Nup107 (nucleoporin 107) - Rat Genome Database

Name: Nup107
Creator: Rat Genome Database
License: Creative Commons CC BY 4.0
Keywords: Rat Gene RGD Genome

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Gene: Nup107 (nucleoporin 107) Rattus norvegicus

Analyze

Symbol:

Nup107

Name:

nucleoporin 107

RGD ID:

621160

Description:

Predicted to be a structural constituent of nuclear pore. Predicted to be involved in several processes, including nuclear pore complex assembly; nucleocytoplasmic transport; and posttranscriptional tethering of RNA polymerase II gene DNA at nuclear periphery. Localizes to nuclear membrane and nuclear pore. Predicted to colocalize with kinetochore. Human ortholog(s) of this gene implicated in Galloway-Mowat syndrome; nephrotic syndrome type 11; and ovarian dysgenesis 6. Orthologous to human NUP107 (nucleoporin 107); PARTICIPATES IN mRNA nuclear export pathway; RNA transport pathway; INTERACTS WITH 17beta-estradiol; acetamide; bisphenol A.

Type:

protein-coding

RefSeq Status:

VALIDATED

Also known as:

107 kDa nucleoporin; nuclear pore complex protein Nup107; nucleoporin Nup107; p105

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):	NUP107 (nucleoporin 107)	HGNC	EggNOG, Ensembl, HomoloGene, Inparanoid, NCBI, OMA, OrthoDB, OrthoMCL, Panther, Treefam
Mus musculus (house mouse):	Nup107 (nucleoporin 107)	HGNC	Treefam, EggNOG, OrthoMCL, NCBI, OMA, HomoloGene, Inparanoid, Panther, OrthoDB, Ensembl
Chinchilla lanigera (long-tailed chinchilla):	Nup107 (nucleoporin 107)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Pan paniscus (bonobo/pygmy chimpanzee):	NUP107 (nucleoporin 107)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Canis lupus familiaris (dog):	NUP107 (nucleoporin 107)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Ictidomys tridecemlineatus (thirteen-lined ground squirrel):	Nup107 (nucleoporin 107)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Sus scrofa (pig):	NUP107 (nucleoporin 107)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chlorocebus sabaeus (African green monkey):	NUP107 (nucleoporin 107)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Heterocephalus glaber (naked mole-rat):	Nup107 (nucleoporin 107)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Alliance orthologs ³
Homo sapiens (human):	NUP107 (nucleoporin 107)	Alliance	DIOPT (HGNC\|Hieranoid\|InParanoid\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|TreeFam)
Mus musculus (house mouse):	Nup107 (nucleoporin 107)	Alliance	DIOPT (Hieranoid\|InParanoid\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|TreeFam)
Danio rerio (zebrafish):	nup107 (nucleoporin 107)	Alliance	DIOPT (PhylomeDB\|TreeFam)
Saccharomyces cerevisiae (baker's yeast):	NUP84	Alliance	DIOPT (Hieranoid\|InParanoid\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB)
Drosophila melanogaster (fruit fly):	Nup107	Alliance	DIOPT (Hieranoid\|InParanoid\|OrthoFinder\|OrthoInspector\|PANTHER\|TreeFam)
Caenorhabditis elegans (roundworm):	npp-5	Alliance	DIOPT (OrthoFinder\|OrthoInspector\|PANTHER)

Latest Assembly:

Rnor_6.0 - RGSC Genome Assembly v6.0

Position:

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
mRatBN7.2	7	53,353,740 - 53,398,345 (-)	NCBI
Rnor_6.0 Ensembl	7	60,781,729 - 60,825,242 (-)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_6.0	7	60,781,724 - 60,825,225 (-)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_5.0	7	60,781,687 - 60,825,188 (-)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	7	57,059,744 - 57,104,512 (-)	NCBI	RGSC3.4		rn4	RGSC3.4
RGSC_v3.1	7	57,080,475 - 57,125,256 (-)	NCBI
Celera	7	50,124,939 - 50,169,469 (-)	NCBI		Celera
Cytogenetic Map	7	q22	NCBI

JBrowse:

View Region in Genome Browser (JBrowse)

Model

Annotation Click to see Annotation Detail View

Disease Annotations Click to see Annotation Detail View

Developmental Disabilities (ISO)

focal segmental glomerulosclerosis 1 (ISO)

Galloway-Mowat Syndrome 7 (ISO)

nephrotic syndrome type 11 (ISO)

ovarian dysgenesis 6 (ISO)

primary ovarian insufficiency (ISO)

