Wdr38 (WD repeat domain 38) - Rat Genome Database

Name: Wdr38
Creator: Rat Genome Database
License: Creative Commons CC BY 4.0
Keywords: Rat Gene RGD Genome

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Gene: Wdr38 (WD repeat domain 38) Rattus norvegicus

Analyze

Symbol:

Wdr38

Name:

WD repeat domain 38

RGD ID:

1562587

Description:

Predicted to be involved in hematopoietic progenitor cell differentiation. Orthologous to human WDR38 (WD repeat domain 38); INTERACTS WITH amphetamine; bisphenol A; 1,2-dichloroethane (ortholog).

Type:

protein-coding

RefSeq Status:

MODEL

Also known as:

LOC366035; RGD1562587; similar to cis-Golgi matrix protein GM130; WD repeat-containing protein 38

RGD Orthologs

Human

Mouse

Bonobo

Dog

Squirrel

Pig

Green Monkey

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):	WDR38 (WD repeat domain 38)	HGNC	Ensembl, HomoloGene, Inparanoid, NCBI, OMA, OrthoDB, OrthoMCL, PhylomeDB, Treefam
Mus musculus (house mouse):	Wdr38 (WD repeat domain 38)	HGNC	Treefam, OrthoMCL, NCBI, OMA, HomoloGene, Inparanoid, PhylomeDB, OrthoDB, Ensembl
Pan paniscus (bonobo/pygmy chimpanzee):	WDR38 (WD repeat domain 38)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Canis lupus familiaris (dog):	WDR38 (WD repeat domain 38)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Ictidomys tridecemlineatus (thirteen-lined ground squirrel):	Wdr38 (WD repeat domain 38)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Sus scrofa (pig):	WDR38 (WD repeat domain 38)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chlorocebus sabaeus (African green monkey):	WDR38 (WD repeat domain 38)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Alliance orthologs ³
Mus musculus (house mouse):	Wdr38 (WD repeat domain 38)	Alliance	DIOPT (Hieranoid\|InParanoid\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|TreeFam)
Homo sapiens (human):	WDR38 (WD repeat domain 38)	Alliance	DIOPT (HGNC\|Hieranoid\|InParanoid\|OrthoFinder\|OrthoInspector\|PANTHER\|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
Rnor_6.0	3	23,291,712 - 23,294,818 (+)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	3	23,290,819 - 23,294,670 (+)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	3	28,513,529 - 28,516,644 (+)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	3	18,781,680 - 18,787,996 (+)	NCBI	RGSC3.4		rn4	RGSC3.4
Celera	3	21,183,440 - 21,186,546 (+)	NCBI		Celera
Cytogenetic Map	3	q12	NCBI

JBrowse:

View Region in Genome Browser (JBrowse)

Model

Annotation Click to see Annotation Detail View

Gene-Chemical Interaction Annotations Click to see Annotation Detail View

1,2-dichloroethane (ISO)

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

4,4'-sulfonyldiphenol (ISO)

4-hydroxyphenyl retinamide (ISO)

aflatoxin B1 (ISO)

amphetamine (EXP)

benzo[e]pyrene (ISO)

bisphenol A (EXP)

carbon nanotube (ISO)

lead(0) (ISO)

lead(2+) (ISO)

methapyrilene (ISO)

tebuconazole (ISO)

titanium dioxide (ISO)

valproic acid (ISO)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

hematopoietic progenitor cell differentiation (ISO)

References

References - curated


1.	RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
2.	RGD automated import pipeline for gene-chemical interactions

Additional References at PubMed

PMID:24029230

Genomics

Comparative Map Data

Wdr38
(Rattus norvegicus - Norway rat)

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Rnor_6.0	3	23,291,712 - 23,294,818 (+)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	3	23,290,819 - 23,294,670 (+)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	3	28,513,529 - 28,516,644 (+)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	3	18,781,680 - 18,787,996 (+)	NCBI	RGSC3.4		rn4	RGSC3.4
Celera	3	21,183,440 - 21,186,546 (+)	NCBI		Celera
Cytogenetic Map	3	q12	NCBI

WDR38
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38.p13 Ensembl	9	124,853,417 - 124,857,890 (+)	Ensembl	GRCh38		hg38	GRCh38
GRCh38	9	124,853,460 - 124,857,884 (+)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh37	9	127,615,627 - 127,620,170 (+)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	9	126,655,576 - 126,659,981 (+)	NCBI	NCBI36		hg18	NCBI36
Celera	9	98,263,706 - 98,268,110 (+)	NCBI
Cytogenetic Map	9	q33.3	NCBI
HuRef	9	97,228,194 - 97,232,664 (+)	NCBI		HuRef
CHM1_1	9	127,764,472 - 127,768,945 (+)	NCBI		CHM1_1

