKERDGMRAILGSYDSELTQAEYSPQLTQRMW
EAEDMVQKVHAHSSEMEAQLSQALEELGVQKQRADTLEMELKMLRAQTSSAEASFPFCKEEVDA
LRLKVEELEGERSRLEQEKQALEMQMERLTLQGDYNQSRTKVLHMSLNPASMARQRQREDHDRL
QEECERLRGLVHALERGGPIPADLEAASSLPSSKEVAELRKQVESAELKNQRLKEVFQTKIQEF
RKVCYTLTGYQIDVTTESQYRLTSRYAEHQTDCLIFKATGPSGSKMQLLETEFSRSVPELIELH
LLQQDSIPAFLSALTIELFSRQTSV

hide sequence

RefSeq Acc Id:

ENSRNOP00000001709 ⟸ ENSRNOT00000001709

RefSeq Acc Id:

ENSRNOP00000087168 ⟸ ENSRNOT00000114435

Transcriptome

eQTL		View at Phenogen
WGCNA		View at Phenogen
Tissue/Strain Expression		View at Phenogen

Promoters

RGD ID:

13698458

Promoter ID:

EPDNEW_R8983

Type:

initiation region

Name:

Mad1l1_1

Description:

mitotic arrest deficient 1 like 1

SO ACC ID:

SO:0000170

Source:

EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)

Experiment Methods:

Single-end sequencing.

Position:

Rat Assembly	Chr	Position (strand)	Source
Rnor_6.0	12	16,410,086 - 16,410,146	EPDNEW

Strain Variation

Strain Sequence Variants (Rnor 6.0)

ACI/EurMcwi (2019)

Visual

CSV

TAB

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

ACI/EurMcwi (MCW)

Visual

CSV

TAB

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Sequenced By:	Medical College of Wisconsin (Dr. Howard Jacob)
Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA v0.7.7 and GATK v3.2-2
Breeder:	Medical College of Wisconsin
Description:	Provided by the Medical College of Wisconsin (Dr. Howard Jacob)

ACI/EurMcwi (RGD)

Visual

CSV

TAB

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

ACI/N (2020)

Visual

CSV

TAB

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	NIH
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

ACI/N (MCW)

Visual

CSV

TAB

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Sequenced By:	Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen) Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform:	SOLiD 4 and 5500
Secondary Analysis:	liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder:	National Institutes of Health
Description:	Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

BBDP/Wor (RGD)

Visual

CSV

TAB

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

BN-Lx/CubMcwi (2019)

Visual

CSV

TAB

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

BN/NHsdMcwi (2019)

Visual

CSV

TAB

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

BN/NHsdMcwi (2020)

Visual

CSV

TAB

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

BN/SsN (2020)

Visual

CSV

TAB

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	NIH
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

BN/SsN (MCW)

Visual

CSV

TAB

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Sequenced By:	Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen) Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform:	SOLiD 4 and 5500
Secondary Analysis:	liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder:	National Institutes of Health
Description:	Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

BUF/N (2020)

Visual

CSV

TAB

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	NIH
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

BXH2/CubMcwi (2020)

Visual

CSV

TAB

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

BXH3/CubMcwi (2020)

Visual

CSV

TAB

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

Buf/N (MCW)

Visual

CSV

TAB

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Sequenced By:	Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen) Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform:	SOLiD 4 and 5500
Secondary Analysis:	liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder:	National Institutes of Health
Description:	Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

COP/CrCrl (MCW & UW)

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CSV

TAB

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Sequenced By:	Medical College of Wisconsin (Dr. Howard Jacob) University of Wisconsin (Dr. James Shull)
Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA v0.7.7 and GATK v3.2-2
Breeder:	Charles River Laboratories
Description:	Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)

DA/OlaHsd (2019)

Visual

CSV

TAB

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Envigo
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

F344/DuCrl (2019)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Charles River
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

F344/N (2020)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	NIH
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

F344/NCrl (2019)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Charles River
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

F344/NCrl (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

F344/NRrrc (MCW)

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Sequenced By:	Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen) Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform:	SOLiD 4 and 5500
Secondary Analysis:	liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder:	National Institutes of Health
Description:	Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

F344/Stm (2019)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Japan
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

FHH/EurMcwi (2019)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

FHH/EurMcwi (MCW)

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Sequenced By:	Medical College of Wisconsin (Dr. Howard Jacob)
Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA v0.7.7 and GATK v3.2-2
Breeder:	Medical College of Wisconsin
Description:	Provided by the Medical College of Wisconsin (Dr. Howard Jacob)

FHH/EurMcwi (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

FHL/EurMcwi (MCW)

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Sequenced By:	Medical College of Wisconsin (Dr. Howard Jacob)
Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA v0.7.7 and GATK v3.2-2
Breeder:	Medical College of Wisconsin
Description:	Provided by the Medical College of Wisconsin (Dr. Howard Jacob)