Gene-Chemical Interaction Annotations Click to see Annotation Detail View

(-)-epigallocatechin 3-gallate (ISO)

17beta-estradiol (EXP,ISO)

2,2',4,4'-Tetrabromodiphenyl ether (ISO)

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

2,3-dimethoxynaphthalene-1,4-dione (ISO)

2-methylcholine (ISO)

3,4-methylenedioxymethamphetamine (ISO)

acetamide (EXP)

aflatoxin B1 (ISO)

arsenous acid (ISO)

benzo[a]pyrene diol epoxide I (ISO)

bisphenol A (EXP)

calcitriol (ISO)

clofibrate (ISO)

copper(II) chloride (ISO)

coumestrol (ISO)

cyclosporin A (ISO)

diarsenic trioxide (ISO)

dicrotophos (ISO)

Enterolactone (ISO)

enzyme inhibitor (ISO)

ethanol (ISO)

menadione (ISO)

mercury atom (ISO)

mercury(0) (ISO)

paracetamol (ISO)

pentachlorophenol (ISO)

potassium chromate (ISO)

resveratrol (ISO)

testosterone (EXP,ISO)

thapsigargin (ISO)

thioacetamide (EXP)

triptonide (ISO)

troglitazone (ISO)

tunicamycin (ISO)

urethane (ISO)

valproic acid (ISO)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

biological_process (ND)

female gonad development (IEA,ISO)

mRNA export from nucleus (IBA,IEA,ISO,ISS)

nephron development (IEA,ISO,ISS)

nuclear pore complex assembly (IEA,ISO,ISS)

posttranscriptional tethering of RNA polymerase II gene DNA at nuclear periphery (IBA)

protein import into nucleus (IBA,IEA)

regulation of transcription, DNA-templated (IBA)

transmembrane transport (IEA)

Cellular Component

kinetochore (IEA,ISO,ISS)

nuclear membrane (IDA,IEA,ISO,ISS)

nuclear periphery (IEA,ISO,ISS)

nuclear pore (IDA,ISO,ISS)

nuclear pore outer ring (IBA,IEA,ISO,ISS)

pore complex (IEA)

Molecular Function

molecular_function (ND)

porin activity (IEA)

protein binding (ISO)

structural constituent of nuclear pore (IBA,IEA,ISO,ISS)

Molecular Pathway Annotations Click to see Annotation Detail View

mRNA nuclear export pathway (ISO)

RNA transport pathway (IEA)

References

References - curated


1.	Bonnet A and Palancade B, Genes (Basel). 2014 Sep 2;5(3):767-91. doi: 10.3390/genes5030767.
2.	D'Angelo MA, etal., Cell. 2009 Jan 23;136(2):284-95. doi: 10.1016/j.cell.2008.11.037.
3.	Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
4.	GOA data from the GO Consortium
5.	NCBI rat LocusLink and RefSeq merged data July 26, 2002
6.	Pipeline to import KEGG annotations from KEGG into RGD
7.	Radu A, etal., J Biol Chem 1994 Jul 1;269(26):17600-5.
8.	RGD automated data pipeline
9.	RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
10.	RGD automated import pipeline for gene-chemical interactions
11.	RGD comprehensive gene curation
12.	Vasu S, etal., J Cell Biol. 2001 Oct 29;155(3):339-54. Epub 2001 Oct 29.

Additional References at PubMed

PMID:8889548	PMID:11564755	PMID:12802065	PMID:15229283	PMID:17360435	PMID:17363900	PMID:19946888	PMID:26411495	PMID:26485283	PMID:30179222	PMID:30506890

Genomics

Comparative Map Data

Nup107
(Rattus norvegicus - Norway rat)

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
mRatBN7.2	7	53,353,740 - 53,398,345 (-)	NCBI
Rnor_6.0 Ensembl	7	60,781,729 - 60,825,242 (-)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_6.0	7	60,781,724 - 60,825,225 (-)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_5.0	7	60,781,687 - 60,825,188 (-)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	7	57,059,744 - 57,104,512 (-)	NCBI	RGSC3.4		rn4	RGSC3.4
RGSC_v3.1	7	57,080,475 - 57,125,256 (-)	NCBI
Celera	7	50,124,939 - 50,169,469 (-)	NCBI		Celera
Cytogenetic Map	7	q22	NCBI

