Sdcbp (syndecan binding protein) - Rat Genome Database

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

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Gene: Sdcbp (syndecan binding protein) Rattus norvegicus

Analyze

Symbol:

Sdcbp

Name:

syndecan binding protein

RGD ID:

621497

Description:

Exhibits several functions, including protein C-terminus binding activity; signaling receptor binding activity; and syndecan binding activity. Involved in presynapse assembly. Predicted to localize to several cellular components, including extracellular exosome; interleukin-5 receptor complex; and nucleus. Orthologous to human SDCBP (syndecan binding protein); PARTICIPATES IN interleukin-5 signaling pathway; syndecan signaling pathway; INTERACTS WITH 3H-1,2-dithiole-3-thione; acetamide; ammonium chloride.

Type:

protein-coding

RefSeq Status:

VALIDATED

Also known as:

mda-9; syndecan-binding protein 1; syntenin; syntenin-1; TACIP18

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):	SDCBP (syndecan binding protein)	HGNC	EggNOG, Ensembl, HomoloGene, Inparanoid, NCBI, OMA, OrthoDB, OrthoMCL, Panther, PhylomeDB, Treefam
Mus musculus (house mouse):	Sdcbp (syndecan binding protein)	HGNC	Treefam, EggNOG, OrthoMCL, NCBI, OMA, HomoloGene, Inparanoid, Panther, PhylomeDB, OrthoDB, Ensembl
Chinchilla lanigera (long-tailed chinchilla):	Sdcbp (syndecan binding protein)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Pan paniscus (bonobo/pygmy chimpanzee):	SDCBP (syndecan binding protein)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Canis lupus familiaris (dog):	LOC482977 (syndecan binding protein)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Ictidomys tridecemlineatus (thirteen-lined ground squirrel):	Sdcbp (syndecan binding protein)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Sus scrofa (pig):	SDCBP (syndecan binding protein)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chlorocebus sabaeus (African green monkey):	LOC103236850 (syndecan binding protein)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Heterocephalus glaber (naked mole-rat):	Sdcbp (syndecan binding protein)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Alliance orthologs ³
Mus musculus (house mouse):	Sdcbp (syndecan binding protein)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|TreeFam)
Homo sapiens (human):	SDCBP (syndecan binding protein)	Alliance	DIOPT (Ensembl Compara\|HGNC\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|TreeFam)
Danio rerio (zebrafish):	sdcbp2 (syndecan binding protein (syntenin) 2)	Alliance	DIOPT (Hieranoid\|InParanoid\|OMA\|OrthoInspector\|PANTHER)
Drosophila melanogaster (fruit fly):	CG31342	Alliance	DIOPT (Ensembl Compara\|PANTHER\|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	5	19,473,499 - 19,517,188 (+)	NCBI
Rnor_6.0 Ensembl	5	19,471,664 - 19,498,485 (+)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_6.0	5	19,471,664 - 19,498,499 (+)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_5.0	5	24,256,110 - 24,283,037 (+)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	5	19,822,440 - 19,849,223 (+)	NCBI	RGSC3.4		rn4	RGSC3.4
RGSC_v3.1	5	19,822,439 - 19,849,220 (+)	NCBI
Celera	5	18,790,757 - 18,817,395 (+)	NCBI		Celera
Cytogenetic Map	5	q12	NCBI

JBrowse:

View Region in Genome Browser (JBrowse)

Model

Annotation Click to see Annotation Detail View

Disease Annotations Click to see Annotation Detail View

osteoarthritis (ISO)

Gene-Chemical Interaction Annotations Click to see Annotation Detail View

(-)-demecolcine (ISO)

1,2-dichloroethane (ISO)

1,2-dimethylhydrazine (ISO)

17beta-estradiol (ISO)

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

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

2-hydroxypropanoic acid (ISO)

3H-1,2-dithiole-3-thione (EXP)

5-azacytidine (ISO)