FHL/EurMcwi (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

FXLE16/Stm (2020)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Japan
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

FXLE18/Stm (2020)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Japan
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

GH/OmrMcwi (MCW)

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Sequenced By:	Medical College of Wisconsin (Dr. Howard Jacob)
Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA v0.7.7 and GATK v3.2-2
Breeder:	Medical College of Wisconsin
Description:	Provided by the Medical College of Wisconsin (Dr. Howard Jacob)

GK/FarMcwi (2019)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

GK/Ox (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

HXB10/IpcvMcwi (2019)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

HXB2/IpcvMcwi (2019)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

HXB20/IpcvMcwi (2020)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

HXB31/IpcvMcwi (2019)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

HXB4/IpcvMcwi (2020)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

LE/Stm (2019)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Japan
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

LE/Stm (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

LEW/Crl (2019)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Charles River
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

LEW/Crl (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

LEW/NCrlBR (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

LEXF10A/StmMcwi (2020)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

LEXF11/Stm (2020)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Japan
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

LEXF1A/Stm (2019)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Japan
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

LEXF1C/Stm (2019)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Japan
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

LEXF2B/Stm (2019)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Japan
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

LEXF3/Stm (2020)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Japan
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

LEXF4/Stm (2020)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Japan
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

LH/MavRrrc (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

LH/MavRrrcAek (2020)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Kwitek
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

LL/MavRrrc (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

LL/MavRrrcAek (2020)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Kwitek
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

LN/MavRrrc (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

LN/MavRrrcAek (2020)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Kwitek
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

M520/N (2020)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	NIH
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

M520/N (MCW)

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Sequenced By:	Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen) Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform:	SOLiD 4 and 5500
Secondary Analysis:	liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder:	National Institutes of Health
Description:	Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

M520/NRrrcMcwi (2019)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

MHS/Gib (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

MNS/Gib (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

MR/N (2020)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	NIH
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

MR/N (MCW)

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Sequenced By:	Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen) Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform:	SOLiD 4 and 5500
Secondary Analysis:	liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder:	National Institutes of Health
Description:	Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

MWF/Hsd (2019)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

PVG/Seac (2019)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Japan
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

SBH/Ygl (MCW)

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Sequenced By:	Medical College of Wisconsin (Dr. Howard Jacob)
Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA v0.7.7 and GATK v3.2-2
Breeder:	Medical College of Wisconsin
Description:	SBH/Ygl sequenced by MCW

SBH/Ygl (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

SBN/Ygl (MCW)

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Sequenced By:	Medical College of Wisconsin (Dr. Howard Jacob)
Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA v0.7.7 and GATK v3.2-2
Breeder:	Medical College of Wisconsin
Description:	SBN/Ygl sequenced by MCW

SBN/Ygl (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

SHR/NHsd (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

SHR/OlalpcvMcwi (2019)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

SHRSP/A3NCrl (2019)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Charles River
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

SHRSP/Gcrc (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

SR/JrHsd (2020)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Envigo
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

SR/JrHsd (MCW)

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Sequenced By:	Medical College of Wisconsin (Dr. Howard Jacob)
Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA v0.7.7 and GATK v3.2-2
Breeder:	Harlan Laboratories
Description:	Provided by the Medical College of Wisconsin (Dr. Howard Jacob)

SR/JrHsd (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

SS/Jr (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

SS/JrHsdMcwi (2019)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

SS/JrHsdMcwi (MCW)

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Sequenced By:	Medical College of Wisconsin (Dr. Howard Jacob)
Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA v0.7.7 and GATK v3.2-2
Breeder:	Medical College of Wisconsin
Description:	Provided by the Medical College of Wisconsin (Dr. Howard Jacob)

SS/JrHsdMcwi (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

WAG/Rij (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

WAG/RijCrl (2020)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Charles River
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

WKY/Gcrc (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

WKY/N (2020)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	NIH
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

WKY/N (MCW)

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Sequenced By:	Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen) Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform:	SOLiD 4 and 5500
Secondary Analysis:	liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder:	National Institutes of Health
Description:	Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

WKY/NCrl (2019)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Charles River
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

WKY/NCrl (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

WKY/NHsd (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

WN/N (2020)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	NIH
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

WN/N (MCW)

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Sequenced By:	Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen) Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform:	SOLiD 4 and 5500
Secondary Analysis:	liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder:	National Institutes of Health
Description:	Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

Damaging Variants

Assembly: Rnor_5.0

Chromosome	Start Pos	End Pos	Reference Nucleotide	Variant Nucleotide	Variant Type	Strain
12	18616424	18616425	C	A	snv	SHRSP/Gcrc (KNAW)

