Shisa4 (shisa family member 4) - Rat Genome Database

Name: Shisa4
Creator: Rat Genome Database
License: Creative Commons CC BY 4.0
Keywords: Rat Gene RGD Genome

	Submit Data \| Help \| Video Tutorials \| News \| Publications \| FTP Download \| REST API \| Citing RGD \| Contact
	Search RGD Grant Resources Citing RGD About Us Contact Us Genes QTLs Strains Markers Genome Information Ontologies Cell Lines References FTP Download Submit Data OntoMate (Literature Search) JBrowse (Genome Browser) Variant Visualizer Multi-Ontology Enrichment (MOET) Gene-Ortholog Location Finder (GOLF) InterViewer (Protein-Protein Interactions) PhenoMiner (Quatitative Phenotypes) Gene Annotator OLGA (Gene List Generator) RatMine GViewer (Genome Viewer) Overgo Probe Designer ACP Haplotyper Genome Scanner Aging & Age-Related Disease Cancer Cardiovascular Disease COVID-19 Developmental Disease Diabetes Hematologic Disease Immune & Inflammatory Disease Liver Disease Neurological Disease Obesity & Metabolic Syndrome Renal Disease Respiratory Disease Sensory Organ Disease Find Models new Genetic Models Autism Models PhenoMiner (Quantitative Phenotypes) Expected Ranges (Quantitative Phenotype) PhenoMiner Term Comparison Hybrid Rat Diversity Panel Phenotypes GERRC (Gene Editing Rat Resource Center) Phenotypes in Other Animal Models Animal Husbandry Strain Medical Records Phylogenetics Strain Availability Calendar Rats 101 Submissions Photo Archive Pathways Rat Community Forum Directory of Rat Laboratories Video Tutorials News RGD Publications RGD Poster Archive Nomenclature Guidelines Resource Links Laboratory Resources Employment Resources
	Advanced Search (OLGA)

Gene: Shisa4 (shisa family member 4) Rattus norvegicus

Analyze

Symbol:

Shisa4

Name:

shisa family member 4

RGD ID:

1312041

Description:

Predicted to localize to integral component of membrane. Orthologous to human SHISA4 (shisa family member 4); INTERACTS WITH 17beta-estradiol; 2,3,7,8-tetrachlorodibenzodioxine; acrylamide.

Type:

protein-coding

RefSeq Status:

PROVISIONAL

Also known as:

LOC360848; Prmp; proline rich membrane protein; protein shisa-4; RGD1312041; shisa homolog 4; shisa homolog 4 (Xenopus laevis); similar to scotin; Tmem58; transmembrane protein 58

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):	SHISA4 (shisa family member 4)	HGNC	EggNOG, Ensembl, HomoloGene, Inparanoid, NCBI, OMA, OrthoDB, OrthoMCL, Panther, PhylomeDB, Treefam
Mus musculus (house mouse):	Shisa4 (shisa family member 4)	HGNC	Treefam, EggNOG, OrthoMCL, NCBI, OMA, HomoloGene, Inparanoid, Panther, PhylomeDB, OrthoDB, Ensembl
Chinchilla lanigera (long-tailed chinchilla):	Shisa4 (shisa family member 4)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Pan paniscus (bonobo/pygmy chimpanzee):	SHISA4 (shisa family member 4)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Canis lupus familiaris (dog):	SHISA4 (shisa family member 4)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Ictidomys tridecemlineatus (thirteen-lined ground squirrel):	Shisa4 (shisa family member 4)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Sus scrofa (pig):	SHISA4 (shisa family member 4)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chlorocebus sabaeus (African green monkey):	SHISA4 (shisa family member 4)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Heterocephalus glaber (naked mole-rat):	Shisa4 (shisa family member 4)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Alliance orthologs ³
Homo sapiens (human):	SHISA4 (shisa family member 4)	Alliance	DIOPT (Ensembl Compara\|HGNC\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|TreeFam)
Mus musculus (house mouse):	Shisa4 (shisa family member 4)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|TreeFam)
Danio rerio (zebrafish):	shisa4 (shisa family member 4)	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	13	46,800,487 - 46,803,703 (-)	NCBI
Rnor_6.0 Ensembl	13	52,193,989 - 52,197,205 (-)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_6.0	13	52,193,989 - 52,197,205 (-)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_5.0	13	57,244,749 - 57,248,270 (-)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	13	48,368,910 - 48,372,126 (-)	NCBI	RGSC3.4		rn4	RGSC3.4
RGSC_v3.1	13	48,382,485 - 48,386,271 (-)	NCBI
Celera	13	47,120,498 - 47,123,714 (-)	NCBI		Celera
Cytogenetic Map	13	q13	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-dimethylhydrazine (ISO)