Wdr38
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	2	38,888,287 - 38,891,600 (+)	NCBI	GRCm39		mm39
GRCm38	2	38,998,309 - 39,001,584 (+)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	2	38,997,476 - 39,006,168 (+)	Ensembl	GRCm38		mm10	GRCm38
MGSCv37	2	38,853,829 - 38,857,104 (+)	NCBI	GRCm37		mm9	NCBIm37
MGSCv36	2	38,819,485 - 38,828,177 (+)	NCBI			mm8
Celera	2	40,724,185 - 40,727,330 (+)	NCBI		Celera
Cytogenetic Map	2	B	NCBI

WDR38
(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	9	124,491,753 - 124,496,140 (+)	NCBI	panpan1.1	PanPan1.1	panPan2
PanPan1.1 Ensembl	9	124,491,733 - 124,496,133 (+)	Ensembl	panpan1.1		panPan2
Mhudiblu_PPA_v0	9	95,973,932 - 95,978,398 (+)	NCBI	Mhudiblu_PPA_v0		panPan3

WDR38
(Canis lupus familiaris - dog)

No map positions available.

Wdr38
(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_004936487	13,052,665 - 13,056,191 (+)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

WDR38
(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	265,633,677 - 265,637,267 (+)	Ensembl	Sscrofa11.1		susScr11	Sscrofa11.1
Sscrofa11.1	1	265,632,153 - 265,637,098 (+)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1
Sscrofa10.2	1	299,458,604 - 299,462,243 (+)	NCBI	Sscrofa10.2	Sscrofa10.2	susScr3

WDR38
(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	12	13,290,713 - 13,296,075 (-)	NCBI
ChlSab1.1 Ensembl	12	13,290,954 - 13,295,025 (-)	Ensembl