Assembly: Rnor_6.0

Chromosome	Start Pos	End Pos	Reference Nucleotide	Variant Nucleotide	Variant Type	Strain
12	16624657	16624658	C	A	snv	SHRSP/Gcrc (RGD)

Assembly: RGSC_v3.4

Chromosome	Start Pos	End Pos	Reference Nucleotide	Variant Nucleotide	Variant Type	Strain
12	15012314	15012315	C	A	snv	SHRSP/Gcrc (ICL), SHRSP/Gcrc (MDC)

Additional Information

External Database Links

Database	Acc Id	Source(s)
AGR Gene	RGD:1596881	AgrOrtholog
Ensembl Genes	ENSRNOG00000001265	Ensembl, UniProtKB/TrEMBL
Ensembl Protein	ENSRNOP00000001709	UniProtKB/TrEMBL
Ensembl Transcript	ENSRNOT00000001709	UniProtKB/TrEMBL
InterPro	MAD	UniProtKB/TrEMBL
KEGG Report	rno:680006	UniProtKB/TrEMBL
NCBI Gene	680006	ENTREZGENE
PANTHER	PTHR23168	UniProtKB/TrEMBL
Pfam	MAD	UniProtKB/TrEMBL
PhenoGen	Mad1l1	PhenoGen
UniProt	D3ZIV3	ENTREZGENE, UniProtKB/TrEMBL

Nomenclature History

Date	Current Symbol	Current Name	Previous Symbol	Previous Name	Description	Reference	Status
2017-09-28	Mad1l1	mitotic arrest deficient 1 like 1	Mad1l1	MAD1 mitotic arrest deficient like 1	Nomenclature updated to reflect human and mouse nomenclature	1299863	APPROVED
2016-04-20	Mad1l1	MAD1 mitotic arrest deficient like 1	Mad1l1	MAD1 mitotic arrest deficient-like 1 (yeast)	Nomenclature updated to reflect human and mouse nomenclature	1299863	APPROVED
2008-10-23	Mad1l1	MAD1 mitotic arrest deficient-like 1 (yeast)	Mad1l1	mitotic arrest deficient 1-like 1	Nomenclature updated to reflect human and mouse nomenclature	1299863	APPROVED
2008-07-08	Mad1l1	mitotic arrest deficient 1-like 1	LOC686419	similar to Mitotic spindle assembly checkpoint protein MAD1 (Mitotic arrest deficient-like protein 1) (MAD1-like 1)	Data Merged	1643240	APPROVED
2008-03-05	Mad1l1	mitotic arrest deficient 1-like 1	LOC680006	similar to Mitotic spindle assembly checkpoint protein MAD1 (Mitotic arrest deficient-like protein 1) (MAD1-like 1)	Nomenclature updated to reflect human and mouse nomenclature	1299863	APPROVED
2006-11-20	LOC680006	similar to Mitotic spindle assembly checkpoint protein MAD1 (Mitotic arrest deficient-like protein 1) (MAD1-like 1)			Symbol and Name status set to provisional	70820	PROVISIONAL
2006-11-20	LOC686419	similar to Mitotic spindle assembly checkpoint protein MAD1 (Mitotic arrest deficient-like protein 1) (MAD1-like 1)			Symbol and Name status set to provisional	70820	PROVISIONAL

Gene Annotator (Functional Annotation) unavailable	Gene Annotator (Annotation Distribution) unavailable	Variant Visualizer (Genomic Variants) unavailble Variant Visualizer (Genomic Variants) unavailable
Gene Annotator (Functional Annotation)	Gene Annotator (Annotation Distribution)	Variant Visualizer (Genomic Variants)

InterViewer (Protein-Protein Interactions) unavailable	Gviewer (Genome Viewer) unavailable	Variant Visualizer (Damaging Variants) unavailble Variant Visualizer (Damaging Variants) unavailable
InterViewer (Protein-Protein Interactions)	GViewer (Genome Viewer)	Variant Visualizer (Damaging Variants)

Gene Annotator (Annotation Comparison) unavailable	OLGA (Gene List Generator) unavailable
Gene Annotator (Annotation Comparison)	OLGA (Gene List Generator)	Excel (Download)

MOET (Multi-Ontology Enrichement) unavailable	GOLF (Gene-Ortholog Location Finder) unavailable
MOET (Multi-Ontology Enrichement)	GOLF (Gene-Ortholog Location Finder)

Imported Disease Annotations - ClinVar

Imported Disease Annotations - CTD

Imported Disease Annotations - OMIM

Imported Annotations - KEGG (archival)

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Imported Disease Annotations - ClinVar

Imported Disease Annotations - CTD

Imported Disease Annotations - OMIM

Imported Annotations - KEGG (archival)