17beta-estradiol (EXP)

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

2-hydroxypropanoic acid (ISO)

acrylamide (EXP)

aflatoxin B1 (ISO)

aflatoxin B2 (ISO)

atrazine (ISO)

benzo[a]pyrene (ISO)

bis(2-ethylhexyl) phthalate (ISO)

bisphenol A (EXP,ISO)

calcitriol (ISO)

carbon nanotube (ISO)

copper atom (EXP)

copper(0) (EXP)

decabromodiphenyl ether (ISO)

dioxygen (ISO)

doxorubicin (ISO)

lead(0) (ISO)

lead(2+) (ISO)

orphenadrine (EXP)

pirinixic acid (ISO)

pravastatin (EXP,ISO)

rac-lactic acid (ISO)

sunitinib (ISO)

testosterone (ISO)

titanium dioxide (ISO)

trichloroethene (ISO)

vancomycin (ISO)

zaragozic acid A (EXP,ISO)

Gene Ontology Annotations Click to see Annotation Detail View

Cellular Component

integral component of membrane (IEA)

Molecular Function

protein binding (ISO)

References

References - curated


1.	RGD automated import pipeline for gene-chemical interactions

Additional References at PubMed

PMID:12477932	PMID:17005852

Genomics

Comparative Map Data

Shisa4
(Rattus norvegicus - Norway rat)

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
mRatBN7.2	13	46,800,487 - 46,803,703 (-)	NCBI
Rnor_6.0 Ensembl	13	52,193,989 - 52,197,205 (-)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_6.0	13	52,193,989 - 52,197,205 (-)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_5.0	13	57,244,749 - 57,248,270 (-)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	13	48,368,910 - 48,372,126 (-)	NCBI	RGSC3.4		rn4	RGSC3.4
RGSC_v3.1	13	48,382,485 - 48,386,271 (-)	NCBI
Celera	13	47,120,498 - 47,123,714 (-)	NCBI		Celera
Cytogenetic Map	13	q13	NCBI

SHISA4
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38.p13 Ensembl	1	201,888,680 - 201,892,587 (+)	Ensembl	GRCh38		hg38	GRCh38
GRCh38.p13 Ensembl	1	201,888,680 - 201,892,306 (+)	Ensembl	GRCh38		hg38	GRCh38
GRCh38	1	201,888,677 - 201,892,587 (+)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh37	1	201,857,797 - 201,861,715 (+)	NCBI	GRCh37	GRCh37	hg19	GRCh37
GRCh37	1	201,857,805 - 201,861,715 (+)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	1	200,124,655 - 200,128,050 (+)	NCBI	NCBI36		hg18	NCBI36
Build 34	1	198,589,688 - 198,593,083	NCBI
Celera	1	174,981,622 - 174,985,540 (+)	NCBI
Cytogenetic Map	1	q32.1	NCBI
HuRef	1	173,023,711 - 173,027,629 (+)	NCBI		HuRef
CHM1_1	1	203,280,041 - 203,283,959 (+)	NCBI		CHM1_1