7,12-dimethyltetraphene (ISO)

acetamide (EXP)

acrolein (ISO)

all-trans-retinoic acid (ISO)

alpha-pinene (ISO)

ammonium chloride (EXP)

amphetamine (EXP)

arsane (ISO)

arsenic atom (ISO)

arsenite(3-) (ISO)

arsenous acid (ISO)

benzo[a]pyrene (ISO)

bisphenol A (EXP,ISO)

bucladesine (ISO)

cadmium dichloride (EXP)

calcitriol (ISO)

carbon nanotube (ISO)

cisplatin (ISO)

copper(II) sulfate (ISO)

cyclosporin A (ISO)

dexamethasone (ISO)

diarsenic trioxide (ISO)

dibutyl phthalate (EXP)

dicrotophos (ISO)

ethanol (ISO)

ethyl methanesulfonate (ISO)

flavonoids (EXP)

flutamide (EXP)

folic acid (ISO)

formaldehyde (ISO)

medroxyprogesterone acetate (ISO)

mercury dichloride (EXP)

methyl methanesulfonate (ISO)

N-nitrosodiethylamine (EXP)

ozone (ISO)

paracetamol (ISO)

phenobarbital (ISO)

potassium dichromate (ISO)

rac-lactic acid (ISO)

sarin (ISO)

silver atom (ISO)

silver(0) (ISO)

sodium arsenate (ISO)

sulforaphane (ISO)

sunitinib (ISO)

tamoxifen (ISO)

tetrachloromethane (ISO)

thioacetamide (EXP)

trichostatin A (ISO)

uranium atom (ISO)

urethane (ISO)

valproic acid (ISO)

vincristine (ISO)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

actin cytoskeleton organization (IEA)

chemical synaptic transmission (IEA)

negative regulation of proteasomal ubiquitin-dependent protein catabolic process (ISO,ISS)

negative regulation of receptor internalization (ISO,ISS)

positive regulation of cell growth (ISO,ISS)

positive regulation of cell migration (ISO,ISS)

positive regulation of cell population proliferation (ISO,ISS)

positive regulation of epithelial to mesenchymal transition (ISO,ISS)

positive regulation of exosomal secretion (ISO)

positive regulation of extracellular exosome assembly (ISO)

positive regulation of pathway-restricted SMAD protein phosphorylation (IBA,ISO,ISS)

positive regulation of phosphorylation (ISO)

positive regulation of transforming growth factor beta receptor signaling pathway (IBA,ISO,ISS)

presynapse assembly (IDA,IMP)

Ras protein signal transduction (ISO)

regulation of mitotic cell cycle (ISO,ISS)

Cellular Component

adherens junction (IEA)

cytoplasm (IBA,ISO)

cytoskeleton (IEA)

cytosol (IEA,ISO)

endoplasmic reticulum membrane (IEA)

extracellular exosome (ISO)

focal adhesion (IEA)

interleukin-5 receptor complex (ISO,ISS)

melanosome (IEA)

membrane raft (ISO,ISS)

nuclear membrane (IEA,ISO)

nucleoplasm (IEA,ISO)

plasma membrane (IBA,ISO,ISS)

synapse (IEA)

Molecular Function

cell adhesion molecule binding (IPI)

ephrin receptor binding (IPI)

frizzled binding (ISO)

growth factor binding (IPI)

identical protein binding (IPI,ISO)

interleukin-5 receptor binding (ISO,ISS)

neurexin family protein binding (IPI,NAS)

phosphatidylinositol-4,5-bisphosphate binding (ISO)

protein binding (IPI,ISO)

protein C-terminus binding (IPI)

protein heterodimerization activity (ISO)

protein N-terminus binding (ISO)

protein-containing complex binding (IPI)

syndecan binding (IBA,IPI,ISO)

