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:

Enables several functions, including identical protein binding activity; signaling receptor binding activity; and syndecan binding activity. Involved in presynapse assembly. Located in mitochondrion and postsynaptic density. Is active in presynapse. Orthologous to human SDCBP (syndecan binding protein); PARTICIPATES IN interleukin-5 signaling pathway; syndecan signaling pathway; INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 3-chloropropane-1,2-diol; 3H-1,2-dithiole-3-thione.

Type:

protein-coding

RefSeq Status:

VALIDATED

Previously known as:

LOC108350925; mda-9; syndecan-binding protein 1; syntenin; syntenin-1; TACIP18; uncharacterized LOC108350925

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)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
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):	SDCBP (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 (green monkey):	SDCBP (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\|SonicParanoid)
Homo sapiens (human):	SDCBP (syndecan binding protein)	Alliance	DIOPT (Ensembl Compara\|HGNC\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|SonicParanoid)
Danio rerio (zebrafish):	sdcbp2 (syndecan binding protein (syntenin) 2)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OrthoInspector\|PANTHER\|SonicParanoid)
Danio rerio (zebrafish):	sdcbp (syndecan binding protein (syntenin))	Alliance	DIOPT (Ensembl Compara\|OMA\|OrthoFinder\|PANTHER)
Drosophila melanogaster (fruit fly):	CG31342	Alliance	DIOPT (Ensembl Compara\|PANTHER)

Latest Assembly:

mRatBN7.2 - mRatBN7.2 Assembly

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	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	5	19,489,961 - 19,527,572 (+)	Ensembl		mRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx	5	21,697,118 - 21,724,119 (+)	NCBI	Rnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.0	5	23,288,429 - 23,315,152 (+)	NCBI	Rnor_SHRSP
UTH_Rnor_WKY_Bbb_1.0	5	23,068,735 - 23,095,458 (+)	NCBI	Rnor_WKY
Rnor_6.0	5	19,471,664 - 19,498,499 (+)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	5	19,471,664 - 19,498,485 (+)	Ensembl	Rnor6.0		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	RGSC_v3.4	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 (EXP,ISO)

2-hydroxypropanoic acid (ISO)

3-chloropropane-1,2-diol (EXP)

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)

aristolochic acid A (ISO)

arsane (ISO)

arsenic atom (ISO)

arsenite(3-) (ISO)

arsenous acid (ISO)

benzatropine (ISO)

benzo[a]pyrene (ISO)

bisphenol A (EXP,ISO)

bucladesine (ISO)

cadmium dichloride (EXP)

caffeine (ISO)

calcitriol (ISO)

cannabidiol (ISO)

carbon nanotube (ISO)

cisplatin (ISO)

clozapine (ISO)

copper(II) sulfate (ISO)

coumarin (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)

gentamycin (EXP)

ivermectin (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)

temozolomide (ISO)

tetrachloromethane (ISO)

thapsigargin (EXP)

thioacetamide (EXP)

trichostatin A (ISO)

triptonide (ISO)

uranium atom (ISO)

urethane (ISO)

valproic acid (ISO)

vincristine (ISO)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

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

negative regulation of receptor internalization (ISO,ISS)

negative regulation of transcription by RNA polymerase II (ISO)

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)

proteolysis (IEA)

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 (IEA)

membrane raft (ISO,ISS)

mitochondrion (IDA)

nuclear membrane (IEA,ISO)

nucleoplasm (IEA,ISO)

plasma membrane (IBA,ISO,ISS)

postsynaptic density (IDA)

presynapse (IDA,IEP)

synapse (IDA)

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)

ionotropic glutamate receptor binding (IPI)

metalloendopeptidase activity (IEA)

neurexin family protein binding (IPI,NAS)

obsolete protein N-terminus binding (ISO)

phosphatidylinositol-4,5-bisphosphate binding (ISO)

protein binding (IPI,ISO)

protein heterodimerization activity (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

