Ndn (necdin, MAGE family member) - Rat Genome Database

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

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Gene: Ndn (necdin, MAGE family member) Rattus norvegicus

Analyze

Symbol:

Ndn

Name:

necdin, MAGE family member

RGD ID:

1310526

Description:

Predicted to have several functions, including DNA-binding transcription activator activity, RNA polymerase II-specific; gamma-tubulin binding activity; and promoter-specific chromatin binding activity. Predicted to be involved in several processes, including nervous system development; neurotrophin TRK receptor signaling pathway; and regulation of transcription, DNA-templated. Localizes to cytoplasm. Human ortholog(s) of this gene implicated in Prader-Willi syndrome. Orthologous to human NDN (necdin, MAGE family member); INTERACTS WITH 17alpha-ethynylestradiol; 2,3,7,8-tetrachlorodibenzodioxine; 6-propyl-2-thiouracil.

Type:

protein-coding

RefSeq Status:

PROVISIONAL

Also known as:

MGC105768; necdin; necdin homolog; necdin homolog (mouse); necdin, melanoma antigen (MAGE) family member

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):	NDN (necdin, MAGE family member)	HGNC	EggNOG, Ensembl, HomoloGene, Inparanoid, NCBI, OMA, OrthoDB, OrthoMCL, Panther, PhylomeDB, Treefam
Mus musculus (house mouse):	Ndn (necdin, MAGE family member)	HGNC	Treefam, EggNOG, OrthoMCL, NCBI, OMA, HomoloGene, Inparanoid, Panther, PhylomeDB, OrthoDB, Ensembl
Chinchilla lanigera (long-tailed chinchilla):	Ndn (necdin, MAGE family member)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Pan paniscus (bonobo/pygmy chimpanzee):	NDN (necdin, MAGE family member)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Canis lupus familiaris (dog):	NDN (necdin, MAGE family member)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Ictidomys tridecemlineatus (thirteen-lined ground squirrel):	Ndn (necdin, MAGE family member)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Sus scrofa (pig):	NDN (necdin, MAGE family member)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chlorocebus sabaeus (African green monkey):	NDN (necdin, MAGE family member)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Heterocephalus glaber (naked mole-rat):	Ndn (necdin, MAGE family member)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Alliance orthologs ³
Homo sapiens (human):	NDN (necdin, MAGE family member)	Alliance	DIOPT (HGNC\|PhylomeDB\|TreeFam)
Mus musculus (house mouse):	Ndn (necdin, MAGE family member)	Alliance	DIOPT (PhylomeDB\|TreeFam)

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	1	115,849,168 - 115,850,767 (+)	NCBI
Rnor_6.0 Ensembl	1	122,981,755 - 122,983,351 (+)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_6.0	1	122,981,755 - 122,983,354 (+)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_5.0	1	124,119,141 - 124,120,740 (+)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	1	116,594,603 - 116,596,202 (+)	NCBI	RGSC3.4		rn4	RGSC3.4
RGSC_v3.1	1	116,672,945 - 116,674,545 (+)	NCBI
Celera	1	108,120,324 - 108,121,923 (+)	NCBI		Celera
Cytogenetic Map	1	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

Angelman syndrome (ISO)

Animal Mammary Neoplasms (ISO)

autism spectrum disorder (ISO)

autistic disorder (ISO)

Birth Weight (ISO)

carcinoma (ISO)

chromosome 15q11.2 deletion syndrome (ISO)

Neurodevelopmental Disorders (ISO)

Prader-Willi syndrome (ISO)

schizophrenia (ISO)

Gene-Chemical Interaction Annotations Click to see Annotation Detail View

1,1-dichloroethene (ISO)

17alpha-ethynylestradiol (EXP)

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

3-isobutyl-1-methyl-7H-xanthine (ISO)

4-hydroperoxycyclophosphamide (ISO)

4-hydroxyphenyl retinamide (ISO)

5-aza-2'-deoxycytidine (ISO)

