Neurod6 (neuronal differentiation 6)

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Gene: Neurod6 (neuronal differentiation 6) Rattus norvegicus

Analyze

Symbol:

Neurod6

Name:

neuronal differentiation 6

RGD ID:

1562793

Description:

Predicted to have DNA-binding transcription activator activity, RNA polymerase II-specific and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Predicted to be involved in dentate gyrus development; neuron differentiation; and positive regulation of transcription by RNA polymerase II. Predicted to localize to nucleus. Orthologous to human NEUROD6 (neuronal differentiation 6); INTERACTS WITH benzo[a]pyrene; bisphenol A; C60 fullerene.

Type:

protein-coding

RefSeq Status:

PROVISIONAL

Also known as:

LOC500137; neurogenic differentiation 6; neurogenic differentiation factor 6; RGD1562793; similar to NEX-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):	NEUROD6 (neuronal differentiation 6)	HGNC	Ensembl, HomoloGene, Inparanoid, NCBI, OMA, OrthoDB, OrthoMCL, Panther, PhylomeDB, Treefam
Mus musculus (house mouse):	Neurod6 (neurogenic differentiation 6)	HGNC	Treefam, OrthoMCL, NCBI, OMA, HomoloGene, Inparanoid, Panther, PhylomeDB, OrthoDB, Ensembl
Chinchilla lanigera (long-tailed chinchilla):	Neurod6 (neuronal differentiation 6)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Pan paniscus (bonobo/pygmy chimpanzee):	NEUROD6 (neuronal differentiation 6)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Canis lupus familiaris (dog):	NEUROD6 (neuronal differentiation 6)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Ictidomys tridecemlineatus (thirteen-lined ground squirrel):	Neurod6 (neuronal differentiation 6)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Sus scrofa (pig):	NEUROD6 (neuronal differentiation 6)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chlorocebus sabaeus (African green monkey):	NEUROD6 (neuronal differentiation 6)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Heterocephalus glaber (naked mole-rat):	Neurod6 (neuronal differentiation 6)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Alliance orthologs ³
Homo sapiens (human):	NEUROD6 (neuronal differentiation 6)	Alliance	DIOPT (Ensembl Compara\|HGNC\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|TreeFam)
Mus musculus (house mouse):	Neurod6 (neurogenic differentiation 6)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|TreeFam)
Danio rerio (zebrafish):	neurod6b (neuronal differentiation 6b)	Alliance	DIOPT (Ensembl Compara\|OMA\|OrthoFinder\|PANTHER\|TreeFam)
Danio rerio (zebrafish):	neurod6a (neuronal differentiation 6a)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|TreeFam)
Caenorhabditis elegans (roundworm):	cnd-1	Alliance	DIOPT (Ensembl Compara\|InParanoid\|OrthoFinder\|OrthoInspector)

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	4	84,846,659 - 84,849,905 (-)	NCBI
Rnor_6.0 Ensembl	4	85,911,861 - 85,915,099 (-)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_6.0	4	85,911,861 - 85,915,107 (-)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_5.0	4	150,564,266 - 150,567,512 (-)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	4	84,476,070 - 84,479,316 (-)	NCBI	RGSC3.4		rn4	RGSC3.4
Celera	4	79,712,924 - 79,716,170 (-)	NCBI		Celera
Cytogenetic Map	4	q24	NCBI

JBrowse:

View Region in Genome Browser (JBrowse)

Model

Annotation Click to see Annotation Detail View

Disease Annotations Click to see Annotation Detail View

pleomorphic xanthoastrocytoma (ISO)

Gene-Chemical Interaction Annotations Click to see Annotation Detail View

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

4,4'-sulfonyldiphenol (ISO)

aflatoxin B1 (ISO)

benzo[a]pyrene (EXP,ISO)

bis(2-chloroethyl) sulfide (ISO)

bisphenol A (EXP)

C60 fullerene (EXP)

cyclosporin A (ISO)

entinostat (ISO)

ethanol (ISO)

ketamine (EXP)

lipopolysaccharide (ISO)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

dentate gyrus development (ISO)

neuron differentiation (IBA)

positive regulation of transcription by RNA polymerase II (ISO)

regulation of transcription by RNA polymerase II (IBA)