#	Reference Title	Reference Citation
1.	Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium.	Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
2.	Cytokine-specific transcriptional regulation through an IL-5Ralpha interacting protein.	Geijsen N, etal., Science. 2001 Aug 10;293(5532):1136-8.
3.	Rat ISS GO annotations from GOA human gene data--August 2006	GOA data from the GO Consortium
4.	Rapid and differential regulation of AMPA and kainate receptors at hippocampal mossy fibre synapses by PICK1 and GRIP.	Hirbec H, etal., Neuron. 2003 Feb 20;37(4):625-38. doi: 10.1016/s0896-6273(02)01191-1.
5.	The neural cell recognition molecule neurofascin interacts with syntenin-1 but not with syntenin-2, both of which reveal self-associating activity.	Koroll M, etal., J Biol Chem 2001 Apr 6;276(14):10646-54.
6.	Ephrin-B1 and ephrin-B2 mediate EphB-dependent presynaptic development via syntenin-1.	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.
7.	Rat ISS GO annotations from MGI mouse gene data--August 2006	MGD data from the GO Consortium
8.	Electronic Transfer of LocusLink and RefSeq Data	NCBI rat LocusLink and RefSeq merged data July 26, 2002
9.	The neuronal glycine transporter 2 interacts with the PDZ domain protein syntenin-1.	Ohno K, etal., Mol Cell Neurosci. 2004 Aug;26(4):518-29. doi: 10.1016/j.mcn.2004.04.007.
10.	PID Annotation Import Pipeline	Pipeline to import Pathway Interaction Database annotations from NCI into RGD
11.	GOA pipeline	RGD automated data pipeline
12.	Data Import for Chemical-Gene Interactions	RGD automated import pipeline for gene-chemical interactions
13.	Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences.	Strausberg RL, etal., Proc Natl Acad Sci U S A. 2002 Dec 24;99(26):16899-903. Epub 2002 Dec 11.
14.	Characterization of syntenin, a syndecan-binding PDZ protein, as a component of cell adhesion sites and microfilaments.	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: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	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	5	19,489,961 - 19,527,572 (+)	Ensembl		mRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx	5	21,697,118 - 21,724,119 (+)	NCBI	Rnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.0	5	23,288,429 - 23,315,152 (+)	NCBI	Rnor_SHRSP
UTH_Rnor_WKY_Bbb_1.0	5	23,068,735 - 23,095,458 (+)	NCBI	Rnor_WKY
Rnor_6.0	5	19,471,664 - 19,498,499 (+)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	5	19,471,664 - 19,498,485 (+)	Ensembl	Rnor6.0		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	RGSC_v3.4	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	8	58,553,261 - 58,582,858 (+)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh38.p13 Ensembl	8	58,552,924 - 58,582,859 (+)	Ensembl	GRCh38		hg38	GRCh38
GRCh37	8	59,465,820 - 59,495,417 (+)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	8	59,628,282 - 59,657,973 (+)	NCBI	NCBI36	Build 36	hg18	NCBI36
Build 34	8	59,628,281 - 59,657,972	NCBI
Celera	8	55,458,752 - 55,488,443 (+)	NCBI		Celera
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
T2T-CHM13v2.0	8	58,974,408 - 59,004,011 (+)	NCBI		T2T-CHM13v2.0

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	GRCm39	mm39
GRCm39 Ensembl	4	6,365,650 - 6,408,423 (+)	Ensembl		GRCm39 Ensembl
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	MGSCv37	mm9	NCBIm37
MGSCv36	4	6,292,868 - 6,322,797 (+)	NCBI		MGSCv36	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	Mhudiblu_PPA_v0	panPan3

SDCBP
(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
Dog10K_Boxer_Tasha	29	9,644,617 - 9,683,238 (+)	NCBI		Dog10K_Boxer_Tasha
ROS_Cfam_1.0	29	9,417,267 - 9,455,907 (+)	NCBI		ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl	29	9,417,305 - 9,455,885 (+)	Ensembl		ROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1	29	9,415,389 - 9,453,988 (+)	NCBI		UMICH_Zoey_3.1
UNSW_CanFamBas_1.0	29	9,541,083 - 9,579,672 (+)	NCBI		UNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0	29	9,820,349 - 9,859,247 (+)	NCBI		UU_Cfam_GSD_1.0

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
HiC_Itri_2	NW_024405303	60,438,300 - 60,453,495 (+)	NCBI		HiC_Itri_2
SpeTri2.0 Ensembl	NW_004936496	14,331,662 - 14,347,197 (-)	Ensembl	SpeTri2.0
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

SDCBP
(Chlorocebus sabaeus - green monkey)