Molecular Pathway Annotations Click to see Annotation Detail View

interleukin-5 signaling pathway (ISO)

syndecan signaling pathway (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.	Geijsen N, etal., Science. 2001 Aug 10;293(5532):1136-8.
3.	GOA data from the GO Consortium
4.	Koroll M, etal., J Biol Chem 2001 Apr 6;276(14):10646-54.
5.	McClelland AC, etal., Proc Natl Acad Sci U S A. 2009 Dec 1;106(48):20487-92. doi: 10.1073/pnas.0811862106. Epub 2009 Nov 13.
6.	MGD data from the GO Consortium
7.	NCBI rat LocusLink and RefSeq merged data July 26, 2002
8.	Pipeline to import Pathway Interaction Database annotations from NCI into RGD
9.	RGD automated data pipeline
10.	RGD automated import pipeline for gene-chemical interactions
11.	Strausberg RL, etal., Proc Natl Acad Sci U S A. 2002 Dec 24;99(26):16899-903. Epub 2002 Dec 11.
12.	Zimmermann P, etal., Mol Biol Cell 2001 Feb;12(2):339-50.

Additional References at PubMed

PMID:9391086	PMID:9883737	PMID:10230395	PMID:11434923	PMID:11891216	PMID:12037664	PMID:15014045	PMID:15276154	PMID:15371445	PMID:15458844	PMID:15489334	PMID:15797720
PMID:16421316	PMID:16502470	PMID:18256285	PMID:19056867	PMID:19199708	PMID:20458337	PMID:21082674	PMID:21362503	PMID:22516433	PMID:22660413	PMID:22673509	PMID:23376485
PMID:23533145	PMID:24769233	PMID:25468996	PMID:25893292	PMID:26539120	PMID:27386966	PMID:27830760

Genomics

Comparative Map Data

Sdcbp
(Rattus norvegicus - Norway rat)

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
mRatBN7.2	5	19,473,499 - 19,517,188 (+)	NCBI
Rnor_6.0 Ensembl	5	19,471,664 - 19,498,485 (+)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_6.0	5	19,471,664 - 19,498,499 (+)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_5.0	5	24,256,110 - 24,283,037 (+)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	5	19,822,440 - 19,849,223 (+)	NCBI	RGSC3.4		rn4	RGSC3.4
RGSC_v3.1	5	19,822,439 - 19,849,220 (+)	NCBI
Celera	5	18,790,757 - 18,817,395 (+)	NCBI		Celera
Cytogenetic Map	5	q12	NCBI

SDCBP
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38.p13 Ensembl	8	58,552,924 - 58,582,859 (+)	Ensembl	GRCh38		hg38	GRCh38
GRCh38	8	58,553,261 - 58,582,860 (+)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh37	8	59,465,820 - 59,495,417 (+)	NCBI	GRCh37	GRCh37	hg19	GRCh37
GRCh37	8	59,465,566 - 59,495,419 (+)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	8	59,628,282 - 59,657,973 (+)	NCBI	NCBI36		hg18	NCBI36
Build 34	8	59,628,281 - 59,657,972	NCBI
Celera	8	55,458,752 - 55,488,443 (+)	NCBI
Cytogenetic Map	8	q12.1	NCBI
HuRef	8	54,952,903 - 54,982,593 (+)	NCBI		HuRef
CHM1_1	8	59,517,611 - 59,547,302 (+)	NCBI		CHM1_1

Sdcbp
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	4	6,365,654 - 6,396,122 (+)	NCBI	GRCm39		mm39
GRCm38	4	6,365,680 - 6,396,122 (+)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	4	6,365,650 - 6,408,423 (+)	Ensembl	GRCm38		mm10	GRCm38
MGSCv37	4	6,292,827 - 6,323,269 (+)	NCBI	GRCm37		mm9	NCBIm37
MGSCv36	4	6,292,868 - 6,322,797 (+)	NCBI			mm8
Celera	4	6,283,969 - 6,314,409 (+)	NCBI		Celera
Cytogenetic Map	4	A1	NCBI

Sdcbp
(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_004955454	17,089,232 - 17,113,484 (+)	Ensembl	ChiLan1.0
ChiLan1.0	NW_004955454	17,093,930 - 17,113,491 (+)	NCBI	ChiLan1.0	ChiLan1.0