Shisa4
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	1	135,299,194 - 135,302,801 (-)	NCBI	GRCm39		mm39
GRCm38	1	135,371,057 - 135,375,298 (-)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	1	135,371,057 - 135,375,237 (-)	Ensembl	GRCm38		mm10	GRCm38
MGSCv37	1	137,268,033 - 137,271,640 (-)	NCBI	GRCm37		mm9	NCBIm37
MGSCv36	1	137,187,867 - 137,191,474 (-)	NCBI			mm8
Celera	1	137,999,630 - 138,003,194 (-)	NCBI		Celera
Cytogenetic Map	1	E4	NCBI

Shisa4
(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_004955406	37,957,326 - 37,962,468 (+)	Ensembl	ChiLan1.0
ChiLan1.0	NW_004955406	37,959,156 - 37,961,972 (+)	NCBI	ChiLan1.0	ChiLan1.0

SHISA4
(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	1	181,787,839 - 181,791,472 (+)	NCBI	panpan1.1	PanPan1.1	panPan2
PanPan1.1 Ensembl	1	181,787,839 - 181,791,472 (+)	Ensembl	panpan1.1		panPan2
Mhudiblu_PPA_v0	1	177,485,825 - 177,489,458 (+)	NCBI	Mhudiblu_PPA_v0		panPan3

SHISA4
(Canis lupus familiaris - dog)

Dog Assembly	Chr	Position (strand)	Source	Genome Browsers
Dog Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
CanFam3.1	7	1,064,833 - 1,066,591 (-)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1

Shisa4
(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_004936567	2,600,309 - 2,604,201 (-)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

SHISA4
(Sus scrofa - pig)

Pig Assembly	Chr	Position (strand)	Source	Genome Browsers
Pig Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Sscrofa11.1 Ensembl	10	24,158,470 - 24,169,536 (+)	Ensembl	Sscrofa11.1		susScr11	Sscrofa11.1
Sscrofa11.1	10	24,158,648 - 24,161,504 (+)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1

SHISA4
(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	25	27,517,915 - 27,521,536 (-)	NCBI
ChlSab1.1 Ensembl	25	27,518,369 - 27,521,219 (-)	Ensembl

Shisa4
(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_004624807	8,884,641 - 8,888,164 (-)	NCBI