NUP107
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38.p13 Ensembl	12	68,686,951 - 68,745,809 (+)	Ensembl	GRCh38		hg38	GRCh38
GRCh38	12	68,686,971 - 68,745,809 (+)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh37	12	69,080,758 - 69,139,589 (+)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	12	67,366,998 - 67,422,740 (+)	NCBI	NCBI36		hg18	NCBI36
Build 34	12	67,366,997 - 67,422,739	NCBI
Celera	12	68,744,181 - 68,799,945 (+)	NCBI
Cytogenetic Map	12	q15	NCBI
HuRef	12	66,131,401 - 66,186,887 (+)	NCBI		HuRef
CHM1_1	12	69,048,911 - 69,104,658 (+)	NCBI		CHM1_1

Nup107
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	10	117,586,526 - 117,628,641 (-)	NCBI	GRCm39		mm39
GRCm39 Ensembl	10	117,586,526 - 117,628,610 (-)	Ensembl
GRCm38	10	117,750,621 - 117,792,736 (-)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	10	117,750,621 - 117,792,705 (-)	Ensembl	GRCm38		mm10	GRCm38
MGSCv37	10	117,187,699 - 117,229,761 (-)	NCBI	GRCm37		mm9	NCBIm37
MGSCv36	10	117,153,636 - 117,195,698 (-)	NCBI			mm8
Celera	10	119,688,469 - 119,730,534 (-)	NCBI		Celera
Cytogenetic Map	10	D2	NCBI

Nup107
(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_004955458	15,149,054 - 15,201,635 (+)	Ensembl	ChiLan1.0
ChiLan1.0	NW_004955458	15,148,773 - 15,201,717 (+)	NCBI	ChiLan1.0	ChiLan1.0

NUP107
(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	12	68,981,409 - 69,035,637 (+)	NCBI	panpan1.1	PanPan1.1	panPan2
PanPan1.1 Ensembl	12	68,981,409 - 69,035,642 (+)	Ensembl	panpan1.1		panPan2
Mhudiblu_PPA_v0	12	66,198,838 - 66,254,505 (+)	NCBI	Mhudiblu_PPA_v0		panPan3

NUP107
(Canis lupus familiaris - dog)

Dog Assembly	Chr	Position (strand)	Source	Genome Browsers
Dog Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
CanFam3.1	10	10,838,881 - 10,887,347 (+)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1
CanFam3.1 Ensembl	10	10,838,944 - 10,887,197 (+)	Ensembl	CanFam3.1		canFam3	CanFam3.1
Dog10K_Boxer_Tasha	10	10,771,659 - 10,820,324 (+)	NCBI
ROS_Cfam_1.0	10	10,962,858 - 11,011,548 (+)	NCBI
UMICH_Zoey_3.1	10	10,830,697 - 10,879,383 (+)	NCBI
UNSW_CanFamBas_1.0	10	11,077,119 - 11,125,774 (+)	NCBI
UU_Cfam_GSD_1.0	10	11,199,135 - 11,247,756 (+)	NCBI

Nup107
(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_024404945	47,467,288 - 47,510,017 (-)	NCBI
SpeTri2.0	NW_004936545	6,600,124 - 6,642,839 (+)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

NUP107
(Sus scrofa - pig)

Pig Assembly	Chr	Position (strand)	Source	Genome Browsers
Pig Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Sscrofa11.1 Ensembl	5	32,989,794 - 33,042,575 (+)	Ensembl	Sscrofa11.1		susScr11	Sscrofa11.1
Sscrofa11.1	5	32,989,661 - 33,040,565 (+)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1
Sscrofa10.2	5	35,773,502 - 35,824,699 (+)	NCBI	Sscrofa10.2	Sscrofa10.2	susScr3

NUP107
(Chlorocebus sabaeus - African green monkey)

Vervet Assembly	Chr	Position (strand)	Source	Genome Browsers
Vervet Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
ChlSab1.1	11	64,317,489 - 64,375,609 (+)	NCBI
ChlSab1.1 Ensembl	11	64,317,521 - 64,375,398 (+)	Ensembl

Nup107
(Heterocephalus glaber - naked mole-rat)

Molerat Assembly	Chr	Position (strand)	Source	Genome Browsers
Molerat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
HetGla 1.0	NW_004624948	556,054 - 604,381 (-)	NCBI

Position Markers

RH131443

Rat Assembly	Chr	Position (strand)	Source	JBrowse
Rnor_6.0	7	60,781,831 - 60,782,031	NCBI	Rnor6.0
Rnor_5.0	7	60,781,794 - 60,781,994	UniSTS	Rnor5.0
RGSC_v3.4	7	57,059,851 - 57,060,051	UniSTS	RGSC3.4
Celera	7	50,125,046 - 50,125,246	UniSTS
RH 3.4 Map	7	487.7	UniSTS
Cytogenetic Map	7	q22	UniSTS

BI288689

Rat Assembly	Chr	Position (strand)	Source	JBrowse
Rnor_6.0	7	60,799,979 - 60,800,164	NCBI	Rnor6.0
Rnor_5.0	7	60,799,942 - 60,800,127	UniSTS	Rnor5.0
RGSC_v3.4	7	57,077,964 - 57,078,149	UniSTS	RGSC3.4
Celera	7	50,143,159 - 50,143,344	UniSTS
RH 3.4 Map	7	487.6	UniSTS
Cytogenetic Map	7	q22	UniSTS

QTLs in Region (Rnor_6.0)

The following QTLs overlap with this region.