SDCBP
(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	8	56,643,962 - 56,673,834 (+)	NCBI	panpan1.1	PanPan1.1	panPan2
PanPan1.1 Ensembl	8	56,643,962 - 56,673,833 (+)	Ensembl	panpan1.1		panPan2
Mhudiblu_PPA_v0	8	54,992,627 - 55,022,560 (+)	NCBI	Mhudiblu_PPA_v0		panPan3

LOC482977
(Canis lupus familiaris - dog)

Dog Assembly	Chr	Position (strand)	Source	Genome Browsers
Dog Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
CanFam3.1	29	9,331,876 - 9,370,489 (+)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1

Sdcbp
(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_004936496	14,331,971 - 14,347,123 (-)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

SDCBP
(Sus scrofa - pig)

Pig Assembly	Chr	Position (strand)	Source	Genome Browsers
Pig Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Sscrofa11.1 Ensembl	4	74,295,922 - 74,341,085 (-)	Ensembl	Sscrofa11.1		susScr11	Sscrofa11.1
Sscrofa11.1	4	74,295,941 - 74,357,720 (-)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1
Sscrofa10.2	4	81,090,105 - 81,122,727 (-)	NCBI	Sscrofa10.2	Sscrofa10.2	susScr3

LOC103236850
(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	8	54,536,286 - 54,565,884 (+)	NCBI

Sdcbp
(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_004624744	33,524,045 - 33,558,963 (-)	NCBI

Position Markers

RH129294

Rat Assembly	Chr	Position (strand)	Source	JBrowse
Rnor_6.0	5	19,498,257 - 19,498,447	NCBI	Rnor6.0
Rnor_5.0	5	24,282,795 - 24,282,985	UniSTS	Rnor5.0
RGSC_v3.4	5	19,848,981 - 19,849,171	UniSTS	RGSC3.4
Celera	5	18,817,153 - 18,817,343	UniSTS
Cytogenetic Map	5	q12	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
1331771	Rf35	Renal function QTL 35	4.36965		kidney blood vessel physiology trait (VT:0100012)	absolute change in renal blood flow rate (CMO:0001168)	5	1	89432042	Rat
1331756	Rf34	Renal function QTL 34	4.16275		kidney blood vessel physiology trait (VT:0100012)	absolute change in renal blood flow rate (CMO:0001168)	5	1	93273395	Rat
70212	Niddm25	Non-insulin dependent diabetes mellitus QTL 25	3.54		blood glucose amount (VT:0000188)	blood glucose level (CMO:0000046)	5	1	136640934	Rat
2312562	Pur18	Proteinuria QTL 18	2.6	0.001	total urine protein amount (VT:0000032)	urine total protein excretion rate (CMO:0000756)	5	1525098	33001026	Rat
1576314	Eutr1	Estrogen induced uterine response QTL 1			uterus integrity trait (VT:0010575)	pyometritis severity score (CMO:0002009)	5	1525098	78720537	Rat
8662454	Vetf3	Vascular elastic tissue fragility QTL 3	27.4		artery integrity trait (VT:0010639)	number of ruptures of the internal elastic lamina of the abdominal aorta and iliac arteries (CMO:0002562)	5	1666587	71552720	Rat
2313085	Bss59	Bone structure and strength QTL 59	2.9	0.0001	long bone metaphysis morphology trait (VT:0000133)	tibia midshaft total cross-sectional area (CMO:0001715)	5	3251329	26252076	Rat
1300117	Hrtrt8	Heart rate QTL 8	3.49		heart pumping trait (VT:2000009)	heart rate (CMO:0000002)	5	3251329	48722188	Rat
61462	Niddm10	Non-insulin dependent diabetes mellitus QTL 10	3.9	0.001	blood glucose amount (VT:0000188)	plasma glucose level (CMO:0000042)	5	4525738	47978104	Rat
2293666	Bmd38	Bone mineral density QTL 38	4.4		femur size trait (VT:1000369)	femoral neck cortical cross-sectional area (CMO:0001702)	5	8632285	53632285	Rat
7394712	Emca13	Estrogen-induced mammary cancer QTL 13			mammary gland integrity trait (VT:0010552)	mammary tumor number (CMO:0000343)	5	9514842	103580403	Rat
634305	Mamtr1	Mammary tumor resistance QTL 1		0.0001	mammary gland integrity trait (VT:0010552)	mammary tumor number (CMO:0000343)	5	12651967	117554267	Rat
1641903	Alcrsp3	Alcohol response QTL 3			response to alcohol trait (VT:0010489)	duration of loss of righting reflex (CMO:0002289)	5	13288888	58288888	Rat
1600358	Mamtr5	Mammary tumor resistance QTL 5			mammary gland integrity trait (VT:0010552)	mammary tumor number (CMO:0000343)	5	18847913	63847913	Rat
1358353	Srcrtb2	Stress Responsive Cort Basal QTL 2	3.48	0.003	blood corticosterone amount (VT:0005345)	plasma corticosterone level (CMO:0001173)	5	18847913	76608178	Rat