6-propyl-2-thiouracil (EXP)

aflatoxin B1 (ISO)

antirheumatic drug (ISO)

benzo[a]pyrene (ISO)

bis(2-chloroethyl) sulfide (ISO)

bisphenol A (EXP,ISO)

bisphenol F (ISO)

cadmium atom (ISO)

cyclosporin A (ISO)

dexamethasone (ISO)

diazinon (EXP)

dibutyl phthalate (ISO)

dieldrin (EXP)

diethylstilbestrol (EXP)

diuron (EXP)

doxorubicin (ISO)

ethanol (ISO)

indometacin (ISO)

methoxychlor (EXP)

methylmercury chloride (ISO)

N-ethyl-N-nitrosourea (ISO)

nitric oxide (ISO)

oxaliplatin (EXP)

PhIP (EXP)

pirinixic acid (ISO)

S-butyl-DL-homocysteine (S,R)-sulfoximine (ISO)

silicon dioxide (EXP)

sodium fluoride (ISO)

sunitinib (ISO)

tetrachloromethane (EXP,ISO)

topotecan (EXP)

valproic acid (ISO)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

axon extension (ISO)

axonal fasciculation (ISO)

axonogenesis (ISO)

central nervous system development (ISO)

genetic imprinting (ISO)

glial cell migration (ISO)

multicellular organismal homeostasis (ISO)

negative regulation of cell population proliferation (IEA)

negative regulation of DNA-binding transcription factor activity (ISO)

negative regulation of transcription by RNA polymerase II (ISO)

neuron development (ISO)

neuron differentiation (ISO)

neuron migration (ISO)

neurotrophin TRK receptor signaling pathway (ISO,NAS)

positive regulation of protein deacetylation (ISO)

positive regulation of transcription by RNA polymerase II (ISO)

post-embryonic development (ISO)

regulation of transcription, DNA-templated (ISO)

respiratory gaseous exchange by respiratory system (ISO)

respiratory system process (ISO)

sensory perception of pain (ISO)

Cellular Component

cell projection (ISO)

centrosome (ISO)

cytoplasm (IDA,ISO)

cytosol (ISO)

nucleoplasm (IEA,ISO)

nucleus (ISO)

protein-containing complex (ISO)

Molecular Function

DNA-binding transcription activator activity, RNA polymerase II-specific (ISO)

gamma-tubulin binding (ISO)

promoter-specific chromatin binding (ISO)

protein binding (IPI,ISO)

RNA polymerase II cis-regulatory region sequence-specific DNA binding (ISO)

References

References - curated


1.	GOA data from the GO Consortium
2.	Liu X, etal., Mol Cell Neurosci. 2009 May;41(1):51-61. Epub 2009 Feb 6.
3.	MGD data from the GO Consortium
4.	Nakada Y, etal., Gene. 1998 Jun 15;213(1-2):65-72.
5.	OMIM Disease Annotation Pipeline
6.	RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
7.	RGD automated import pipeline for gene-chemical interactions
8.	Tcherpakov M, etal., J Biol Chem 2002 Dec 20;277(51):49101-4.

Additional References at PubMed

PMID:10508517	PMID:10965153	PMID:12477932	PMID:12629158	PMID:14593116	PMID:15649943	PMID:15972963	PMID:16049186	PMID:19818769	PMID:20220004	PMID:20663865	PMID:21150695
PMID:22442722	PMID:24349431

Genomics

Comparative Map Data

Ndn
(Rattus norvegicus - Norway rat)

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
mRatBN7.2	1	115,849,168 - 115,850,767 (+)	NCBI
Rnor_6.0 Ensembl	1	122,981,755 - 122,983,351 (+)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_6.0	1	122,981,755 - 122,983,354 (+)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_5.0	1	124,119,141 - 124,120,740 (+)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	1	116,594,603 - 116,596,202 (+)	NCBI	RGSC3.4		rn4	RGSC3.4
RGSC_v3.1	1	116,672,945 - 116,674,545 (+)	NCBI
Celera	1	108,120,324 - 108,121,923 (+)	NCBI		Celera
Cytogenetic Map	1	q22	NCBI