Cellular Component

nucleus (IBA)

Molecular Function

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

DNA-binding transcription factor activity, RNA polymerase II-specific (IBA)

protein dimerization activity (IEA)

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

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.	RGD automated import pipeline for gene-chemical interactions

Additional References at PubMed

PMID:10804213	PMID:12477932	PMID:12562512	PMID:15659228	PMID:19610105	PMID:20517466

Genomics

Comparative Map Data

Neurod6
(Rattus norvegicus - Norway rat)

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
mRatBN7.2	4	84,846,659 - 84,849,905 (-)	NCBI
Rnor_6.0 Ensembl	4	85,911,861 - 85,915,099 (-)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_6.0	4	85,911,861 - 85,915,107 (-)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_5.0	4	150,564,266 - 150,567,512 (-)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	4	84,476,070 - 84,479,316 (-)	NCBI	RGSC3.4		rn4	RGSC3.4
Celera	4	79,712,924 - 79,716,170 (-)	NCBI		Celera
Cytogenetic Map	4	q24	NCBI

NEUROD6
(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	31,337,465 - 31,340,726 (-)	Ensembl	GRCh38		hg38	GRCh38
GRCh38	7	31,337,465 - 31,340,726 (-)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh37	7	31,377,079 - 31,380,340 (-)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	7	31,343,604 - 31,347,063 (-)	NCBI	NCBI36		hg18	NCBI36
Build 34	7	31,150,319 - 31,153,778	NCBI
Celera	7	31,365,996 - 31,369,454 (-)	NCBI
Cytogenetic Map	7	p14.3	NCBI
HuRef	7	31,259,879 - 31,263,342 (-)	NCBI		HuRef
CHM1_1	7	31,376,632 - 31,380,087 (-)	NCBI		CHM1_1
CRA_TCAGchr7v2	7	31,426,277 - 31,429,739 (-)	NCBI

Neurod6
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	6	55,654,803 - 55,658,248 (-)	NCBI	GRCm39		mm39
GRCm39 Ensembl	6	55,654,807 - 55,658,248 (-)	Ensembl
GRCm38	6	55,677,818 - 55,681,263 (-)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	6	55,677,822 - 55,681,263 (-)	Ensembl	GRCm38		mm10	GRCm38
MGSCv37	6	55,627,812 - 55,631,257 (-)	NCBI	GRCm37		mm9	NCBIm37
MGSCv36	6	55,607,401 - 55,610,647 (-)	NCBI			mm8
Celera	6	56,208,451 - 56,211,896 (-)	NCBI		Celera
Cytogenetic Map	6	B3	NCBI
cM Map	6	27.53	NCBI

Neurod6
(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_004955410	32,408,052 - 32,411,273 (-)	Ensembl	ChiLan1.0
ChiLan1.0	NW_004955410	32,408,052 - 32,411,273 (-)	NCBI	ChiLan1.0	ChiLan1.0

NEUROD6
(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	32,068,515 - 32,071,974 (-)	NCBI	panpan1.1	PanPan1.1	panPan2
Mhudiblu_PPA_v0	7	31,949,900 - 31,953,353 (-)	NCBI	Mhudiblu_PPA_v0		panPan3

NEUROD6
(Canis lupus familiaris - dog)

Dog Assembly	Chr	Position (strand)	Source	Genome Browsers
Dog Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
CanFam3.1	14	43,913,351 - 43,916,818 (-)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1
CanFam3.1 Ensembl	14	43,914,149 - 43,915,162 (-)	Ensembl	CanFam3.1		canFam3	CanFam3.1
Dog10K_Boxer_Tasha	14	43,346,323 - 43,349,875 (-)	NCBI
ROS_Cfam_1.0	14	43,855,211 - 43,858,777 (-)	NCBI
UMICH_Zoey_3.1	14	43,980,567 - 43,984,107 (-)	NCBI
UNSW_CanFamBas_1.0	14	43,647,051 - 43,650,594 (-)	NCBI
UU_Cfam_GSD_1.0	14	44,009,200 - 44,012,762 (-)	NCBI