RGD ID	Symbol	Name	LOD	P Value	Trait	Sub Trait	Chr	Start	Stop	Species
634336	Anxrr17	Anxiety related response QTL 17	3.66		locomotor behavior trait (VT:0001392)	number of entries into a discrete space in an experimental apparatus (CMO:0000960)	7	2920071	124838025	Rat
2298547	Neuinf5	Neuroinflammation QTL 5	3.7		nervous system integrity trait (VT:0010566)	spinal cord Cd74 protein level (CMO:0002131)	7	12328467	67193263	Rat
1643004	Pain2	Pain QTL 2	1		mechanical nociception trait (VT:0002734)	self mutilation severity score (CMO:0002145)	7	12328467	106995532	Rat
1578652	Bmd15	Bone mineral density QTL 15	5.2		femur mineral mass (VT:0010011)	trabecular volumetric bone mineral density (CMO:0001729)	7	12687850	67801690	Rat
738033	Anxrr6	Anxiety related response QTL 6	4.1		exploratory behavior trait (VT:0010471)	percentage of entries into a discrete space in an experimental apparatus (CMO:0000961)	7	22168412	67168412	Rat
10755451	Coatc11	Coat color QTL 11		0	coat/hair pigmentation trait (VT:0010463)	pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)	7	24731465	69731465	Rat
1300132	Bp182	Blood pressure QTL 182	3.49		arterial blood pressure trait (VT:2000000)	blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)	7	25365633	93155402	Rat
7411569	Bw137	Body weight QTL 137		0.001	body mass (VT:0001259)	body weight gain (CMO:0000420)	7	28204653	73204653	Rat
1641885	Alcrsp9	Alcohol response QTL 9			alcohol metabolism trait (VT:0015089)	blood ethanol level (CMO:0000535)	7	31381529	76381529	Rat
1549840	Bss5	Bone structure and strength QTL 5	9.8		femur strength trait (VT:0010010)	femur midshaft polar moment of inertia (CMO:0001669)	7	32035053	77035053	Rat
61439	Cia8	Collagen induced arthritis QTL 8	5.1		joint integrity trait (VT:0010548)	joint inflammation composite score (CMO:0000919)	7	32572942	77572942	Rat
70190	Mcs6	Mammary carcinoma susceptibility QTL 6	2.29		mammary gland integrity trait (VT:0010552)	mammary tumor number (CMO:0000343)	7	33044449	71352127	Rat
1300138	Hrtrt9	Heart rate QTL 9	4.72		heart pumping trait (VT:2000009)	heart rate (CMO:0000002)	7	35867729	61047824	Rat
10402855	Bp379	Blood pressure QTL 379		0.21	arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	7	35867729	80867729	Rat
1300127	Srn1	Serum renin concentration QTL 1	3.87		blood renin amount (VT:0003349)	plasma renin activity level (CMO:0000116)	7	35867729	93155402	Rat
10755453	Coatc12	Coat color QTL 12		0	coat/hair pigmentation trait (VT:0010463)	pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)	7	38547706	83547706	Rat
631534	Lnnr1	Liver neoplastic nodule remodeling QTL 1	3.85	0.001	liver integrity trait (VT:0010547)	liver remodeling tumorous lesion number to liver total tumorous lesion number ratio (CMO:0001705)	7	40872682	85872682	Rat
7411605	Foco14	Food consumption QTL 14	24.1	0.001	eating behavior trait (VT:0001431)	feed conversion ratio (CMO:0001312)	7	40872682	85872682	Rat
631513	Scl7	Serum cholesterol level QTL 7	4.1		blood cholesterol amount (VT:0000180)	serum total cholesterol level (CMO:0000363)	7	45301573	90301573	Rat
2303629	Vencon3	Ventilatory control QTL 3	7.25		respiration trait (VT:0001943)	respiration rate (CMO:0000289)	7	47895099	63372754	Rat