Green Monkey Assembly	Chr	Position (strand)	Source	Genome Browsers
Green Monkey Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
ChlSab1.1	8	54,536,286 - 54,565,884 (+)	NCBI	ChlSab1.1	ChlSab1.1	chlSab2
Vero_WHO_p1.0	NW_023666039	87,157,660 - 87,187,388 (-)	NCBI	Vero_WHO_p1.0	Vero_WHO_p1.0

Sdcbp
(Heterocephalus glaber - naked mole-rat)

Naked Mole-rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Naked Mole-rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
HetGla_female_1.0 Ensembl	NW_004624744	33,524,416 - 33,557,025 (-)	Ensembl	HetGla_female_1.0	HetGla_female_1.0 Ensembl	hetGla2
HetGla 1.0	NW_004624744	33,524,045 - 33,558,963 (-)	NCBI	HetGla_female_1.0	HetGla 1.0	hetGla2

Variants

Variants in Sdcbp
164 total Variants

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.

QTLs in Region (mRatBN7.2)

The following QTLs overlap with this region.

RGD ID	Symbol	Name	LOD	P Value	Trait	Sub Trait	Chr	Start	Stop	Species
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	90450412	Rat
70212	Niddm25	Non-insulin dependent diabetes mellitus QTL 25	3.54		blood glucose amount (VT:0000188)	blood glucose level (CMO:0000046)	5	1	131345958	Rat
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	729470	86724018	Rat
2312562	Pur18	Proteinuria QTL 18	2.6	0.001	urine total protein amount (VT:0000032)	urine total protein excretion rate (CMO:0000756)	5	2138965	32656739	Rat
1576314	Eutr1	Estrogen induced uterine response QTL 1			uterus integrity trait (VT:0010575)	pyometritis severity score (CMO:0002009)	5	2138965	166875058	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	2282226	69540447	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	3844018	26141981	Rat
1300117	Hrtrt8	Heart rate QTL 8	3.49		heart pumping trait (VT:2000009)	heart rate (CMO:0000002)	5	3844018	47869213	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	5112159	47171491	Rat
2293666	Bmd38	Bone mineral density QTL 38	4.4		femur size trait (VT:1000369)	femoral neck cortical cross-sectional area (CMO:0001702)	5	8948228	53948228	Rat
7394712	Emca13	Estrogen-induced mammary cancer QTL 13			mammary gland integrity trait (VT:0010552)	mammary tumor number (CMO:0000343)	5	9823266	99753708	Rat
1641903	Alcrsp3	Alcohol response QTL 3			response to alcohol trait (VT:0010489)	duration of loss of righting reflex (CMO:0002289)	5	12689285	57689285	Rat
634305	Mamtr1	Mammary tumor resistance QTL 1		0.0001	mammary gland integrity trait (VT:0010552)	mammary tumor number (CMO:0000343)	5	12789751	113558310	Rat
1600358	Mamtr5	Mammary tumor resistance QTL 5			mammary gland integrity trait (VT:0010552)	mammary tumor number (CMO:0000343)	5	18873947	63873947	Rat
1358353	Srcrtb2	Stress Responsive Cort Basal QTL 2	3.48	0.003	blood corticosterone amount (VT:0005345)	plasma corticosterone level (CMO:0001173)	5	18873947	74251464	Rat

Markers in Region

RH129294

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	5	19,516,940 - 19,517,131 (+)	MAPPER	mRatBN7.2
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

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
mRatBN7.2 Ensembl	5	19,489,967 - 19,517,187 (+)	Ensembl
Rnor_6.0 Ensembl	5	19,471,664 - 19,498,485 (+)	Ensembl

RefSeq Acc Id:

ENSRNOT00000098340 ⟹ ENSRNOP00000079793

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2 Ensembl	5	19,503,468 - 19,517,872 (+)	Ensembl

RefSeq Acc Id:

ENSRNOT00000110124 ⟹ ENSRNOP00000084825

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2 Ensembl	5	19,489,970 - 19,527,572 (+)	Ensembl

RefSeq Acc Id:

ENSRNOT00000115856 ⟹ ENSRNOP00000081603

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2 Ensembl	5	19,489,961 - 19,517,175 (+)	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
- UniProtKB:	Q9JI92 (UniProtKB/Swiss-Prot)