Neurod6
(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_024405118	88,313,184 - 88,316,659 (-)	NCBI
SpeTri2.0	NW_004936478	7,524,912 - 7,528,395 (-)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

NEUROD6
(Sus scrofa - pig)

Pig Assembly	Chr	Position (strand)	Source	Genome Browsers
Pig Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Sscrofa11.1 Ensembl	18	41,760,546 - 41,763,837 (+)	Ensembl	Sscrofa11.1		susScr11	Sscrofa11.1
Sscrofa11.1	18	41,757,356 - 41,763,837 (+)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1

NEUROD6
(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	21	27,042,482 - 27,049,611 (+)	NCBI
ChlSab1.1 Ensembl	21	27,047,809 - 27,048,822 (+)	Ensembl

Neurod6
(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_004624783	533,727 - 537,180 (-)	NCBI

Position Markers

D44480

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	4	84,847,242 - 84,847,383 (+)	MAPPER
Rnor_6.0	4	85,912,445 - 85,912,585	NCBI	Rnor6.0
Rnor_5.0	4	150,564,850 - 150,564,990	UniSTS	Rnor5.0
RGSC_v3.4	4	84,476,654 - 84,476,794	UniSTS	RGSC3.4
Celera	4	79,713,508 - 79,713,648	UniSTS
Cytogenetic Map	4	q24	UniSTS

BF386980

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	4	84,847,352 - 84,847,506 (+)	MAPPER
Rnor_6.0	4	85,912,555 - 85,912,708	NCBI	Rnor6.0
Rnor_5.0	4	150,564,960 - 150,565,113	UniSTS	Rnor5.0
RGSC_v3.4	4	84,476,764 - 84,476,917	UniSTS	RGSC3.4
Celera	4	79,713,618 - 79,713,771	UniSTS
RH 3.4 Map	4	526.11	UniSTS
Cytogenetic Map	4	q24	UniSTS

PMC57740P1

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	4	84,847,505 - 84,847,750 (+)	MAPPER
Rnor_6.0	4	85,912,708 - 85,912,952	NCBI	Rnor6.0
Rnor_5.0	4	150,565,113 - 150,565,357	UniSTS	Rnor5.0
RGSC_v3.4	4	84,476,917 - 84,477,161	UniSTS	RGSC3.4
Celera	4	79,713,771 - 79,714,015	UniSTS
Cytogenetic Map	4	q24	UniSTS

NEUROD6

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	4	84,847,358 - 84,847,795 (+)	MAPPER
Rnor_6.0	4	85,912,561 - 85,912,997	NCBI	Rnor6.0
Rnor_5.0	4	150,564,966 - 150,565,402	UniSTS	Rnor5.0
RGSC_v3.4	4	84,476,770 - 84,477,206	UniSTS	RGSC3.4
Celera	4	79,713,624 - 79,714,060	UniSTS
Cytogenetic Map	4	q24	UniSTS

Neurod6

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	4	84,847,441 - 84,848,455 (+)	MAPPER
Rnor_6.0	4	85,912,644 - 85,913,657	NCBI	Rnor6.0
Rnor_5.0	4	150,565,049 - 150,566,062	UniSTS	Rnor5.0
RGSC_v3.4	4	84,476,853 - 84,477,866	UniSTS	RGSC3.4
Celera	4	79,713,707 - 79,714,720	UniSTS
Cytogenetic Map	4	q24	UniSTS