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
631679	Cm10	Cardiac mass QTL 10	7.34	0.0001	heart left ventricle mass (VT:0007031)	heart left ventricle weight to body weight ratio (CMO:0000530)	3	1	25786001	Rat
70202	Alc19	Alcohol consumption QTL 19	2.5		drinking behavior trait (VT:0001422)	ethanol intake volume to total fluid intake volume ratio (CMO:0001591)	3	1	28136884	Rat
631545	Bp85	Blood pressure QTL 85	3.1		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	3	1	28500807	Rat
61468	Bp15	Blood pressure QTL 15	4.4		blood pressure trait (VT:0000183)	pulse pressure (CMO:0000292)	3	1	28500807	Rat
61468	Bp15	Blood pressure QTL 15	4.4		blood pressure trait (VT:0000183)	systolic blood pressure (CMO:0000004)	3	1	28500807	Rat
61468	Bp15	Blood pressure QTL 15	4.4		blood pressure trait (VT:0000183)	diastolic blood pressure (CMO:0000005)	3	1	28500807	Rat
631831	Alc8	Alcohol consumption QTL 8	2.7		consumption behavior trait (VT:0002069)	calculated ethanol drink intake rate (CMO:0001615)	3	1	32972944	Rat
4889966	Bss95	Bone structure and strength QTL 95	4.4		tibia area (VT:1000281)	tibia-fibula cross-sectional area (CMO:0001718)	3	1	37891710	Rat
2312664	Scl62	Serum cholesterol level QTL 62		0.05	blood cholesterol amount (VT:0000180)	serum total cholesterol level (CMO:0000363)	3	1	39773425	Rat
2290452	Scl56	Serum cholesterol level QTL 56	2.26		blood cholesterol amount (VT:0000180)	plasma total cholesterol level (CMO:0000585)	3	1	95176874	Rat
1298526	Arunc3	Aerobic running capacity QTL 3	2.2		exercise endurance trait (VT:0002332)	maximum distance run on treadmill (CMO:0001406)	3	2631421	33477544	Rat
10401810	Kidm53	Kidney mass QTL 53			kidney mass (VT:0002707)	both kidneys wet weight to body weight ratio (CMO:0000340)	3	2631421	48562146	Rat
70203	Gcr2	Gastric cancer resistance QTL 2	2.6		stomach morphology trait (VT:0000470)	stomach tumor susceptibility score (CMO:0002043)	3	3285929	28136884	Rat
1358357	Srcrtb1	Stress Responsive Cort Basal QTL 1	6.36	0.002	blood corticosterone amount (VT:0005345)	plasma corticosterone level (CMO:0001173)	3	3285929	28136884	Rat
8693641	Alc30	Alcohol consumption QTL 30	2	0.739	drinking behavior trait (VT:0001422)	calculated ethanol drink intake rate (CMO:0001615)	3	5654639	25105730	Rat
1558654	Bw56	Body weight QTL 56	4.5	0.0000171	body mass (VT:0001259)	body weight (CMO:0000012)	3	6000748	34394365	Rat
6893355	Bw101	Body weight QTL 101	0.4	0.38	body mass (VT:0001259)	body weight (CMO:0000012)	3	6000748	34394365	Rat
6893363	Bw105	Body weight QTL 105	2.6	0.0036	body mass (VT:0001259)	body weight (CMO:0000012)	3	6000748	34394365	Rat
70191	BpQTLcluster4	Blood pressure QTL cluster 4	3		arterial blood pressure trait (VT:2000000)	absolute change in systolic blood pressure (CMO:0000607)	3	6000748	51687917	Rat
70191	BpQTLcluster4	Blood pressure QTL cluster 4	3		arterial blood pressure trait (VT:2000000)	absolute change in mean arterial blood pressure (CMO:0000533)	3	6000748	51687917	Rat
1558647	Cm46	Cardiac mass QTL 46	5.4	0.0000055	heart mass (VT:0007028)	heart wet weight (CMO:0000069)	3	6000866	34394121	Rat
1558650	Cm48	Cardiac mass QTL 48	4	0.0001	heart mass (VT:0007028)	heart weight to body weight ratio (CMO:0000074)	3	6000866	34394121	Rat
1558657	Cm43	Cardiac mass QTL 43	6.6	0.0000000293	heart mass (VT:0007028)	heart wet weight (CMO:0000069)	3	6000866	34394121	Rat
1358905	Hrtrt17	Heart rate QTL 17	5.9	0.000014	heart pumping trait (VT:2000009)	heart rate (CMO:0000002)	3	10094081	93415837	Rat
2298542	Neuinf11	Neuroinflammation QTL 11	3.9		nervous system integrity trait (VT:0010566)	spinal cord complement component 1, q subcomponent, B chain mRNA level (CMO:0002126)	3	10119318	79772001	Rat
1358885	Bp251	Blood pressure QTL 251	3.8		arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	3	10639528	127023997	Rat
1358888	Bp264	Blood pressure QTL 264	4.43		arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	3	10639528	127023997	Rat
634306	Bp140	Blood pressure QTL 140	3.3	0.0013	arterial blood pressure trait (VT:2000000)	body weight (CMO:0000012)	3	13126914	36600143	Rat
634306	Bp140	Blood pressure QTL 140	3.3	0.0013	arterial blood pressure trait (VT:2000000)	body weight (CMO:0000012)	3	13126914	36600143	Rat
634306	Bp140	Blood pressure QTL 140	3.3	0.0013	arterial blood pressure trait (VT:2000000)	heart rate (CMO:0000002)	3	13126914	36600143	Rat
634306	Bp140	Blood pressure QTL 140	3.3	0.0013	arterial blood pressure trait (VT:2000000)	heart rate (CMO:0000002)	3	13126914	36600143	Rat
634306	Bp140	Blood pressure QTL 140	3.3	0.0013	arterial blood pressure trait (VT:2000000)	diastolic blood pressure (CMO:0000005)	3	13126914	36600143	Rat
634306	Bp140	Blood pressure QTL 140	3.3	0.0013	arterial blood pressure trait (VT:2000000)	diastolic blood pressure (CMO:0000005)	3	13126914	36600143	Rat
634306	Bp140	Blood pressure QTL 140	3.3	0.0013	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	3	13126914	36600143	Rat
634306	Bp140	Blood pressure QTL 140	3.3	0.0013	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	3	13126914	36600143	Rat
631568	Bp92	Blood pressure QTL 92	2.2	0.005	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	3	13126914	41510346	Rat
2325840	Bp345	Blood pressure QTL 345		0.001	arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	3	14090411	29084626	Rat
731172	Bp151	Blood pressure QTL 151		0.04	arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	3	14090411	48562146	Rat
12879849	Bw180	Body weight QTL 180		0.037	body mass (VT:0001259)	body weight (CMO:0000012)	3	14090411	48562146	Rat
12879850	Cm91	Cardiac mass QTL 91		0.001	heart mass (VT:0007028)	heart wet weight to body weight ratio (CMO:0002408)	3	14090411	48562146	Rat
12879851	Cm92	Cardiac mass QTL 92		0.001	heart left ventricle mass (VT:0007031)	heart left ventricle weight to body weight ratio (CMO:0000530)	3	14090411	48562146	Rat
12879852	Cm93	Cardiac mass QTL 93		0.001	heart right ventricle mass (VT:0007033)	heart right ventricle weight to body weight ratio (CMO:0000914)	3	14090411	48562146	Rat
12879853	Am5	Aortic mass QTL 5		0.001	aorta mass (VT:0002845)	aorta weight to aorta length to body weight ratio (CMO:0002722)	3	14090411	48562146	Rat
12879854	Kidm63	Kidney mass QTL 63		0.001	kidney mass (VT:0002707)	both kidneys wet weight to body weight ratio (CMO:0000340)	3	14090411	48562146	Rat
631676	Cm8	Cardiac mass QTL 8	7.03	0.0001	aorta mass (VT:0002845)	aorta weight (CMO:0000076)	3	18023664	63023664	Rat
10450794	Scl69	Serum cholesterol level QTL 69	6.3	0.001	blood LDL cholesterol amount (VT:0000181)	blood low density lipoprotein cholesterol level (CMO:0000053)	3	21223803	66223803	Rat
10450804	Scl70	Serum cholesterol level QTL 70	4.7	0.001	blood LDL cholesterol amount (VT:0000181)	blood low density lipoprotein cholesterol level (CMO:0000053)	3	21223803	66223803	Rat