Position Markers

RH143294

Rat Assembly	Chr	Position (strand)	Source	JBrowse
Rnor_6.0	13	52,193,263 - 52,193,486	NCBI	Rnor6.0
Rnor_5.0	13	57,244,023 - 57,244,246	UniSTS	Rnor5.0
RGSC_v3.4	13	48,368,184 - 48,368,407	UniSTS	RGSC3.4
Celera	13	47,119,772 - 47,119,995	UniSTS
RH 3.4 Map	13	197.2	UniSTS
Cytogenetic Map	13	q13	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
1354666	Bp244	Blood pressure QTL 244	4.9		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	13	1	107975663	Rat
1354666	Bp244	Blood pressure QTL 244	4.9		arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	13	1	107975663	Rat
1354666	Bp244	Blood pressure QTL 244	4.9		arterial blood pressure trait (VT:2000000)	diastolic blood pressure (CMO:0000005)	13	1	107975663	Rat
1581554	Pur11	Proteinuria QTL 11			urine albumin amount (VT:0002871)	urine albumin excretion rate (CMO:0000757)	13	9016906	82995569	Rat
1581573	Uae36	Urinary albumin excretion QTL 36			urine albumin amount (VT:0002871)	urine albumin excretion rate (CMO:0000757)	13	9016906	82995569	Rat
1581570	Eae17	Experimental allergic encephalomyelitis QTL 17	4.1		nervous system integrity trait (VT:0010566)	experimental autoimmune encephalomyelitis incidence/prevalence measurement (CMO:0001046)	13	12193394	108478121	Rat
9589141	Insul28	Insulin level QTL 28	10.82	0.001	blood insulin amount (VT:0001560)	plasma insulin level (CMO:0000342)	13	14096330	59096330	Rat
7411662	Foco29	Food consumption QTL 29	20.8	0.001	eating behavior trait (VT:0001431)	feed conversion ratio (CMO:0001312)	13	14096330	59096330	Rat
2317040	Aia21	Adjuvant induced arthritis QTL 21	2.75		joint integrity trait (VT:0010548)	left rear ankle joint diameter (CMO:0002149)	13	14624631	59624631	Rat
2317046	Aia8	Adjuvant induced arthritis QTL 8	3.9700000286102295		joint integrity trait (VT:0010548)	left rear ankle joint diameter (CMO:0002149)	13	14624631	59624631	Rat
631645	Bp121	Blood pressure QTL 121	3.3		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	13	19810814	64810814	Rat
9589164	Gluco66	Glucose level QTL 66	6.67	0.001	blood glucose amount (VT:0000188)	plasma glucose level (CMO:0000042)	13	20052477	65052477	Rat
1331784	Bp222	Blood pressure QTL 222	2.944		arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	13	21482481	58537177	Rat
7207885	Glom27	Glomerulus QTL 27	3.9		kidney glomerulus integrity trait (VT:0010546)	kidney crescentic glomeruli count to kidney normal glomeruli count ratio (CMO:0002139)	13	24502279	108770533	Rat
61391	Bp5	Blood pressure QTL 5	5.6		arterial blood pressure trait (VT:2000000)	diastolic blood pressure (CMO:0000005)	13	28008338	73008338	Rat
70170	Eae14	Experimental allergic encephalomyelitis QTL 14		0.0024	nervous system integrity trait (VT:0010566)	experimental autoimmune encephalomyelitis incidence/prevalence measurement (CMO:0001046)	13	28584452	73584452	Rat
1558644	Cm45	Cardiac mass QTL 45	3.6	0.002	heart mass (VT:0007028)	heart wet weight (CMO:0000069)	13	29076934	74076934	Rat
6893338	Cm76	Cardiac mass QTL 76	0	0.99	heart mass (VT:0007028)	heart weight to body weight ratio (CMO:0000074)	13	29076934	74076934	Rat
1354621	Rf47	Renal function QTL 47	3.7		kidney renin amount (VT:0010559)	kidney renin level (CMO:0002166)	13	35301263	107975663	Rat
2301962	Cm72	Cardiac mass QTL 72	4.12		heart left ventricle mass (VT:0007031)	heart left ventricle weight (CMO:0000776)	13	36147533	64868393	Rat
70181	BpQTLcluster11	Blood pressure QTL cluster 11	6.922		arterial blood pressure trait (VT:2000000)	absolute change in mean arterial blood pressure (CMO:0000533)	13	36147533	99968921	Rat
70181	BpQTLcluster11	Blood pressure QTL cluster 11	6.922		arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	13	36147533	99968921	Rat
70181	BpQTLcluster11	Blood pressure QTL cluster 11	6.922		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	13	36147533	99968921	Rat
70181	BpQTLcluster11	Blood pressure QTL cluster 11	6.922		arterial blood pressure trait (VT:2000000)	diastolic blood pressure (CMO:0000005)	13	36147533	99968921	Rat
2303563	Bw89	Body weight QTL 89	6		body mass (VT:0001259)	body weight (CMO:0000012)	13	37346348	82346348	Rat
61340	Bp25	Blood pressure QTL 25	4.2	0.004	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	13	39372927	84372927	Rat
10755495	Bp387	Blood pressure QTL 387	3.78		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	13	39501300	93652524	Rat
4889861	Pur29	Proteinuria QTL 29	13.8	0.005	total urine protein amount (VT:0000032)	urine total protein excretion rate (CMO:0000756)	13	42310744	86833540	Rat
1331750	Bp220	Blood pressure QTL 220	2.98		arterial blood pressure trait (VT:2000000)	diastolic blood pressure (CMO:0000005)	13	42310744	87310744	Rat
70220	Bp55	Blood pressure QTL 55	5.75		arterial blood pressure trait (VT:2000000)	blood pressure measurement (CMO:0000003)	13	42508345	87508345	Rat
61349	Bp31	Blood pressure QTL 31	5.75		arterial blood pressure trait (VT:2000000)	blood pressure measurement (CMO:0000003)	13	42508345	87508345	Rat
1549897	Stresp12	Stress response QTL 12	3.35		stress-related behavior trait (VT:0010451)	number of approaches toward negative stimulus before onset of defensive burying response (CMO:0001960)	13	43575717	88575717	Rat
619615	Bp80	Blood pressure QTL 80		0.0354	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	13	45676629	90676629	Rat
4145117	Mcs27	Mammary carcinoma susceptibility QTL 27		0.0001	mammary gland integrity trait (VT:0010552)	post-insult time to mammary tumor formation (CMO:0000345)	13	48776655	53264877	Rat
6893344	Cm79	Cardiac mass QTL 79	1.5	0.04	heart mass (VT:0007028)	heart weight to body weight ratio (CMO:0000074)	13	49058507	67207219	Rat
12879472	Bp399	Blood pressure QTL 399			arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	13	50609228	53264877	Rat
12879441	Bp396	Blood pressure QTL 396			arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	13	51080989	96080989	Rat
1298066	Bp159	Blood pressure QTL 159		0.004	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	13	51569248	96569248	Rat
71119	Thym2	Thymus enlargement QTL 2	3.8		thymus mass (VT:0004954)	thymus weight to body weight ratio (CMO:0000612)	13	51577824	90675199	Rat