NDN
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38.p13 Ensembl	15	23,685,400 - 23,687,305 (-)	Ensembl	GRCh38		hg38	GRCh38
GRCh38	15	23,685,400 - 23,687,305 (-)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh37	15	23,930,547 - 23,932,452 (-)	NCBI	GRCh37	GRCh37	hg19	GRCh37
GRCh37	15	23,930,554 - 23,932,450 (-)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	15	21,481,647 - 21,483,543 (-)	NCBI	NCBI36		hg18	NCBI36
Build 34	15	21,481,646 - 21,483,543	NCBI
Celera	15	2,091,460 - 2,093,348 (-)	NCBI
Cytogenetic Map	15	q11.2	NCBI
HuRef	15	2,066,175 - 2,068,071 (-)	NCBI		HuRef
CHM1_1	15	23,880,849 - 23,882,745 (-)	NCBI		CHM1_1

Ndn
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	7	61,998,025 - 61,999,676 (+)	NCBI	GRCm39		mm39
GRCm38	7	62,348,277 - 62,349,928 (+)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	7	62,346,569 - 62,350,262 (+)	Ensembl	GRCm38		mm10	GRCm38
MGSCv37	7	69,493,163 - 69,494,814 (+)	NCBI	GRCm37		mm9	NCBIm37
MGSCv36	7	51,709,553 - 51,711,133 (+)	NCBI			mm8
MGSCv36	7	62,227,298 - 62,228,878 (+)	NCBI			mm8
Cytogenetic Map	7	C	NCBI
cM Map	7	34.36	NCBI

Ndn
(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_004955416	31,125,924 - 31,126,889 (-)	Ensembl	ChiLan1.0
ChiLan1.0	NW_004955416	31,125,354 - 31,127,010 (-)	NCBI	ChiLan1.0	ChiLan1.0

NDN
(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	15	21,176,270 - 21,177,467 (-)	NCBI	panpan1.1	PanPan1.1	panPan2
Mhudiblu_PPA_v0	15	5,977,519 - 5,979,185 (+)	NCBI	Mhudiblu_PPA_v0		panPan3

NDN
(Canis lupus familiaris - dog)

Dog Assembly	Chr	Position (strand)	Source	Genome Browsers
Dog Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
CanFam3.1 Ensembl	3	36,314,104 - 36,315,081 (+)	Ensembl	CanFam3.1		canFam3	CanFam3.1
CanFam3.1	3	36,313,977 - 36,315,661 (+)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1

Ndn
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)

Squirrel Assembly	Chr	Position (strand)	Source	Genome Browsers
Squirrel Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
SpeTri2.0	NW_004936805	849,218 - 850,894 (+)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

NDN
(Sus scrofa - pig)

Pig Assembly	Chr	Position (strand)	Source	Genome Browsers
Pig Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Sscrofa11.1 Ensembl	1	142,412,565 - 142,414,240 (+)	Ensembl	Sscrofa11.1		susScr11	Sscrofa11.1
Sscrofa11.1	1	142,412,688 - 142,413,665 (+)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1
Sscrofa10.2	1	158,275,444 - 158,276,423 (+)	NCBI	Sscrofa10.2	Sscrofa10.2	susScr3

NDN
(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	26	57,939,212 - 57,940,868 (+)	NCBI
ChlSab1.1 Ensembl	26	57,939,330 - 57,940,295 (+)	Ensembl

Ndn
(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_004624768	579,607 - 581,302 (+)	NCBI

Position Markers

AI528698

Rat Assembly	Chr	Position (strand)	Source	JBrowse
Rnor_6.0	1	122,983,147 - 122,983,238	NCBI	Rnor6.0
Rnor_5.0	1	124,120,533 - 124,120,624	UniSTS	Rnor5.0
RGSC_v3.4	1	116,595,995 - 116,596,086	UniSTS	RGSC3.4
Celera	1	108,121,716 - 108,121,807	UniSTS
Cytogenetic Map	1	q22	UniSTS

Ndn

Rat Assembly	Chr	Position (strand)	Source	JBrowse
Rnor_6.0	1	122,982,150 - 122,983,096	NCBI	Rnor6.0
Rnor_5.0	1	124,119,536 - 124,120,482	UniSTS	Rnor5.0
RGSC_v3.4	1	116,594,998 - 116,595,944	UniSTS	RGSC3.4
Celera	1	108,120,719 - 108,121,665	UniSTS
Cytogenetic Map	1	q22	UniSTS