Neurod6

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	4	84,848,336 - 84,848,452 (+)	MAPPER
Rnor_6.0	4	85,913,539 - 85,913,654	NCBI	Rnor6.0
Rnor_5.0	4	150,565,944 - 150,566,059	UniSTS	Rnor5.0
Celera	4	79,714,602 - 79,714,717	UniSTS
Cytogenetic Map	4	q24	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
2303168	Bp330	Blood pressure QTL 330	4.25	0.017	arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	4	3043231	145254791	Rat
631261	Tcas3	Tongue tumor susceptibility QTL 3	6.88		tongue integrity trait (VT:0010553)	number of squamous cell tumors of the tongue with diameter greater than 3 mm (CMO:0001950)	4	7342404	92484039	Rat
2316958	Gluco58	Glucose level QTL 58	10		blood glucose amount (VT:0000188)	blood glucose level (CMO:0000046)	4	7850904	182171018	Rat
10755501	Bp390	Blood pressure QTL 390	2.5		arterial blood pressure trait (VT:2000000)	diastolic blood pressure (CMO:0000005)	4	23850384	169318094	Rat
12798520	Anxrr55	Anxiety related response QTL 55	4.45	0.01	locomotor behavior trait (VT:0001392)	number of rearing movements with lid-pushing in an experimental apparatus (CMO:0002715)	4	29549895	112807890	Rat
8655961	Kidm43	Kidney mass QTL 43	18		kidney mass (VT:0002707)	both kidneys wet weight (CMO:0000085)	4	34277932	99067150	Rat
1358352	Srcrt3	Stress Responsive Cort QTL 3	2.29		blood corticosterone amount (VT:0005345)	plasma corticosterone level (CMO:0001173)	4	36615599	145611886	Rat
1300139	Hrtrt6	Heart rate QTL 6	2.85		heart pumping trait (VT:2000009)	heart rate (CMO:0000002)	4	37703272	115372927	Rat
6893678	Bw108	Body weight QTL 108	2.6	0.006	body mass (VT:0001259)	body weight (CMO:0000012)	4	42415777	87415777	Rat
1576305	Emca6	Estrogen-induced mammary cancer QTL 6	5.8		mammary gland integrity trait (VT:0010552)	mammary tumor number (CMO:0000343)	4	43414605	155469929	Rat
1354660	Salc1	Saline consumption QTL 1	11.26		drinking behavior trait (VT:0001422)	saline drink intake rate (CMO:0001627)	4	43414792	146942075	Rat
1354612	Foco1	Food consumption QTL 1	8.87		eating behavior trait (VT:0001431)	food intake rate (CMO:0000427)	4	43414792	146942075	Rat
1298082	Stresp4	Stress response QTL 4			blood corticosterone amount (VT:0005345)	plasma corticosterone level (CMO:0001173)	4	46898276	145611886	Rat
2312567	Glom19	Glomerulus QTL 19	1.9	0.006	kidney glomerulus morphology trait (VT:0005325)	index of glomerular damage (CMO:0001135)	4	49906054	145611886	Rat
70200	Alc18	Alcohol consumption QTL 18	9.2		drinking behavior trait (VT:0001422)	ethanol intake volume to total fluid intake volume ratio (CMO:0001591)	4	55324953	148360954	Rat
1641833	Alc21	Alcohol consumption QTL 21	8.6	0.0001	drinking behavior trait (VT:0001422)	ethanol drink intake rate (CMO:0001407)	4	55375865	125671711	Rat
631546	Bp86	Blood pressure QTL 86	3.2		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	4	55791564	92484312	Rat
1578657	Bss12	Bone structure and strength QTL 12	8.9		femur morphology trait (VT:0000559)	femoral neck cross-sectional area (CMO:0001697)	4	56092756	101092756	Rat
1578658	Bss13	Bone structure and strength QTL 13	8		femur strength trait (VT:0010010)	femoral neck polar moment of inertia (CMO:0001670)	4	56092756	101092756	Rat
1558651	Swd3	Spike wave discharge measurement QTL 3	4.62	0.000024	brain electrophysiology trait (VT:0010557)	brain spike-and-wave discharge frequency (CMO:0001742)	4	57101077	92990863	Rat
1358363	Sradr3	Stress Responsive Adrenal Weight QTL 3	6.19		adrenal gland mass (VT:0010420)	both adrenal glands wet weight (CMO:0000164)	4	58166424	103166424	Rat
738009	Sach4	Saccharine consumption QTL 4	4.9	0.000016	consumption behavior trait (VT:0002069)	saccharin intake volume to total fluid intake volume ratio (CMO:0001601)	4	58640017	154427984	Rat
738016	Alc16	Alcohol consumption QTL 16	3.6	0.00015	consumption behavior trait (VT:0002069)	ethanol drink intake rate to body weight ratio (CMO:0001616)	4	58640017	154427984	Rat
738031	Alc14	Alcohol consumption QTL 14	7.6	0.00003	consumption behavior trait (VT:0002069)	ethanol drink intake rate to body weight ratio (CMO:0001616)	4	58640017	154427984	Rat
1549843	Bw53	Body weight QTL 53		0.0001	body mass (VT:0001259)	body weight gain (CMO:0000420)	4	60439127	99066957	Rat
1549839	Bw52	Body weight QTL 52		0.0001	body mass (VT:0001259)	body weight gain (CMO:0000420)	4	60439127	113416139	Rat
61418	Pia5	Pristane induced arthritis QTL 5	4.5		joint integrity trait (VT:0010548)	joint inflammation composite score (CMO:0000919)	4	61038901	127777403	Rat
7394826	Bw126	Body weight QTL 126		0.002	body mass (VT:0001259)	body weight gain (CMO:0000420)	4	61708103	88565113	Rat
70192	BpQTLcluster5	Blood pressure QTL cluster 5	4.183		arterial blood pressure trait (VT:2000000)	diastolic blood pressure (CMO:0000005)	4	61708341	113100992	Rat