miRNA Target Status

Predicted Target Of

	Summary Value
Count of predictions:	97
Count of miRNA genes:	79
Interacting mature miRNAs:	81
Transcripts:	ENSRNOT00000018921
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											10	10
Low	3	10	23	7	19	7	7	7	57	15	8	1	7
Below cutoff		5	6	6		6	1	4	11	10	14		1

View RNA-SEQ Expression Data

Sequence

Nucleotide Sequences


RefSeq Transcripts	XM_003753718	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_575125	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	AABR07051827	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	AAHX01021246	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	CH473983	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	FQ213095	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

Reference Sequences

RefSeq Acc Id:

ENSRNOT00000018921 ⟹ ENSRNOP00000018921

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
Rnor_6.0 Ensembl	3	23,290,819 - 23,294,670 (+)	Ensembl

RefSeq Acc Id:

XM_003753718 ⟹ XP_003753766

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
Celera	3	21,183,440 - 21,186,546 (+)	NCBI

Sequence:

show sequence

TTCCCTTCCCCTTCTACCGAGGCCCCTCCAACGGGACTGGTGCCCGCTTAGGAGGGAGCCCTCC
CGGTTCTGGAGCGGGCTCCCATGAACATCAGAGCTCCAACAAAATTGGCCGTGGGCAGAGTGAG
GTTCTACGGTCAACACCACGGGGAGGTCAACTGCTCTGCCTTCTCCCCTGATGGCCGGAACCTG
ATCACAGCCTCAGATGATGGTTGTGTGTATGTATGGGGGACGAAGAGTGGGCGACTGCTGTGGA
GACTGGCAGGCCACAAAGGCCCAGTGAAGTCTTGCCGTTTCTCTCCCGATGGCCGCCTCGTTGC
CAGCTCCTCCTGTGACCACACCATCCGCCTGTGGGATGTGGCAAAAGCCAAATGCCTGCATGTG
CTGAAAGGTCACCAGAGGAGTGTGGAAACTGTCAGCTTCAGCCCTGACTCAAAGCAGCTGGCAT
CAGGTGGCTGGGACAAGAGGGTGATTCTCTGGGAAGTGCAGTCCGGCCGCAATGTGCGCTTCTT
GCCTGGGCATTGTGATTCCATCCAGAGCAGTGACTTCTCTCCAACCTCGGATTCTCTGGCCACT
GGCTCCTGGGACTCGACTGTGCACATCTGGGACTTGCGGGCATCAAGCCCAGCTGTCTCCTTCC
GTAATTTGGAGGGCCACACTGGCAACATCAGCTGCTTGAAGTACTCAGCATCTGGCCTCTTGGC
ATCTGGCTCCTGGGACAAGACAGTCCGCATCTGGAAGCCCACAACCAACAACCTGCTTCTGCAG
CTCAGGGGCCACGCCACCTGGGTCAATAGCCTAGCCTTCTCTCCCGATGAGCTAAAGCTGGCCA
GTGCTGGTTACTCTCGTATGGTCAAAGTCTGGGACTGCCTCACAGGGAAATGCCTTGAGACCCT
AAAGGGCATGCTGGATGTGGCCCATGCCTGCATTTTCACTCCAAATGGCAAACTCTTAGTGTCA
GGGATTGCTGACGCGACAAGATGACAAGTCTGCTGAAAGTCAAGAACTTCATCCATGTAACTTA
CCCACAGGCCTAAGGTAACTAAGCCACCAGATCTCCAAGGCAGGGACTACCTAGCCTATCCCGT
AAGGTGGTTGTCACCTGCTGTAGGCAAGCGATCACCTAACCTCACCCCCTGGACCCTGGGCGGC
CAGTGTCAAACAGGAAGCAGAGAGCTCGTCA