RefSeq Acc Id:	XP_038966785 ⟸ XM_039110857
- Peptide Label:	isoform X1
- UniProtKB:	Q9JI92 (UniProtKB/Swiss-Prot)

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

RefSeq Acc Id:	XP_038966783 ⟸ XM_039110855
- Peptide Label:	isoform X1
- UniProtKB:	Q9JI92 (UniProtKB/Swiss-Prot)

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

RefSeq Acc Id:	XP_038966786 ⟸ XM_039110858
- Peptide Label:	isoform X1
- UniProtKB:	Q9JI92 (UniProtKB/Swiss-Prot)

RefSeq Acc Id:	XP_038966788 ⟸ XM_039110860
- Peptide Label:	isoform X1
- UniProtKB:	Q9JI92 (UniProtKB/Swiss-Prot)

RefSeq Acc Id:	XP_038966789 ⟸ XM_039110861
- Peptide Label:	isoform X1
- UniProtKB:	Q9JI92 (UniProtKB/Swiss-Prot)

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

RefSeq Acc Id:	XP_038966787 ⟸ XM_039110859
- Peptide Label:	isoform X1
- UniProtKB:	Q9JI92 (UniProtKB/Swiss-Prot)

RefSeq Acc Id:

ENSRNOP00000079793 ⟸ ENSRNOT00000098340

RefSeq Acc Id:

ENSRNOP00000084825 ⟸ ENSRNOT00000110124

RefSeq Acc Id:

ENSRNOP00000081603 ⟸ ENSRNOT00000115856

Protein Domains

PDZ

Protein Structures

Name	Modeler	Protein Id	AA Range	Protein Structure
AF-Q9JI92-F1-model_v2	AlphaFold	Q9JI92	1-300	view protein structure

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

Additional Information

External Database Links

Database	Acc Id	Source(s)
AGR Gene	RGD:621497	AgrOrtholog
BioCyc Gene	G2FUF-42071	BioCyc
Ensembl Genes	ENSRNOG00000009683	Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Ensembl Protein	ENSRNOP00000013563.5	UniProtKB/TrEMBL
	ENSRNOP00000079793	ENTREZGENE
	ENSRNOP00000079793.1	UniProtKB/TrEMBL
	ENSRNOP00000081603	ENTREZGENE, UniProtKB/Swiss-Prot
	ENSRNOP00000084825.1	UniProtKB/TrEMBL
Ensembl Transcript	ENSRNOT00000013563.8	UniProtKB/TrEMBL
	ENSRNOT00000098340	ENTREZGENE
	ENSRNOT00000098340.1	UniProtKB/TrEMBL
	ENSRNOT00000110124.1	UniProtKB/TrEMBL
	ENSRNOT00000115856	ENTREZGENE, UniProtKB/Swiss-Prot
Gene3D-CATH	2.30.42.10	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
IMAGE_CLONE	IMAGE:5598152	IMAGE-MGC_LOAD
InterPro	PDZ	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	PDZ_sf	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	Peptidase_M50	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	SDCBP	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report	rno:83841	UniProtKB/Swiss-Prot
MGC_CLONE	MGC:72376	IMAGE-MGC_LOAD
NCBI Gene	83841	ENTREZGENE
PANTHER	PTHR12345:SF10	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam	PDZ	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	Peptidase_M50	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen	Sdcbp	PhenoGen
PROSITE	PDZ	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
SMART	PDZ	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP	SSF50156	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt	A0A8I6A1Z6_RAT	UniProtKB/TrEMBL
	A0A8I6G5R4_RAT	UniProtKB/TrEMBL
	A0A8L2Q6V7_RAT	UniProtKB/TrEMBL
	Q9JI92	ENTREZGENE, UniProtKB/Swiss-Prot

Nomenclature History

Date	Current Symbol	Current Name	Previous Symbol	Previous Name	Description	Reference	Status
2021-03-09	Sdcbp	syndecan binding protein	LOC108350925	uncharacterized LOC108350925	Data Merged	737654	PROVISIONAL
2016-08-02	LOC108350925	uncharacterized LOC108350925			Symbol and Name status set to provisional	70820	PROVISIONAL
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)

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Imported Disease Annotations - CTD

Imported Annotations - PID (archival)