61357	Bp38	Blood pressure QTL 38	1.6	0.052	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	7	48118835	128611831	Rat
634326	Hc3	Hypercalciuria QTL 3	2.1		urine calcium amount (VT:0002985)	urine calcium excretion rate (CMO:0000763)	7	50252103	95252103	Rat
631504	Cm27	Cardiac mass QTL 27	3.45		heart left ventricle mass (VT:0007031)	heart left ventricle wet weight (CMO:0000071)	7	50704769	128085642	Rat
10053722	Scort27	Serum corticosterone level QTL 27	2.41	0.0083	blood corticosterone amount (VT:0005345)	plasma corticosterone level (CMO:0001173)	7	50793818	95793818	Rat
1358361	Sradr5	Stress Responsive Adrenal Weight QTL 5	5.55		adrenal gland mass (VT:0010420)	both adrenal glands wet weight (CMO:0000164)	7	51251919	118477612	Rat
1300179	Kidm5	Kidney mass QTL 5	3.51		kidney mass (VT:0002707)	left kidney wet weight (CMO:0000083)	7	51251919	145729302	Rat
1300149	Cm6	Cardiac mass QTL 6	4.09		heart mass (VT:0007028)	heart left ventricle weight to body weight ratio (CMO:0000530)	7	51252005	111589099	Rat
61428	Scl3	Serum cholesterol level QTL 3	3.2		blood cholesterol amount (VT:0000180)	serum total cholesterol level (CMO:0000363)	7	53200344	98200344	Rat
738030	Anxrr8	Anxiety related response QTL 8	4.1		exploratory behavior trait (VT:0010471)	number of entries into a discrete space in an experimental apparatus (CMO:0000960)	7	54259512	99259512	Rat
10059605	Kidm47	Kidney mass QTL 47	2.91	0.05	kidney mass (VT:0002707)	both kidneys wet weight to body weight ratio (CMO:0000340)	7	54534996	73293934	Rat
2317059	Aia15	Adjuvant induced arthritis QTL 15	2.46		joint integrity trait (VT:0010548)	right rear ankle joint diameter (CMO:0002150)	7	55072862	69399731	Rat
2316947	Rf58	Renal function QTL 58	7.8		kidney glomerulus morphology trait (VT:0005325)	index of glomerular damage (CMO:0001135)	7	55072862	123602998	Rat
2316952	Pur22	Proteinuria QTL 22	5.2		urine protein amount (VT:0005160)	urine protein level (CMO:0000591)	7	55072862	123602998	Rat
2316955	Stl24	Serum triglyceride level QTL 24	7.1		blood triglyceride amount (VT:0002644)	plasma triglyceride level (CMO:0000548)	7	55072862	123602998	Rat
2300178	Bmd54	Bone mineral density QTL 54	5.3	0.0001	femur mineral mass (VT:0010011)	volumetric bone mineral density (CMO:0001553)	7	55495689	100495689	Rat
2293644	Bmd29	Bone mineral density QTL 29	5.4	0.0001	femur size trait (VT:1000369)	femoral neck cross-sectional area (CMO:0001697)	7	55495689	100495689	Rat
2293667	Bss42	Bone structure and strength QTL 42	7.25	0.0001	lumbar vertebra size trait (VT:0010518)	lumbar vertebra cross-sectional area (CMO:0001689)	7	55495689	100495689	Rat
2293678	Bss24	Bone structure and strength QTL 24	6.71	0.0001	femur morphology trait (VT:0000559)	femur cross-sectional area (CMO:0001661)	7	55495689	100495689	Rat
2293685	Bmd21	Bone mineral density QTL 21	4.2	0.0003	femur mineral mass (VT:0010011)	total volumetric bone mineral density (CMO:0001728)	7	55495689	100495689	Rat
2293696	Bmd32	Bone mineral density QTL 32	5.1	0.0001	femur strength trait (VT:0010010)	femoral neck polar moment of inertia (CMO:0001670)	7	55495689	100495689	Rat
2293707	Bss32	Bone structure and strength QTL 32	7.64	0.0001	femur strength trait (VT:0010010)	femur midshaft polar moment of inertia (CMO:0001669)	7	55495689	100495689	Rat