miRNA Target Status

Predicted Target Of

	Summary Value
Count of predictions:	673
Count of miRNA genes:	268
Interacting mature miRNAs:	333
Transcripts:	ENSRNOT00000013563
Prediction methods:	Microtar, Miranda
Result types:	miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.

Expression

RNA-SEQ Expression

High: > 1000 TPM value Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM Below Cutoff: < 0.5 TPM

	alimentary part of gastrointestinal system	circulatory system	endocrine system	exocrine system	hemolymphoid system	hepatobiliary system	integumental system	musculoskeletal system	nervous system	renal system	reproductive system	respiratory system	appendage
High
Medium	3	43	57	41	19	41	8	11	74	35	41	11	8
Low
Below cutoff

View RNA-SEQ Expression Data

Sequence

Nucleotide Sequences


RefSeq Transcripts	NM_031986	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_039110855	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_039110856	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_039110857	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_039110858	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_039110859	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_039110860	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_039110861	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_039110862	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_039110863	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_039110864	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	AC135473	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	AF248548	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	AJ292243	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	BC064651	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	CH473984	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	FQ225374	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	FQ226774	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	FQ230274	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	JACYVU010000160	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

Reference Sequences

RefSeq Acc Id:

ENSRNOT00000013563 ⟹ ENSRNOP00000013563

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
Rnor_6.0 Ensembl	5	19,471,664 - 19,498,485 (+)	Ensembl

RefSeq Acc Id:

NM_031986 ⟹ NP_114192

RefSeq Status:

VALIDATED

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	5	19,489,977 - 19,517,188 (+)	NCBI
Rnor_6.0	5	19,471,664 - 19,498,499 (+)	NCBI
Rnor_5.0	5	24,256,110 - 24,283,037 (+)	NCBI
RGSC_v3.4	5	19,822,440 - 19,849,223 (+)	RGD
Celera	5	18,790,757 - 18,817,395 (+)	RGD

Sequence:

show sequence

GACCCACGCGTCCGGGAGCCGGAGCGAGCGGCAGGAACAACGCGGTGTTCGGGGCAGAAAACAC
CTGCAAAAATGTCTCTCTATCCATCTCTTGAAGATTTGAAGGTAGACAAAGTAATTCAGGCTCA
AACTGCCTCTTCTGCTAATCCTGCCAGCCAGGCCTTTTTTTTAAATGTGGTCGATTCTGCTGCC
TTCCCTCCAGGTGGAAATCTCTATCCTAAACTGTATCCAGAACTCTCTCAATACATGGGACTGT
CTTTAAGTGAAGCTGAAATATGTGAAAACATGCCTGTGGTCTCTGGAGCGCCAACCCAAGGGCA
GTTGGTAGCAAGGCCATCCAGTGTGAACTACATGGTAGCACCTGTGACAGGTAACGATGCGGGG
ATTAGGAGAGCAGAGATTAAGCAAGGGATTCGGGAAGTCATTTTGTGTAAGGATCAAGATGGAA
AAATTGGGCTCAGACTGAAGTCAGTAGATAATGGTATATTTGTTCAACTAGTCCAGGCTAATTC
CCCAGCCTCCTTGGTTGGGCTGCGATTTGGGGACCAGGTGCTCCAGATCAATGGTGAAAACTGT
GCCGGCTGGAGCTCCGATAAGGCACACAAGGTGCTCAAGCAGGCCTTTGGAGAGAAGATTACCA
TGACCATTCGTGATAGACCCTTTGAACGGACAGTTACCATGCATAAGGACAGCAGTGGACATGT
TGGCTTTATCTTTAAAAGTGGAAAAATCACATCCATAGTGAAAGACAGTTCTGCTGCCAGAAAC
GGCCTTCTCACTGATCACCACATCTGTGAGATCAACGGACAGAACGTCATTGGCTTGAAGGATG
CTCAGATTGCAGATATACTGTCAACAGCTGGGACTGTGGTCACCATCACAATCATGCCTGCCTT
TATCTTCGAACATATTATTAAACGGATGGCTCCCAGCATTATGAAAAGCCTGATGGATCACACC
ATTCCTGAAGTTTAAACCTTGTACAGTGCATCACCGCCGAACGCTTCCAGTCTTCCTCTTCGGC
AACTTCTCTATTTCACCGCACATGAAGCTTTCCCGGATCCAGGGAGACTGTGCTGCATGGAGAC
CTGTCTATCTTCCACCATGGCTGGGAACCTCACTCTATCTGAGAGCGTCTTCAGATTTTAAGAT
AGGTGTAGCCTTATCCTGGTTTTACAGATGTGAACTCTCAAAAGATTCCCTGACTTTCTAGACT
TGGTTCTTTACTGGGAACCTGATGTTTTTCTATAAGCCATTGTGATTAGGATGACTGGTGTAGG
CTTAGCTGTGTCCGAGAACTGGTCTGCTTTCTCCGAGAAGTGCACAGTGCTAGGCACGTGCTTC
AGTTCTGTGGCATATGTGGAGTGTAGTACATCAGCATAGTACCTGTAGGATGAGTGCCTTTGAT
CGCAACTTTTTAAGTGTGTGTGTGAGTGTGTAAAATTCCAGTTAATCAACACTTCATTCACAAA
AGCATTATACAGTTCTGTGTAGGTGGCAAGAGACTAATGATTGTCACTAAATTCTAACACCTTC
ACCTAATGTGCTTCAGTTGTCGCCTAACACAGAAGCATTTAGATAAAGCAAATAGAAATTATTG
CTGCCTTCTGAAACCTGAGAGGTAGCTCTCTATCAAGCTGTTCTATGCTAGCCCTGAGCAGCTT
ACTGGTGTCGCAGAGCTGCCTAGCTGTACCAAGATTTTCTAGTCACTGCATAAAGGAAACGCCT
AAGAGTTGCCGTATTGCTTTCTGAGATACAAATTGCTATATATTTCATGTAAAAGTTGTTATAC
TAAATAGGATAAATTTTGGAGTCTCTTTTCACTCGTAGATAAAGTGGGTAATATCTAATTTGGC
ACTTGAGTCCTAACATTATGTAACTTTAGCTAGGTTGGGGTGGGTTTAGAATGTTTCCCTAGTC
ATCTCAGTTTGTTCCATTTTCTGACTCTATCCTGCAAACAAAAATGGCAATGACACTTTATCCT
GACTCTTTCCTTCTTAGTTTGTGCCTATCTTATTATTTTATGTGATATTATCCTATTAAATGTA
TAAAAATATTAAAAAAAAAAAAAAAAAAA

hide sequence

RefSeq Acc Id:

XM_039110855 ⟹ XP_038966783

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	5	19,489,960 - 19,517,188 (+)	NCBI

RefSeq Acc Id:

XM_039110856 ⟹ XP_038966784

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	5	19,473,499 - 19,517,188 (+)	NCBI

RefSeq Acc Id:

XM_039110857 ⟹ XP_038966785

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	5	19,473,640 - 19,517,188 (+)	NCBI

RefSeq Acc Id:

XM_039110858 ⟹ XP_038966786

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	5	19,489,970 - 19,517,188 (+)	NCBI