miRNA Target Status

Predicted Target Of

	Summary Value
Count of predictions:	385
Count of miRNA genes:	195
Interacting mature miRNAs:	239
Transcripts:	ENSRNOT00000009712
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	1	43	4	4		4	8	11	74	20	33	11	8
Low	2		41	25	18	25				15	8
Below cutoff			12	12	1	12

View RNA-SEQ Expression Data

Sequence

Nucleotide Sequences


RefSeq Transcripts	NM_001077826	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	AC096239	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	BC158557	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	CH473958	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	EF044301	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	FQ213412	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	FQ213723	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	FQ214216	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	JACYVU010000242	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

Reference Sequences

RefSeq Acc Id:

ENSRNOT00000009712 ⟹ ENSRNOP00000009712

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
Rnor_6.0 Ensembl	13	52,193,989 - 52,197,205 (-)	Ensembl

RefSeq Acc Id:

NM_001077826 ⟹ NP_001071294

RefSeq Status:

PROVISIONAL

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	13	46,800,487 - 46,803,703 (-)	NCBI
Rnor_6.0	13	52,193,989 - 52,197,205 (-)	NCBI
Rnor_5.0	13	57,244,749 - 57,248,270 (-)	NCBI
RGSC_v3.4	13	48,368,910 - 48,372,126 (-)	RGD
Celera	13	47,120,498 - 47,123,714 (-)	RGD

Sequence:

show sequence

ATGCCGCCCGCCGGGCCCCGCGGGGTCGCGCCACTCGCTGCCGTCGTCCTGCTGGTGCTTGGGG
CTCCTCTGGCACTGGCGAGTGAAGACTGCTTGTGGTATCTGGACCGGAATGGCTCCTGGCATCC
GGGATTTGACTGCGAGTTTTTCACCTTCTGCTGCGGGACCTGCTACCAGCGGTACTGCTGCAGG
GACCTGACCTTACTCATCACCGAGAGACAGCAGAAACACTGCCTGGCCTTCAGTCCCAAGACCA
TAGCAGGCATCGCCTCTGCTGTAATCCTCTTTGTTGCCGTGGTTGCCACCACCATCTGCTGCTT
CCTCTGTTCCTGTTGTTACCTATACCGAAGGCGCCAGCAGCTCCAGAGCACATTTGAAGGCCAA
GAGATTCCGATGACAGGCATCCCAATGCAGCCAGTATACCAGTACCCCCCGGACCCCAAAGCTG
GACCTGGACCCCCACAGCCTGGTTTCATGTACCCACCTAGTGGTCCTGCTCCTCAGTATCCTCT
CTATCCAGCTGGGCCCCCAATCTACAACCCTGCAGCTCCTCCACCCTATATGCCACCACAGCCC
TCTTACCCAGGAGCCTGA