miRNA Target Status

Predicted Target Of

	Summary Value
Count of predictions:	308
Count of miRNA genes:	199
Interacting mature miRNAs:	224
Transcripts:	ENSRNOT00000009203
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	3	26	28	18	19	18	1	1	74	21	38	11	1
Low		17	29	23		23	7	10		14	3		7
Below cutoff

View RNA-SEQ Expression Data

Sequence

Nucleotide Sequences


RefSeq Transcripts	NM_053830	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	BQ191246	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	C07146	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	CB733157	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	CB775175	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	CB792533	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	CH473960	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	CK844566	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	CV120917	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	EV764995	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	JACYVU010000185	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	L31840	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

Reference Sequences

RefSeq Acc Id:

ENSRNOT00000009203 ⟹ ENSRNOP00000009203

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
Rnor_6.0 Ensembl	7	60,781,729 - 60,825,242 (-)	Ensembl

RefSeq Acc Id:

NM_053830 ⟹ NP_446282

RefSeq Status:

VALIDATED

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	7	53,353,740 - 53,398,345 (-)	NCBI
Rnor_6.0	7	60,781,724 - 60,825,225 (-)	NCBI
Rnor_5.0	7	60,781,687 - 60,825,188 (-)	NCBI
RGSC_v3.4	7	57,059,744 - 57,104,512 (-)	RGD
Celera	7	50,124,939 - 50,169,469 (-)	RGD

Sequence:

show sequence

GCTGAAACGCGGTGGCTGGACTGTAATCAAAGTTGCAAGGTTCTATCTAGGTGGAGACGGCTGC
GGCCATGGACAGGAGTGGCTTCGGGGGAATGTCATCCCCTGTGATCCGAGACCCAGAGGTTACG
AGGACTGCACGGAAGCATAGTGCTCACAAAAGAGTTTTAATTCAGGCCAACCAAGATGAAAATT
TTGGTACTACTACACCAAGAAGCCAGATTATTCCTCGAACTCCAAGCTCATTTCGACAACCTTT
TACTCCACCAAGCCGAAGTTTACTAAGACACCCAGATATATCCTACATTTTTGGGACGGAAGGG
AGGTCTCCCCGGCATATACAGTCTTCTGGGTATTTGGGAAATCTTTCCATGGTGACTAACCTTG
ATGACAGCAACTGGGCAGCTGCATTCTCATCCCAGCGTTTAGGGTTCTACACAAACACGGAGCA
CCATAGTATGACTGAGGACATAAACCTAAGTACTGTCATGCTACGGGAGGATGACCCTGGAGAG
GCTGCATCCATGAGTATGTTCTCTGATTTCCTGCAGTCTTTCTTGAAGCACTCTTCAACCACAG
TCTTTGATCTTGTAGAAGAGTATGAAAATATTTGTGCTAGTCAGGTGAACATCCTGAGTAAAAT
CGTGAGCCGAGCAACGCCTGGACTGCAGAAGTTCTCCAAGACAGCCAGCATGCTCTGGCTTCTC