RefSeq Acc Id:

XM_039110859 ⟹ XP_038966787

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	5	19,493,819 - 19,517,188 (+)	NCBI

RefSeq Acc Id:

XM_039110860 ⟹ XP_038966788

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	5	19,490,182 - 19,517,188 (+)	NCBI

RefSeq Acc Id:

XM_039110861 ⟹ XP_038966789

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	5	19,490,386 - 19,517,188 (+)	NCBI

RefSeq Acc Id:

XM_039110862 ⟹ XP_038966790

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	5	19,489,906 - 19,517,188 (+)	NCBI

RefSeq Acc Id:

XM_039110863 ⟹ XP_038966791

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	5	19,489,960 - 19,517,188 (+)	NCBI

RefSeq Acc Id:

XM_039110864 ⟹ XP_038966792

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	5	19,493,808 - 19,517,188 (+)	NCBI

Protein Sequences


Protein RefSeqs	NP_114192	(Get FASTA)	NCBI Sequence Viewer
	XP_038966783	(Get FASTA)	NCBI Sequence Viewer
	XP_038966784	(Get FASTA)	NCBI Sequence Viewer
	XP_038966785	(Get FASTA)	NCBI Sequence Viewer
	XP_038966786	(Get FASTA)	NCBI Sequence Viewer
	XP_038966787	(Get FASTA)	NCBI Sequence Viewer
	XP_038966788	(Get FASTA)	NCBI Sequence Viewer
	XP_038966789	(Get FASTA)	NCBI Sequence Viewer
	XP_038966790	(Get FASTA)	NCBI Sequence Viewer
	XP_038966791	(Get FASTA)	NCBI Sequence Viewer
	XP_038966792	(Get FASTA)	NCBI Sequence Viewer
GenBank Protein	AAF86960	(Get FASTA)	NCBI Sequence Viewer
	AAH64651	(Get FASTA)	NCBI Sequence Viewer
	CAC21602	(Get FASTA)	NCBI Sequence Viewer
	EDM11636	(Get FASTA)	NCBI Sequence Viewer
	EDM11637	(Get FASTA)	NCBI Sequence Viewer
	EDM11638	(Get FASTA)	NCBI Sequence Viewer
	Q9JI92	(Get FASTA)	NCBI Sequence Viewer

Reference Sequences

RefSeq Acc Id:

NP_114192 ⟸ NM_031986

- UniProtKB:

Q9JI92 (UniProtKB/Swiss-Prot)

- Sequence:

show sequence

MSLYPSLEDLKVDKVIQAQTASSANPASQAFFLNVVDSAAFPPGGNLYPKLYPELSQYMGLSLS
EAEICENMPVVSGAPTQGQLVARPSSVNYMVAPVTGNDAGIRRAEIKQGIREVILCKDQDGKIG
LRLKSVDNGIFVQLVQANSPASLVGLRFGDQVLQINGENCAGWSSDKAHKVLKQAFGEKITMTI
RDRPFERTVTMHKDSSGHVGFIFKSGKITSIVKDSSAARNGLLTDHHICEINGQNVIGLKDAQI
ADILSTAGTVVTITIMPAFIFEHIIKRMAPSIMKSLMDHTIPEV

hide sequence

RefSeq Acc Id:

ENSRNOP00000013563 ⟸ ENSRNOT00000013563

RefSeq Acc Id:	XP_038966784 ⟸ XM_039110856
- Peptide Label:	isoform X1

RefSeq Acc Id:	XP_038966785 ⟸ XM_039110857
- Peptide Label:	isoform X1

RefSeq Acc Id:	XP_038966790 ⟸ XM_039110862
- Peptide Label:	isoform X2

RefSeq Acc Id:	XP_038966783 ⟸ XM_039110855
- Peptide Label:	isoform X1

RefSeq Acc Id:	XP_038966791 ⟸ XM_039110863
- Peptide Label:	isoform X2

RefSeq Acc Id:	XP_038966786 ⟸ XM_039110858
- Peptide Label:	isoform X1

RefSeq Acc Id:	XP_038966788 ⟸ XM_039110860
- Peptide Label:	isoform X1

RefSeq Acc Id:	XP_038966789 ⟸ XM_039110861
- Peptide Label:	isoform X1

RefSeq Acc Id:	XP_038966792 ⟸ XM_039110864
- Peptide Label:	isoform X2

RefSeq Acc Id:	XP_038966787 ⟸ XM_039110859
- Peptide Label:	isoform X1

Protein Domains

PDZ

Transcriptome

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

Promoters

RGD ID:

13693554

Promoter ID:

EPDNEW_R4078

Type:

multiple initiation site

Name:

Sdcbp_1

Description:

syndecan binding protein

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	5	19,471,652 - 19,471,712	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

Damaging Variants

Assembly: RGSC_v3.4

Chromosome	Start Pos	End Pos	Reference Nucleotide	Variant Nucleotide	Variant Type	Strain
5	19842993	19842994	G	T	snv	SS/JrHsdMcwi (MCW)

Additional Information

External Database Links

Database	Acc Id	Source(s)
AGR Gene	RGD:621497	AgrOrtholog
Ensembl Genes	ENSRNOG00000009683	Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Protein	ENSRNOP00000013563	ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript	ENSRNOT00000013563	ENTREZGENE, UniProtKB/Swiss-Prot
Gene3D-CATH	2.30.42.10	UniProtKB/Swiss-Prot
IMAGE_CLONE	IMAGE:5598152	IMAGE-MGC_LOAD
InterPro	PDZ	UniProtKB/Swiss-Prot
	PDZ_sf	UniProtKB/Swiss-Prot
	SDCBP	UniProtKB/Swiss-Prot
KEGG Report	rno:83841	UniProtKB/Swiss-Prot
MGC_CLONE	MGC:72376	IMAGE-MGC_LOAD
NCBI Gene	83841	ENTREZGENE
PANTHER	PTHR12345:SF10	UniProtKB/Swiss-Prot
Pfam	PDZ	UniProtKB/Swiss-Prot
PhenoGen	Sdcbp	PhenoGen
PROSITE	PDZ	UniProtKB/Swiss-Prot
SMART	PDZ	UniProtKB/Swiss-Prot
Superfamily-SCOP	SSF50156	UniProtKB/Swiss-Prot
UniProt	Q9JI92	ENTREZGENE, UniProtKB/Swiss-Prot

Nomenclature History

Date	Current Symbol	Current Name	Previous Symbol	Previous Name	Description	Reference	Status
2005-01-20	Sdcbp	syndecan binding protein		syntenin	Name updated	1299863	APPROVED
2002-08-07	Sdcbp	syntenin			Symbol and Name status set to provisional	70820	PROVISIONAL

RGD Curation Notes

Note Type	Note	Reference
gene_physical_interaction	interacts with syntenin-2	633988
gene_protein	forms homodimers	633988

Gene Annotator (Functional Annotation) unavailable	Gene Annotator (Annotation Distribution) unavailable	Variant Visualizer (Genomic Variants) unavailble Variant Visualizer (Genomic Variants) unavailable
Gene Annotator (Functional Annotation)	Gene Annotator (Annotation Distribution)	Variant Visualizer (Genomic Variants)

InterViewer (Protein-Protein Interactions) unavailable	Gviewer (Genome Viewer) unavailable	Variant Visualizer (Damaging Variants) unavailble Variant Visualizer (Damaging Variants) unavailable
InterViewer (Protein-Protein Interactions)	GViewer (Genome Viewer)	Variant Visualizer (Damaging Variants)

Gene Annotator (Annotation Comparison) unavailable	OLGA (Gene List Generator) unavailable
Gene Annotator (Annotation Comparison)	OLGA (Gene List Generator)	Excel (Download)

MOET (Multi-Ontology Enrichement) unavailable	GOLF (Gene-Ortholog Location Finder) unavailable
MOET (Multi-Ontology Enrichement)	GOLF (Gene-Ortholog Location Finder)

Imported Disease Annotations - CTD

Imported Annotations - PID (archival)