70192	BpQTLcluster5	Blood pressure QTL cluster 5	4.183		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	4	61708341	113100992	Rat
70192	BpQTLcluster5	Blood pressure QTL cluster 5	4.183		arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	4	61708341	113100992	Rat
70192	BpQTLcluster5	Blood pressure QTL cluster 5	4.183		arterial blood pressure trait (VT:2000000)	percent change in mean arterial blood pressure (CMO:0002035)	4	61708341	113100992	Rat
70192	BpQTLcluster5	Blood pressure QTL cluster 5	4.183		arterial blood pressure trait (VT:2000000)	percent change in systolic blood pressure (CMO:0000747)	4	61708341	113100992	Rat
70192	BpQTLcluster5	Blood pressure QTL cluster 5	4.183		arterial blood pressure trait (VT:2000000)	absolute change in pulse pressure (CMO:0001882)	4	61708341	113100992	Rat
70192	BpQTLcluster5	Blood pressure QTL cluster 5	4.183		arterial blood pressure trait (VT:2000000)	absolute change in mean arterial blood pressure (CMO:0000533)	4	61708341	113100992	Rat
2300179	Bmd50	Bone mineral density QTL 50	5.9	0.0001	femur mineral mass (VT:0010011)	volumetric bone mineral density (CMO:0001553)	4	61975371	106975371	Rat
1641919	Alc22	Alcohol consumption QTL 22		0.0005	drinking behavior trait (VT:0001422)	ethanol drink intake rate (CMO:0001407)	4	62947687	125671711	Rat
631674	Iddm14	Insulin dependent diabetes mellitus QTL 14			blood glucose amount (VT:0000188)	plasma glucose level (CMO:0000042)	4	63537179	157286626	Rat
6478684	Anxrr30	Anxiety related response QTL 30		0.00087	defecation behavior trait (VT:0010462)	defecation rate (CMO:0000998)	4	63812687	108812687	Rat
6478743	Anxrr40	Anxiety related response QTL 40		0.83076	defecation behavior trait (VT:0010462)	defecation rate (CMO:0000998)	4	63812687	108812687	Rat
6478772	Anxrr49	Anxiety related response QTL 49		0.15488	defecation behavior trait (VT:0010462)	defecation rate (CMO:0000998)	4	63812687	108812687	Rat
631651	Bp124	Blood pressure QTL 124	3		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	4	63938412	108938412	Rat
2312569	Pur19	Proteinuria QTL 19	3.4	0.001	total urine protein amount (VT:0000032)	urine total protein excretion rate (CMO:0000756)	4	65989243	97759057	Rat
61330	Eau1	Experimental allergic uveoretinitis QTL 1		0.0003	uvea integrity trait (VT:0010551)	experimental autoimmune uveitis score (CMO:0001504)	4	70773471	132455556	Rat
634344	Hcar7	Hepatocarcinoma resistance QTL 7	7.8		liver integrity trait (VT:0010547)	liver tumorous lesion area to total liver area ratio (CMO:0001075)	4	71476518	116476518	Rat
634344	Hcar7	Hepatocarcinoma resistance QTL 7	7.8		liver integrity trait (VT:0010547)	liver tumorous lesion number (CMO:0001068)	4	71476518	116476518	Rat
631646	Stl4	Serum triglyceride level QTL 4	6.5	0.0001	blood triglyceride amount (VT:0002644)	plasma triglyceride level (CMO:0000548)	4	73786419	132455556	Rat
724522	Bp146	Blood pressure QTL 146	2.2	0.0021	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	4	75258970	120258970	Rat
2302051	Pia28	Pristane induced arthritis QTL 28	5.3	0.001	blood autoantibody amount (VT:0003725)	serum immunoglobulin G-type rheumatoid factor level relative to an arbitrary reference serum (CMO:0002112)	4	75258970	120258970	Rat
738015	Pia9	Pristane induced arthritis QTL 9	4.5	0.048	joint integrity trait (VT:0010548)	joint inflammation composite score (CMO:0000919)	4	76567036	121567036	Rat
70167	Bw22	Body weight QTL 22	3.1		body mass (VT:0001259)	body weight (CMO:0000012)	4	77307388	116916073	Rat
1357342	Bw40	Body weight QTL 40		0.001	body mass (VT:0001259)	body weight (CMO:0000012)	4	77307388	116916073	Rat
631662	Hcar2	Hepatocarcinoma resistance QTL 2	3.1	0.0003	liver integrity trait (VT:0010547)	volume of individual liver tumorous lesion (CMO:0001078)	4	79555067	124555067	Rat
631556	Bp135	Blood pressure QTL 135		0.017	arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	4	79557856	116916073	Rat
61364	Iddm2	Insulin dependent diabetes mellitus QTL 2			blood glucose amount (VT:0000188)	blood glucose level (CMO:0000046)	4	79562451	98542106	Rat
2306899	Bp338	Blood pressure QTL 338		0.071	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	4	81874073	119546974	Rat
70177	Xhs1	X-ray hypersensitivity QTL 1	25.1		intestine integrity trait (VT:0010554)	post-insult time to onset of moribundity (CMO:0001896)	4	81959983	152055009	Rat
2306794	Ean2	Experimental allergic neuritis QTL 2	6.4		nervous system integrity trait (VT:0010566)	IFNG-secreting splenocyte count (CMO:0002122)	4	84475257	97479149	Rat
1576316	Ept5	Estrogen-induced pituitary tumorigenesis QTL 5	3.8		pituitary gland mass (VT:0010496)	pituitary gland wet weight (CMO:0000853)	4	84475257	178931073	Rat
634334	Xhs3	X-ray hypersensitivity QTL 3	10		intestine integrity trait (VT:0010554)	post-insult time to onset of moribundity (CMO:0001896)	4	85794049	129615056	Rat