hide sequence

RefSeq Acc Id:

XM_575125 ⟹ XP_575125

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
Rnor_6.0	3	23,291,712 - 23,294,818 (+)	NCBI
Rnor_5.0	3	28,513,529 - 28,516,644 (+)	NCBI
RGSC_v3.4	3	18,781,680 - 18,787,996 (+)	RGD

Sequence:

show sequence

TTCCCTTCCCCTTCTACCGAGGCCCCTCCAACGGGACTGGTGCCCGCTTAGGAGGGAGCCCTCC
CGGTTCTGGAGCGGGCTCCCATGAACATCAGAGCTCCAACAAAATTGGCCGTGGGCAGAGTGAG
GTTCTACGGTCAACACCACGGGGAGGTCAACTGCTCTGCCTTCTCCCCTGATGGCCGGAACCTG
ATCACAGCCTCAGATGATGGTTGTGTGTATGTATGGGGGACGAAGAGTGGGCGACTGCTGTGGA
GACTGGCAGGCCACAAAGGCCCAGTGAAGTCTTGCCGTTTCTCTCCCGATGGCCGCCTCGTTGC
CAGCTCCTCCTGTGACCACACCATCCGCCTGTGGGATGTGGCAAAAGCCAAATGCCTGCATGTG
CTGAAAGGTCACCAGAGGAGTGTGGAAACTGTCAGCTTCAGCCCTGACTCAAAGCAGCTGGCAT
CAGGTGGCTGGGACAAGAGGGTGATTCTCTGGGAAGTGCAGTCCGGCCGCAATGTGCGCTTCTT
GCCTGGGCATTGTGATTCCATCCAGAGCAGTGACTTCTCTCCAACCTCGGATTCTCTGGCCACT
GGCTCCTGGGACTCGACTGTGCACATCTGGGACTTGCGGGCATCAAGCCCAGCTGTCTCCTTCC
GTAATTTGGAGGGCCACACTGGCAACATCAGCTGCTTGAAGTACTCAGCATCTGGCCTCTTGGC
ATCTGGCTCCTGGGACAAGACAGTCCGCATCTGGAAGCCCACAACCAACAACCTGCTTCTGCAG
CTCAGGGGCCACGCCACCTGGGTCAATAGCCTAGCCTTCTCTCCCGATGAGCTAAAGCTGGCCA
GTGCTGGTTACTCTCGTATGGTCAAAGTCTGGGACTGCCTCACAGGGAAATGCCTTGAGACCCT
AAAGGGCATGCTGGATGTGGCCCATGCCTGCATTTTCACTCCAAATGGCAAACTCTTAGTGTCA
GGGATTGCTGACGCGACAAGATGACAAGTCTGCTGAAAGTCAAGAACTTCATCCATGTAACTTA
CCCACAGGCCTAAGGTAACTAAGCCACCAGATCTCCAAGGCAGGGACTACCTAGCCTATCCCGT
AAGGTGGTTGTCACCTGCTGTAGGCAAGCGATCACCTAACCTCACCCCCTGGACCCTGGGCGGC
CAGTGTCAAACAGGAAGCAGAGAGCTCGTCA

hide sequence

Protein Sequences


Protein RefSeqs	XP_003753766	(Get FASTA)	NCBI Sequence Viewer
	XP_575125	(Get FASTA)	NCBI Sequence Viewer
GenBank Protein	EDM00501	(Get FASTA)	NCBI Sequence Viewer
	EDM00502	(Get FASTA)	NCBI Sequence Viewer