Ndn

Rat Assembly	Chr	Position (strand)	Source	JBrowse
Rnor_6.0	1	122,982,068 - 122,982,446	NCBI	Rnor6.0
Rnor_5.0	1	124,119,454 - 124,119,832	UniSTS	Rnor5.0
Celera	1	108,120,637 - 108,121,015	UniSTS
Cytogenetic Map	1	q22	UniSTS

Ndn

Rat Assembly	Chr	Position (strand)	Source	JBrowse
Rnor_6.0	1	122,982,068 - 122,983,339	NCBI	Rnor6.0
Rnor_5.0	1	124,119,454 - 124,120,725	UniSTS	Rnor5.0
Celera	1	108,120,637 - 108,121,908	UniSTS
Cytogenetic Map	1	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
1358359	Sradr1	Stress Responsive Adrenal Weight QTL 1	4.74		adrenal gland mass (VT:0010420)	both adrenal glands wet weight (CMO:0000164)	1	25951907	130917265	Rat
70225	Bp58	Blood pressure QTL 58	3.3		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	1	34993530	173445086	Rat
10059597	Bp377	Blood pressure QTL 377	3.42	0.025	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	1	35377692	217372257	Rat
2313051	Bss57	Bone structure and strength QTL 57	3.7	0.0001	tibia strength trait (VT:1000284)	bone polar moment of inertia (CMO:0001558)	1	43579208	126240667	Rat
2313059	Bss55	Bone structure and strength QTL 55	3.2	0.0001	tibia size trait (VT:0100001)	tibia midshaft cross-sectional area (CMO:0001717)	1	43579208	126240667	Rat
2313072	Bss53	Bone structure and strength QTL 53	4.3	0.0001	tibia length (VT:0004357)	tibia length (CMO:0000450)	1	43579208	126240667	Rat
2313078	Bss54	Bone structure and strength QTL 54	3.5	0.0001	tibia area (VT:1000281)	tibia midshaft cross-sectional area (CMO:0001717)	1	43579208	126240667	Rat
2313094	Bss58	Bone structure and strength QTL 58	3.7	0.0001	tibia strength trait (VT:1000284)	tibia total energy absorbed before break (CMO:0001736)	1	43579208	126240667	Rat
2313098	Bmd70	Bone mineral density QTL 70	3.6	0.0001	tibia mineral mass (VT:1000283)	cortical volumetric bone mineral density (CMO:0001730)	1	43579208	126240667	Rat
2313099	Bss56	Bone structure and strength QTL 56	2.4	0.0001	tibia size trait (VT:0100001)	tibia midshaft endosteal cross-sectional area (CMO:0001716)	1	43579208	126240667	Rat
2313402	Anxrr24	Anxiety related response QTL 24			aggression-related behavior trait (VT:0015014)	tameness/aggressiveness composite score (CMO:0002136)	1	49147799	156446783	Rat
1578654	Bss10	Bone structure and strength QTL 10	4		femur morphology trait (VT:0000559)	femoral neck cortical cross-sectional area (CMO:0001702)	1	49578577	169852184	Rat
634314	Niddm44	Non-insulin dependent diabetes mellitus QTL 44			blood glucose amount (VT:0000188)	blood glucose level (CMO:0000046)	1	49578693	217054291	Rat
2298545	Neuinf8	Neuroinflammation QTL 8	4.6		nervous system integrity trait (VT:0010566)	spinal cord beta-2 microglobulin mRNA level (CMO:0002125)	1	58354072	161711996	Rat
7421628	Bp361	Blood pressure QTL 361		0.001	arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	1	64588516	125875986	Rat
7411712	Strs4	Sensitivity to stroke QTL 4	8.7		cerebrum integrity trait (VT:0010549)	percentage of study population developing cerebrovascular lesions during a period of time (CMO:0000932)	1	79689548	124689548	Rat
1578780	Cm52	Cardiac mass QTL 52	3.3	0.0001	heart mass (VT:0007028)	heart wet weight (CMO:0000069)	1	82788437	239853971	Rat
10054135	Gmadr2	Adrenal mass QTL 2	1.97	0.0129	adrenal gland mass (VT:0010420)	both adrenal glands wet weight (CMO:0000164)	1	83502376	128502376	Rat
2313083	Bmd74	Bone mineral density QTL 74	4	0.0001	tibia mineral mass (VT:1000283)	total volumetric bone mineral density (CMO:0001728)	1	83656882	126240667	Rat
61344	Bp29	Blood pressure QTL 29	7.5		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	1	85779320	130779320	Rat
1582234	Gluco18	Glucose level QTL 18	3.4	0.0003	blood glucose amount (VT:0000188)	blood glucose level (CMO:0000046)	1	85917265	130917265	Rat
4889494	Scort2	Serum corticosterone level QTL 2	4.2		blood corticosterone amount (VT:0005345)	plasma corticosterone level (CMO:0001173)	1	86776571	131776571	Rat
724529	Cm16	Cardiac mass QTL 16	2.7		heart mass (VT:0007028)	calculated heart weight (CMO:0000073)	1	90804143	161321256	Rat
738022	Anxrr13	Anxiety related response QTL 13	4.6	0.00039	locomotor behavior trait (VT:0001392)	number of 20 x 20 cm floor squares crossed into, out of or within a discrete space in an experimental apparatus (CMO:0001514)	1	91093646	136093646	Rat