miRNA Target Status

Predicted Target Of

	Summary Value
Count of predictions:	293
Count of miRNA genes:	181
Interacting mature miRNAs:	227
Transcripts:	ENSRNOT00000016182
Prediction methods:	Microtar, Miranda, 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	hemolymphoid system	integumental system	musculoskeletal system	nervous system	renal system	reproductive system	respiratory system	appendage
High
Medium							64
Low							4		5
Below cutoff	2	1	6	3	3	3		2	17	5	3

View RNA-SEQ Expression Data

Sequence

Nucleotide Sequences


RefSeq Transcripts	NM_001109237	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	BC168855	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	CH474011	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	JACYVU010000142	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

Reference Sequences

RefSeq Acc Id:

ENSRNOT00000016182 ⟹ ENSRNOP00000016182

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
Rnor_6.0 Ensembl	4	85,911,861 - 85,915,099 (-)	Ensembl

RefSeq Acc Id:

NM_001109237 ⟹ NP_001102707

RefSeq Status:

PROVISIONAL

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	4	84,846,659 - 84,849,905 (-)	NCBI
Rnor_6.0	4	85,911,861 - 85,915,107 (-)	NCBI
Rnor_5.0	4	150,564,266 - 150,567,512 (-)	NCBI
RGSC_v3.4	4	84,476,070 - 84,479,316 (-)	RGD
Celera	4	79,712,924 - 79,716,170 (-)	RGD