Reference Sequences

RefSeq Acc Id:

XP_575125 ⟸ XM_575125

- Sequence:

show sequence

MNIRAPTKLAVGRVRFYGQHHGEVNCSAFSPDGRNLITASDDGCVYVWGTKSGRLLWRLAGHKG
PVKSCRFSPDGRLVASSSCDHTIRLWDVAKAKCLHVLKGHQRSVETVSFSPDSKQLASGGWDKR
VILWEVQSGRNVRFLPGHCDSIQSSDFSPTSDSLATGSWDSTVHIWDLRASSPAVSFRNLEGHT
GNISCLKYSASGLLASGSWDKTVRIWKPTTNNLLLQLRGHATWVNSLAFSPDELKLASAGYSRM
VKVWDCLTGKCLETLKGMLDVAHACIFTPNGKLLVSGIADATR

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RefSeq Acc Id:

XP_003753766 ⟸ XM_003753718

- Sequence:

show sequence

MNIRAPTKLAVGRVRFYGQHHGEVNCSAFSPDGRNLITASDDGCVYVWGTKSGRLLWRLAGHKG
PVKSCRFSPDGRLVASSSCDHTIRLWDVAKAKCLHVLKGHQRSVETVSFSPDSKQLASGGWDKR
VILWEVQSGRNVRFLPGHCDSIQSSDFSPTSDSLATGSWDSTVHIWDLRASSPAVSFRNLEGHT
GNISCLKYSASGLLASGSWDKTVRIWKPTTNNLLLQLRGHATWVNSLAFSPDELKLASAGYSRM
VKVWDCLTGKCLETLKGMLDVAHACIFTPNGKLLVSGIADATR

hide sequence

RefSeq Acc Id:

ENSRNOP00000018921 ⟸ ENSRNOT00000018921

Protein Domains

WD_REPEATS_REGION

Transcriptome

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

Promoters

RGD ID:

13692059

Promoter ID:

EPDNEW_R2579

Type:

multiple initiation site

Name:

Wdr38_1

Description:

WD repeat domain 38

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	3	23,290,835 - 23,290,895	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:1562587	AgrOrtholog
Ensembl Genes	ENSRNOG00000014102	Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein	ENSRNOP00000018921	ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript	ENSRNOT00000018921	ENTREZGENE, UniProtKB/TrEMBL
Gene3D-CATH	2.130.10.10	UniProtKB/TrEMBL
InterPro	G-protein_beta_WD-40_rep	UniProtKB/TrEMBL
	WD40/YVTN_repeat-like_dom_sf	UniProtKB/TrEMBL
	WD40_repeat	UniProtKB/TrEMBL
	WD40_repeat_CS	UniProtKB/TrEMBL
	WD40_repeat_dom	UniProtKB/TrEMBL
	WD40_repeat_dom_sf	UniProtKB/TrEMBL
NCBI Gene	366035	ENTREZGENE
Pfam	WD40	UniProtKB/TrEMBL
PhenoGen	Wdr38	PhenoGen
PRINTS	GPROTEINBRPT	UniProtKB/TrEMBL
PROSITE	WD_REPEATS_1	UniProtKB/TrEMBL
	WD_REPEATS_2	UniProtKB/TrEMBL
	WD_REPEATS_REGION	UniProtKB/TrEMBL
SMART	WD40	UniProtKB/TrEMBL
Superfamily-SCOP	WD40_like	UniProtKB/TrEMBL
UniGene	Rn.198114	ENTREZGENE
UniProt	F1LZZ1_RAT	UniProtKB/TrEMBL

Nomenclature History

Date	Current Symbol	Current Name	Previous Symbol	Previous Name	Description	Reference	Status
2008-02-29	Wdr38	WD repeat domain 38	RGD1562587_predicted	similar to cis-Golgi matrix protein GM130 (predicted)	Nomenclature updated to reflect human and mouse nomenclature	1299863	APPROVED
2006-03-07	RGD1562587_predicted	similar to cis-Golgi matrix protein GM130 (predicted)	LOC366035	similar to cis-Golgi matrix protein GM130	Symbol and Name status set to approved	1299863	APPROVED
2006-02-09	LOC366035	similar to cis-Golgi matrix protein GM130			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)