724521	Uae1	Urinary albumin excretion QTL 1	3.8	0.0001	urine albumin amount (VT:0002871)	urine albumin excretion rate (CMO:0000757)	1	94201400	184846632	Rat
1358902	Bw47	Body weight QTL 47	1.67		body mass (VT:0001259)	body weight (CMO:0000012)	1	94201400	197187904	Rat
1302788	Scl19	Serum cholesterol QTL 19	4.6	0.001	blood cholesterol amount (VT:0000180)	plasma total cholesterol level (CMO:0000585)	1	94225372	130917265	Rat
1300153	Bp171	Blood pressure QTL 171	3.37		arterial blood pressure trait (VT:2000000)	diastolic blood pressure (CMO:0000005)	1	94364073	153076991	Rat
724567	Tcas6	Tongue tumor susceptibility QTL 6	6.85		tongue integrity trait (VT:0010553)	number of squamous cell tumors of the tongue with diameter greater than 3 mm (CMO:0001950)	1	95304961	156446783	Rat
1331800	Scl25	Serum cholesterol level QTL 25	3.013		blood cholesterol amount (VT:0000180)	serum total cholesterol level (CMO:0000363)	1	99983293	127203999	Rat
1331793	Bp200	Blood pressure QTL 200	3.71601		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	1	99983293	188289386	Rat
1331751	Bp199	Blood pressure QTL 199	3.60022		arterial blood pressure trait (VT:2000000)	diastolic blood pressure (CMO:0000005)	1	99983293	198656062	Rat
1331749	Hrtrt11	Heart rate QTL 11	2.973		heart pumping trait (VT:2000009)	heart rate (CMO:0000002)	1	99983293	216213510	Rat
70209	Niddm23	Non-insulin dependent diabetes mellitus QTL 23	2.82		blood glucose amount (VT:0000188)	blood glucose level (CMO:0000046)	1	99983293	216325819	Rat
731168	Bp154	Blood pressure QTL 154	3.4		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	1	100131562	236763528	Rat
2293142	Bp314	Blood pressure QTL 314			arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	1	100354344	145354344	Rat
8655649	Arrd1	Age-related retinal degeneration QTL 1	4.89		retinal layer morphology trait (VT:0003727)	percentage of study population developing retinopathy during a period of time (CMO:0002453)	1	106002252	202571904	Rat
61370	Mcs3	Mammary carcinoma susceptibility QTL 3	2.15		mammary gland integrity trait (VT:0010552)	mammary tumor number (CMO:0000343)	1	108057233	167517487	Rat
1641897	Alcrsp1	Alcohol response QTL 1			response to alcohol trait (VT:0010489)	duration of loss of righting reflex (CMO:0002289)	1	108417193	153417193	Rat
2317833	Alcrsp19	Alcohol response QTL 19	12.4	0.001	response to alcohol trait (VT:0010489)	duration of loss of righting reflex (CMO:0002289)	1	108417193	153417193	Rat
1354623	Rf46	Renal function QTL 46	3.8		blood creatinine amount (VT:0005328)	plasma creatinine level (CMO:0000537)	1	108986301	161784422	Rat
1354591	Cm36	Cardiac mass QTL 36	4.1		heart left ventricle mass (VT:0007031)	calculated heart weight (CMO:0000073)	1	108986301	219232156	Rat
1354615	Cm32	Cardiac mass QTL 32	5.2		heart left ventricle mass (VT:0007031)	heart left ventricle wet weight (CMO:0000071)	1	108986301	219232156	Rat
1354606	Bp246	Blood pressure QTL 246	3.6		arterial blood pressure trait (VT:2000000)	pulse pressure (CMO:0000292)	1	108986301	238830534	Rat
2303591	Gluco41	Glucose level QTL 41	2		blood glucose amount (VT:0000188)	blood glucose level (CMO:0000046)	1	109634374	154634374	Rat
9590300	Scort16	Serum corticosterone level QTL 16	4.39	0.001	blood corticosterone amount (VT:0005345)	plasma corticosterone level (CMO:0001173)	1	110620749	155620749	Rat
8694370	Bw154	Body weight QTL 154	8.91	0.001	body lean mass (VT:0010483)	lean tissue morphological measurement (CMO:0002184)	1	110620749	155620749	Rat
61399	Tcat1	Tongue tumor resistance QTL 1	3.3		tongue integrity trait (VT:0010553)	number of squamous cell tumors of the tongue with diameter greater than 5 mm (CMO:0001879)	1	111446783	156446783	Rat
61346	Rf2	Renal disease susceptibility QTL 2	3.7		urine protein amount (VT:0005160)	urine protein level (CMO:0000591)	1	111446783	156446783	Rat
631569	Bp93	Blood pressure QTL 93		0.0001	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	1	113593576	129209407	Rat
631496	Bp97	Blood pressure QTL 97	3.08		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	1	113593576	158593576	Rat
1300158	Bp173	Blood pressure QTL 173	3.48		arterial blood pressure trait (VT:2000000)	blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)	1	122614824	201146953	Rat
7794788	Mcs32	Mammary carcinoma susceptibility QTL 32	2.61		mammary gland integrity trait (VT:0010552)	mammary tumor incidence/prevalence measurement (CMO:0000946)	1	122614824	262664716	Rat