Sequence:

show sequence

CACTTTTTAGAGATCAATGAGATAGTGCAGATACACACAGATCTAGAGGCTCCAGGAGACGATG
CGACACTCAGCCTGAAAAGATTTGGAAGATCCAAAATGAAAACTGATTATTGAATGAAATTAAA
ACCTAAGGTAAATTAAGGTTAAAGAACCATGTTAACACTACCGTTTGACGAGTCTGTCGTAATG
CCCGAATCCCAGATGTGCAGAAAGTTTGCTAGACAATGTGAGGACCAGAAACAAATTAAGAAAC
CAGAGAGTTTTCCAAAACAAGTTGTCCTTCGAGGAAAGAGCATTAAAAGGGCCCCCGGAGAAGA
AACCGAGAAAGAGGAGGAGGAGGAAGACAGAGAGGAAGAAGATGAGAATGGCTTGCCCAGAAGG
AGGGGTCTCAGGAAAAAAAAGACCACCAAACTACGATTGGAAAGGGTCAAGTTCAGGAGACAGG
AAGCCAATGCACGAGAGAGGAACCGGATGCACGGCCTCAATGATGCTCTGGACAATTTGCGAAA
AGTGGTCCCCTGTTACTCTAAAACCCAAAAACTGTCCAAAATAGAAACTTTACGGCTGGCCAAA
AATTACATCTGGGCACTTTCTGAAATTCTGAGGATTGGCAAGAGACCGGATCTGCTCACGTTCG
TCCAAAACTTATGCAAAGGTCTTTCTCAGCCAACTACAAACTTGGTGGCAGGCTGCTTACAGCT
CAACGCCAGGAGTTTCCTGATGGGTCAGGGTGGGGAGGCTGCCCACCACACAAGGTCACCCTAC
TCCACATTCTACCCACCCTACCACAGCCCTGAGCTGGCCACTCCCCCAGGGCATGGGACTCTTG
ATAATTCCAAGTCCATGAAACCCTACAATTACTGCAGTGCATATGAATCCTTCTATGAAAGTAC
TTCCCCTGAGTGTGCCAGCCCTCAGTTTGAAGGTCCCTTAAGTCCTCCCCCAATTAACTATAAT
GGGATATTTTCCCTGAAGCAAGAAGAAACCTTGGACTATGGCAAAAATTACAATTATGGCATGC
ATTACTGTGCAGTGCCACCCAGGGGTCCCCTTGGGCAGGGTGCCATGTTCAGGTTGCCCACCGA
CAGCCACTTCCCTTACGACTTACATCTGCGCAGCCAATCTCTCACTATGCAAGATGAATTAAAT
GCAGTTTTTCATAATTAATGAGGAAAATGAAAATAAACAGTGGTCATTCACCTCCCACTCTAAT
TAAGACAAAGCAGATGCTTGTGGGCTGAGTAATTGGCACAACTCTATCTAAGGTGTTTACTAGT
TTCTGAAGTGTGTTTCAAAGATTGTGAACATTTTCTATGTCATAATAAATCTCTTTTCGTATGA
GAATTTCTTTTCCTTCCCTCTTGTCTGTATCACACTGTGATGATTCTCTCTCTCTCTCTTACTG
GCAGGATTTTTTCTTTCTTGTTTTAGTTCCTTTCAAATTCCCTTAATTTGGTTAACAAGGCGTC
GAAGAGTATGTTGCGGAGTAAAGACAGCACACGGCATACTTCGGTGTCTATTTCGGTTGTACAG
TTATGATGAAGATGCATGTTATAAAAAAATCAGATAAGTAAAATGTGTTTATAATTACTAGGAC
TCATATATGTATCTCTGAAATTTTAGGTTTTTAAACTATCAAGAGCTAACCCTGAAATTAAAAG
ACGCATTCGAGGATGTACAACAATATCAAAAGCTATGCAATTTTCTGTTTATTAGGGACAAAAC
TAAATGTAATGACTATTCCTCCTCAAGCGTTTTCCAGAGGAGGAAACACAGTATTTGGGGGAGG
TTATCAGTGTCATAATTGGGGGACAATTAATTCAGTCACAAAGAAAAATATTAGCACTTGTTTT
GTATTGTTCAGGATTCTTCTGTACAGGTTTGTTACGGTGTATAATTGTGTTTTCCATCCTAGAG
TTTAAAAGCAATTAAACATAGATATTTCCACTT

hide sequence

Protein Sequences


Protein RefSeqs	NP_001102707	(Get FASTA)	NCBI Sequence Viewer
GenBank Protein	AAI68855	(Get FASTA)	NCBI Sequence Viewer
	EDL88072	(Get FASTA)	NCBI Sequence Viewer