CAGCAGGAGATGGTCACGTGGAGGCTGCTTGCCTCTTTGTATAGAGACAGAATACAGTCTTCAT
TAGAAGAGGAAAATATGTTTGCAATTGCTGGTATCAATGCCAGTGAGAAGACGGTTGTGGAAGC
GCTGTTTCAGAGGGACACGCTGGTCCGACAGAGCCAGTTGGTGGTAGATTGGCTAGAGAGCATT
GCCAAAGATGAAATTGGAGATTTCTCAGACAATATTGAGTTTTATGCAAAATCAGTATATTGGG
AAAATACACTCCACTCCTTAAAACAGCGGCAGCTGCTGTCTTATATAGGAAGTACCCGTCCTCT
TGTCACTGAGCTGGACCCAGATGCTCCCATTAGACAGAAAATGCCGCTGGATGATCTGGACAGA
GAAGATGAAGTCAGACTGCTGAAGTACCTCTTCACTCTAATCCGTGCTGGGATGACCGAGGAGG
CACAGAGGCTCTGTAAACGGTGCGGGCAAGCATGGAGAGCTGCAACCCTGGAAGGATGGAAGCT
GCACCACGACCCCAACGTGAATGGAGGGACAGAGCTAGAGCCTGTCGAAGGGAATCCATATAGA
CGGATCTGGAAGATTAGTTGCTGGAGAATGGCTGAAGATGAACTTTTTAATAAATACGAAAGAG
CGATTTATGCAGCACTCAGTGGGAATCTCAAGCAGCTCCTTCCGGTCTGTGACACCTGGGAAGA
CACAGTGTGGGCCTATTTCCGGGTGATGGTGGACAGCCTGGTGGAGCAGGAGATTCGCACCTCA
GTCATGACCCTAGATGAAACTGAGGAGCTCCCTCGGGAGTACATGGAAGCGAATTGGACCTTAG
AAAAAGTTTTTGAAGAGCTTCAAGCCACTGATAAGAAGAGAGTTCTGGAAGAGAATCAAGAACA
TTACCATGTAGTCCAGAAATTCCTTATCCTGGGAGACATTGATGGTTTGATGGATGAATTTAGC
AAATGGCTGTCCAAGAGCAGAAGCAGTCTACCTGGACACCTCCTCCGTTTTATGACTCACCTCA
TTCTGTTTTTCCGCACCCTGGGACTGCAGACCAAAGAAGAAGTTTCCATTGAAGTTCTAAAGAC
GTATATACAGCTGTTAATCAATGAGAAGCACACAAACCTCATAGCGTTCTATACCTGTCATCTG
CCTCAAGACCTTGCGGTTGCCCAATACGCCTTGTTTTTGGAGGGTGTTACGGAGTGTGAGCAGC
GGCACCAGTGCCTGGAGCTGGCTAAGGAGGCAGATTTGGATGTTGCGACTATAACAAAAACTGT
AGTTGAAAATATTCGGAAGAAAGATAATGGTGAATTCAGTCACCATGACCTGGCTCCATCCCTG
GATACTGCCACTACTGAGGAGGACCGTTTGAAGATCGATGTGATTGACTGGCTGGTGTTTGACC
CAGCGCAGAGAGCCGAAGCCCTGAGACAAGGCAACGCCATCATGAGGAAGTTCTTAGCATTAAA
GAAACATGAAGCTGCAAAAGAAGTGTTTGTGAAAATTCCTCAGGATTCCATCGCAGAAATCTAT
AATCAGTGGGAGGAGCAAGGCATGGAGAGCCCTCTTCCTGCCGAGGATGATAACGCTATCCGAG
AGCACTTGTGTATCAGAGCTTATCTGGAAGCCCATGAAACCTTCAATGAGTGGTTTAAACATAT
GAATTCGGCTCCTCAGAAACCTACACTGCTGTCCCAGGCGACTTTTACAGAGAAAGTGGCTCAC
GAGCACAAAGAAAAGAAGTACGAGATGGATCATAATATTTGGAAAGGACATTTGGATGCTCTAA
CTGCTGATGTGAAGGAGAAAATGTACAACGTCTTATTGTTTGTTGATGGAGGATGGATGGTGGA
TGTCAGAGAGGACGCTGAGGAAGACCCGGAACGAGCTCATCAGATGGTTTTGCTGAGAAAGCTC
TGTCTCCCCATGCTGTGCTTCCTGCTTCACACCATACTGCACAGCACCGGGCAATACCAGGAGT
GCCTGCAGCTGGCCGACATGGTGTCCTCTGAGCGCCACAAGCTCTATCTGGTATTTTCTAAGGA
AGAACTAAGGAAACTGCTGCAGAAGTTAAGGGAGTCCTCGCTGATGCTCCTAGACCAGGGGCTT
GACCCGCTCGGCTATGAAATCCAGTCATAATTCACCATTCTCTGCGCCCGTGACTACAAGAGGA
TGCCTGCTTGCTTGGCTGTGTTGCTTAGTTGGTTGGTTTTGGTCAGATATACATATTTGTAATT
ATTGGTTTATTTGTTTGTTTGTTTCCTTTGGCATTCTTGGGGAAAATGTAAAATTTTGGCTTTT
GAATTTTGTATTATATCAGTATTTCCTTATGTATTTTTTAAAGAAATTATACAAAATAAATTTT
TTGTTCTATAGAAAAAAAAAAAAAAAAAA