miRNA Target Status

Predicted Target Of

	Summary Value
Count of predictions:	90
Count of miRNA genes:	70
Interacting mature miRNAs:	86
Transcripts:	ENSRNOT00000013468
Prediction methods:	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	1	28	22	12	7	12	2	2	74	20	33	6	2
Low	2	15	29	23	12	23	6	9		15	8	5	6
Below cutoff			6	6		6

View RNA-SEQ Expression Data

Sequence

Nucleotide Sequences


RefSeq Transcripts	NM_001008558	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	BC087630	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	CH473980	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	JACYVU010000038	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

Reference Sequences

RefSeq Acc Id:

ENSRNOT00000013468 ⟹ ENSRNOP00000013464

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
Rnor_6.0 Ensembl	1	122,981,755 - 122,983,351 (+)	Ensembl

RefSeq Acc Id:

NM_001008558 ⟹ NP_001008558

RefSeq Status:

PROVISIONAL

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	1	115,849,168 - 115,850,767 (+)	NCBI
Rnor_6.0	1	122,981,755 - 122,983,354 (+)	NCBI
Rnor_5.0	1	124,119,141 - 124,120,740 (+)	NCBI
RGSC_v3.4	1	116,594,603 - 116,596,202 (+)	RGD
Celera	1	108,120,324 - 108,121,923 (+)	RGD