Reference Sequences

RefSeq Acc Id:

NP_001102707 ⟸ NM_001109237

- UniProtKB:

B5DEY7 (UniProtKB/TrEMBL)

- Sequence:

show sequence

MLTLPFDESVVMPESQMCRKFARQCEDQKQIKKPESFPKQVVLRGKSIKRAPGEETEKEEEEED
REEEDENGLPRRRGLRKKKTTKLRLERVKFRRQEANARERNRMHGLNDALDNLRKVVPCYSKTQ
KLSKIETLRLAKNYIWALSEILRIGKRPDLLTFVQNLCKGLSQPTTNLVAGCLQLNARSFLMGQ
GGEAAHHTRSPYSTFYPPYHSPELATPPGHGTLDNSKSMKPYNYCSAYESFYESTSPECASPQF
EGPLSPPPINYNGIFSLKQEETLDYGKNYNYGMHYCAVPPRGPLGQGAMFRLPTDSHFPYDLHL
RSQSLTMQDELNAVFHN

hide sequence

RefSeq Acc Id:

ENSRNOP00000016182 ⟸ ENSRNOT00000016182

Protein Domains

bHLH

Transcriptome

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

Promoters

RGD ID:

13693076

Promoter ID:

EPDNEW_R3600

Type:

single initiation site

Name:

Neurod6_1

Description:

neuronal differentiation 6

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	4	85,915,106 - 85,915,166	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:1562793	AgrOrtholog
Ensembl Genes	ENSRNOG00000026055	Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein	ENSRNOP00000016182	ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript	ENSRNOT00000016182	ENTREZGENE, UniProtKB/TrEMBL
Gene3D-CATH	4.10.280.10	UniProtKB/TrEMBL
InterPro	HLH_DNA-bd_sf	UniProtKB/TrEMBL
	HLH_DNA_bd	UniProtKB/TrEMBL
	Neurod6	UniProtKB/TrEMBL
	Neurogenic_DUF	UniProtKB/TrEMBL
	TF_bHLH_NeuroD	UniProtKB/TrEMBL
KEGG Report	rno:500137	UniProtKB/TrEMBL
NCBI Gene	500137	ENTREZGENE
PANTHER	PTHR19290:SF9	UniProtKB/TrEMBL
Pfam	HLH	UniProtKB/TrEMBL
	Neuro_bHLH	UniProtKB/TrEMBL
PhenoGen	Neurod6	PhenoGen
PIRSF	bHLH_NeuroD	UniProtKB/TrEMBL
PROSITE	HLH	UniProtKB/TrEMBL
SMART	HLH	UniProtKB/TrEMBL
Superfamily-SCOP	HLH_basic	UniProtKB/TrEMBL
UniProt	B5DEY7	ENTREZGENE, UniProtKB/TrEMBL

Nomenclature History

Date	Current Symbol	Current Name	Previous Symbol	Previous Name	Description	Reference	Status
2012-10-05	Neurod6	neuronal differentiation 6	Neurod6	neurogenic differentiation 6	Nomenclature updated to reflect human and mouse nomenclature	1299863	APPROVED
2008-02-29	Neurod6	neurogenic differentiation 6	RGD1562793_predicted	similar to NEX-1 (predicted)	Nomenclature updated to reflect human and mouse nomenclature	1299863	APPROVED
2006-03-07	RGD1562793_predicted	similar to NEX-1 (predicted)	LOC500137	similar to NEX-1	Symbol and Name status set to approved	1299863	APPROVED
2006-02-09	LOC500137	similar to NEX-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)

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Imported Disease Annotations - ClinVar