hide sequence

Protein Sequences


Protein RefSeqs	NP_001071294	(Get FASTA)	NCBI Sequence Viewer
GenBank Protein	AAI58558	(Get FASTA)	NCBI Sequence Viewer
	ABK41474	(Get FASTA)	NCBI Sequence Viewer
	EDM09697	(Get FASTA)	NCBI Sequence Viewer

Reference Sequences

RefSeq Acc Id:	NP_001071294 ⟸ NM_001077826
- Peptide Label:	precursor
- UniProtKB:	A0MV40 (UniProtKB/TrEMBL)
- Sequence:	show sequence MPPAGPRGVAPLAAVVLLVLGAPLALASEDCLWYLDRNGSWHPGFDCEFFTFCCGTCYQRYCCR DLTLLITERQQKHCLAFSPKTIAGIASAVILFVAVVATTICCFLCSCCYLYRRRQQLQSTFEGQ EIPMTGIPMQPVYQYPPDPKAGPGPPQPGFMYPPSGPAPQYPLYPAGPPIYNPAAPPPYMPPQP SYPGA hide sequence

RefSeq Acc Id:

ENSRNOP00000009712 ⟸ ENSRNOT00000009712

Transcriptome

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

Strain Variation

Strain Sequence Variants (Rnor 6.0)

ACI/EurMcwi (MCW)

Visual

CSV

TAB

Printer

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

ACI/EurMcwi (RGD)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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

BBDP/Wor (RGD)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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:1312041	AgrOrtholog
Ensembl Genes	ENSRNOG00000007369	Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein	ENSRNOP00000009712	ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript	ENSRNOT00000009712	ENTREZGENE, UniProtKB/TrEMBL
IMAGE_CLONE	IMAGE:7313337	IMAGE-MGC_LOAD
InterPro	Shisa	UniProtKB/TrEMBL
KEGG Report	rno:360848	UniProtKB/TrEMBL
MGC_CLONE	MGC:187232	IMAGE-MGC_LOAD
NCBI Gene	360848	ENTREZGENE
PANTHER	PTHR31395	UniProtKB/TrEMBL
Pfam	Shisa	UniProtKB/TrEMBL
PhenoGen	Shisa4	PhenoGen
UniProt	A0MV40	ENTREZGENE, UniProtKB/TrEMBL

Nomenclature History

Date	Current Symbol	Current Name	Previous Symbol	Previous Name	Description	Reference	Status
2013-08-07	Shisa4	shisa family member 4	Shisa4	shisa homolog 4 (Xenopus laevis)	Nomenclature updated to reflect human and mouse nomenclature	1299863	APPROVED
2008-05-02	Shisa4	shisa homolog 4 (Xenopus laevis)	Tmem58	transmembrane protein 58	Nomenclature updated to reflect human and mouse nomenclature	1299863	APPROVED
2008-04-30	Tmem58	transmembrane protein 58	Tmem58_predicted	transmembrane protein 58 (predicted)	'predicted' is removed	2292626	APPROVED
2006-03-30	Tmem58_predicted	transmembrane protein 58 (predicted)	RGD1312041_predicted	similar to scotin (predicted)	Symbol and Name updated	1299863	APPROVED
2005-01-20	RGD1312041_predicted	similar to scotin (predicted)	LOC360848_predicted		Symbol and Name status set to approved	1331353	APPROVED
2005-01-12	LOC360848_predicted	similar to scotin (predicted)			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)