Sequence:

show sequence

CACTGAGGCAGTGCAGGCTCCGAGAGCTCCGAGTCGCAGCGGTCCTGCTCTGATCAAAAGACGC
AGAATGTCGGAACAAAGTAAGGACCTGAGCGACCCTAACTTTGCCGCTGAGGACCCCGACACTG
AGATGCAGGTCAGCGATGCTGTTCCGGTGGGGGTCCCTCCTCCCGCTCCTCTGGCCGCGAACCT
CTCAGGGCCATCGTGCGCTCCGGAAGGCCCTATGGCAGCCCCACAGGCCTCGCCACCACCTGCA
GAACGGTTTGAAGAGGTTGACCCTAAGATCCTGCAGCAGGCCGCAGAAGAGGGCCGCGCCCACC
AGCCCCAGAGCCCAGCCCGGCCGATCCCAGCACCGCCGGCCCCTGCCCAGCTGGTGCAGAAGGC
GCACGAGCTCATGTGGTACGTGTTGGTCAAGGACCAGAAGAGGATGGTCCTCTGGCTTCCAGAC
ATGGTGAAAGAGGTCATGGGCAGCTACAAGAAGTGGTGCAGAAGCATCCTCAGGCGCACCAGCG
TCATCCTCGCCAGAGTTTTCGGGCTGCACCTGAGGCTGACCAATCTCCACACCATGGAGTTCGC
CCTGGTCAAAGCACTCAGCCCAGAAGAGCTGGACAGAGTCGCGCTGAACAACCGTATGCCCATG
ACAGGTCTCCTGCTCATGATCCTGAGTCTCATCTATGTGAAGGGCCGCGGGGCCAGAGAGGGTG
CGGTCTGGAATGTGCTGCGCATCCTGGGGCTGAGGCCCTGGAAGAAGCACTCCACCTTCGGAGA
TGTGAGAAAGATTATCACCGAGGAGTTCGTCCAGCAGAATTACCTGAAGTACCAGCGTGTGCCC
CACATCGAGCCTCCCGAGTACGAGTTCTTCTGGGGCCCCAGAGCTAACCGTGAAATCACCAAGA
TGCAGATCATGGAGTTCCTGGCCAGAGTCTTTAAGAAGGATCCCCAGGCTTGGCCTTCCCGCTA
CAGAGAGGCTCTGGAGCAGGCCAGAGCTCTGCGGGAGGCTAATCTTGTCGCCCAGGCCCCCCGC
AGCAGTGTCTCTGAGGACTAAAATGTCCAGGAGCACATTGATAGTTTCTGACCCATACTAGGGC
TGTGTAAGGGTGGGGTTGGACATTAGAGTATCCCAGATTCATAGTGCAGTATTTCATGTATAGT
TTTTAAGTTTTCCATCCAGTGCTTTTTTTATCTTGTAATGCAATGTATTCAGTTGTGTACTCGT
GTAGTGTTTAAAATTGATGCATGTGTGTTTTATAAGTGAGCAAGTTGGTACTTTCACTTCTGTG
CTTTCTTGGATTTTTGTACAAGAGATGTGCTGTGCTAAACTTGTGAAATACATTGAGGTGTTCT
GTATCTTGTTCTTTGAATGGGACTGATGGTCCGTATCGACAAAGAAGGCCCTGGAGAGTTAGCA
GGACTTAACAACAACACAGACCTGACCAAGAGAAAGGTCAGGGTCCCTCTCCATATGACTCCAA
CTGGCACAGGAAACATCCATGTGGAATGGACTGATTTGAACTGGACTGTTTTCAGTTTAAGCAC
TTAGCACACTTTGCAAAACATGTATCCAACCCCACCATAAATAAACTTTAAAATGAGCATTAAA
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAGG

hide sequence

Protein Sequences


Protein RefSeqs	NP_001008558	(Get FASTA)	NCBI Sequence Viewer
GenBank Protein	AAH87630	(Get FASTA)	NCBI Sequence Viewer
	EDM08368	(Get FASTA)	NCBI Sequence Viewer

Reference Sequences

RefSeq Acc Id:

NP_001008558 ⟸ NM_001008558

- UniProtKB:

Q5PPL0 (UniProtKB/TrEMBL)

- Sequence:

show sequence

MSEQSKDLSDPNFAAEDPDTEMQVSDAVPVGVPPPAPLAANLSGPSCAPEGPMAAPQASPPPAE
RFEEVDPKILQQAAEEGRAHQPQSPARPIPAPPAPAQLVQKAHELMWYVLVKDQKRMVLWLPDM
VKEVMGSYKKWCRSILRRTSVILARVFGLHLRLTNLHTMEFALVKALSPEELDRVALNNRMPMT
GLLLMILSLIYVKGRGAREGAVWNVLRILGLRPWKKHSTFGDVRKIITEEFVQQNYLKYQRVPH
IEPPEYEFFWGPRANREITKMQIMEFLARVFKKDPQAWPSRYREALEQARALREANLVAQAPRS
SVSED

hide sequence

RefSeq Acc Id:

ENSRNOP00000013464 ⟸ ENSRNOT00000013468

Protein Domains

MAGE

Transcriptome

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

Promoters

RGD ID:

13690090

Promoter ID:

EPDNEW_R615

Type:

multiple initiation site

Name:

Ndn_1

Description:

necdin, MAGE family member

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	1	122,981,735 - 122,981,795	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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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

Additional Information

External Database Links

Database	Acc Id	Source(s)
AGR Gene	RGD:1310526	AgrOrtholog
Ensembl Genes	ENSRNOG00000010146	Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein	ENSRNOP00000013464	ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript	ENSRNOT00000013468	ENTREZGENE, UniProtKB/TrEMBL
Gene3D-CATH	1.10.10.1200	UniProtKB/TrEMBL
	1.10.10.1210	UniProtKB/TrEMBL
IMAGE_CLONE	IMAGE:7319134	IMAGE-MGC_LOAD
InterPro	MAGE	UniProtKB/TrEMBL
	MAGE	UniProtKB/TrEMBL
	MAGE_WH1	UniProtKB/TrEMBL
	MAGE_WH2	UniProtKB/TrEMBL
	Necdin	UniProtKB/TrEMBL
KEGG Report	rno:308690	UniProtKB/TrEMBL
MGC_CLONE	MGC:105768	IMAGE-MGC_LOAD
NCBI Gene	308690	ENTREZGENE
PANTHER	PTHR11736	UniProtKB/TrEMBL
	PTHR11736:SF10	UniProtKB/TrEMBL
Pfam	MAGE	UniProtKB/TrEMBL
PhenoGen	Ndn	PhenoGen
PROSITE	MAGE	UniProtKB/TrEMBL
SMART	MAGE	UniProtKB/TrEMBL
UniProt	G3V7A4_RAT	UniProtKB/TrEMBL
	Q5PPL0	ENTREZGENE, UniProtKB/TrEMBL

Nomenclature History

Date	Current Symbol	Current Name	Previous Symbol	Previous Name	Description	Reference	Status
2015-12-10	Ndn	necdin, MAGE family member	Ndn	necdin, melanoma antigen (MAGE) family member	Nomenclature updated to reflect human and mouse nomenclature	1299863	APPROVED
2012-12-18	Ndn	necdin, melanoma antigen (MAGE) family member	Ndn	necdin homolog (mouse)	Nomenclature updated to reflect human and mouse nomenclature	1299863	APPROVED
2008-09-09	Ndn	necdin homolog (mouse)	Ndn	necdin	Nomenclature updated to reflect human and mouse nomenclature	1299863	APPROVED
2005-12-06	Ndn	necdin	Ndn_predicted	necdin (predicted)	Symbol and Name updated	1559027	APPROVED
2005-01-12	Ndn_predicted	necdin (predicted)			Symbol and Name status set to approved	70820	APPROVED

RGD Curation Notes

Note Type	Note	Reference
gene_mutations_overexpression	ectopic expression of Mageh1 in PC-12 cells caused an acceleration of NGF-induced neuronal differentiation, possibly through synergy between Nectin-Ngfr signaling and a TrkA signaling pathway	729117

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