hide sequence

Protein Sequences


Protein RefSeqs	NP_446282	(Get FASTA)	NCBI Sequence Viewer
GenBank Protein	AAA74476	(Get FASTA)	NCBI Sequence Viewer
	EDM16606	(Get FASTA)	NCBI Sequence Viewer
	EDM16607	(Get FASTA)	NCBI Sequence Viewer
	EDM16608	(Get FASTA)	NCBI Sequence Viewer
	EDM16609	(Get FASTA)	NCBI Sequence Viewer
	EDM16610	(Get FASTA)	NCBI Sequence Viewer
	EDM16611	(Get FASTA)	NCBI Sequence Viewer
	EDM16612	(Get FASTA)	NCBI Sequence Viewer
	P52590	(Get FASTA)	NCBI Sequence Viewer

Reference Sequences

RefSeq Acc Id:

NP_446282 ⟸ NM_053830

- UniProtKB:

F1LSL2 (UniProtKB/TrEMBL)

- Sequence:

show sequence

MDRSGFGGMSSPVIRDPEVTRTARKHSAHKRVLIQANQDENFGTTTPRSQIIPRTPSSFRQPFT
PPSRSLLRHPDISYIFGTEGRSPRHIQSSGYLGNLSMVTNLDDSNWAAAFSSQRLGFYTNTEHH
SMTEDINLSTVMLREDDPGEAASMSMFSDFLQSFLKHSSTTVFDLVEEYENICASQVNILSKIV
SRATPGLQKFSKTASMLWLLQQEMVTWRLLASLYRDRIQSSLEEENMFAIAGINASEKTVVEAL
FQRDTLVRQSQLVVDWLESIAKDEIGDFSDNIEFYAKSVYWENTLHSLKQRQLLSYIGSTRPLV
TELDPDAPIRQKMPLDDLDREDEVRLLKYLFTLIRAGMTEEAQRLCKRCGQAWRAATLEGWKLH
HDPNVNGGTELEPVEGNPYRRIWKISCWRMAEDELFNKYERAIYAALSGNLKQLLPVCDTWEDT
VWAYFRVMVDSLVEQEIRTSVMTLDETEELPREYMEANWTLEKVFEELQATDKKRVLEENQEHY
HVVQKFLILGDIDGLMDEFSKWLSKSRSSLPGHLLRFMTHLILFFRTLGLQTKEEVSIEVLKTY
IQLLINEKHTNLIAFYTCHLPQDLAVAQYALFLEGVTECEQRHQCLELAKEADLDVATITKTVV
ENIRKKDNGEFSHHDLAPSLDTATTEEDRLKIDVIDWLVFDPAQRAEALRQGNAIMRKFLALKK
HEAAKEVFVKIPQDSIAEIYNQWEEQGMESPLPAEDDNAIREHLCIRAYLEAHETFNEWFKHMN
SAPQKPTLLSQATFTEKVAHEHKEKKYEMDHNIWKGHLDALTADVKEKMYNVLLFVDGGWMVDV
REDAEEDPERAHQMVLLRKLCLPMLCFLLHTILHSTGQYQECLQLADMVSSERHKLYLVFSKEE
LRKLLQKLRESSLMLLDQGLDPLGYEIQS

hide sequence

RefSeq Acc Id:

ENSRNOP00000009203 ⟸ ENSRNOT00000009203

Transcriptome

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

Promoters

RGD ID:

13695218

Promoter ID:

EPDNEW_R5743

Type:

initiation region

Name:

Nup107_1

Description:

nucleoporin 107

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	7	60,825,250 - 60,825,310	EPDNEW

Strain Variation

Strain Sequence Variants (Rnor 6.0)

ACI/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)

ACI/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

ACI/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

BBDP/Wor (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

BN/SsN (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

Buf/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

COP/CrCrl (MCW & UW)

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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)

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

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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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

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/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

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 (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

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

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

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

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

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 (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

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

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 (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 (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

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 (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 (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 (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_6.0

Chromosome	Start Pos	End Pos	Reference Nucleotide	Variant Nucleotide	Variant Type	Strain
7	60794503	60794504	A	C	snv	LEW/NCrlBR (RGD)
7	60806223	60806224	T	C	snv	CDS

Additional Information

External Database Links

Database	Acc Id	Source(s)
AGR Gene	RGD:621160	AgrOrtholog
Ensembl Genes	ENSRNOG00000006541	Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein	ENSRNOP00000009203	ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript	ENSRNOT00000009203	ENTREZGENE, UniProtKB/TrEMBL
InterPro	Nup84/Nup107	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report	rno:116555	UniProtKB/TrEMBL
NCBI Gene	116555	ENTREZGENE
PANTHER	PTHR13003	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam	Nup84_Nup100	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen	Nup107	PhenoGen
UniProt	F1LSL2	ENTREZGENE, UniProtKB/TrEMBL
	NU107_RAT	UniProtKB/Swiss-Prot, ENTREZGENE

Nomenclature History

Date	Current Symbol	Current Name	Previous Symbol	Previous Name	Description	Reference	Status
2005-01-20	Nup107	nucleoporin 107		nuclear pore complex protein	Name updated	1299863	APPROVED
2002-08-07	Nup107	nuclear pore complex protein			Symbol and Name status set to provisional	70820	PROVISIONAL

RGD Curation Notes

Note Type	Note	Reference
gene_domains	contains a leucine zipper and kinase consensus sites	729023

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 - OMIM

RGD Manual Annotations

Imported Annotations - KEGG (archival)

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Imported Disease Annotations - ClinVar

Imported Disease Annotations - OMIM

RGD Manual Annotations

Imported Annotations - KEGG (archival)