Sdcbp (syndecan binding protein) - Rat Genome Database

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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. 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 Orthologs
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8524,245,279 - 24,314,712 (+)NCBIGRCr8
mRatBN7.2519,473,499 - 19,517,188 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl519,489,961 - 19,527,572 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx521,697,118 - 21,724,119 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0523,288,429 - 23,315,152 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0523,068,735 - 23,095,458 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0519,471,664 - 19,498,499 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl519,471,664 - 19,498,485 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0524,256,110 - 24,283,037 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4519,822,440 - 19,849,223 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.1519,822,439 - 19,849,220 (+)NCBI
Celera518,790,757 - 18,817,395 (+)NCBICelera
Cytogenetic Map5q12NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

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)
4,4'-sulfonyldiphenol  (ISO)
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)
beta-lapachone  (ISO)
bisphenol A  (EXP,ISO)
Bisphenol B  (ISO)
bisphenol F  (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)
DDE  (ISO)
dexamethasone  (ISO)
diarsenic trioxide  (ISO)
Dibutyl phosphate  (ISO)
dibutyl phthalate  (EXP)
dicrotophos  (ISO)
diuron  (ISO)
ethanol  (ISO)
ethyl methanesulfonate  (ISO)
flavonoids  (EXP)
flutamide  (EXP)
folic acid  (ISO)
formaldehyde  (ISO)
FR900359  (ISO)
gentamycin  (EXP)
ivermectin  (ISO)
medroxyprogesterone acetate  (ISO)
mercury dichloride  (EXP)
methyl methanesulfonate  (ISO)
mono(2-ethylhexyl) phthalate  (ISO)
N-nitrosodiethylamine  (EXP)
ozone  (ISO)
paracetamol  (ISO)
perfluorohexanesulfonic acid  (ISO)
phenobarbital  (ISO)
potassium dichromate  (ISO)
rac-lactic acid  (ISO)
sarin  (ISO)
SB 431542  (ISO)
silver atom  (ISO)
silver(0)  (ISO)
sodium arsenate  (ISO)
sulforaphane  (ISO)
sunitinib  (ISO)
tamoxifen  (ISO)
temozolomide  (ISO)
tetrachloromethane  (ISO)
thapsigargin  (EXP)
thioacetamide  (EXP)
titanium dioxide  (ISO)
trichostatin A  (ISO)
triphenyl phosphate  (ISO)
triptonide  (ISO)
uranium atom  (ISO)
urethane  (ISO)
valproic acid  (ISO)
vincristine  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Pathway Annotations     Click to see Annotation Detail View
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 AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8524,245,279 - 24,314,712 (+)NCBIGRCr8
mRatBN7.2519,473,499 - 19,517,188 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl519,489,961 - 19,527,572 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx521,697,118 - 21,724,119 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0523,288,429 - 23,315,152 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0523,068,735 - 23,095,458 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0519,471,664 - 19,498,499 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl519,471,664 - 19,498,485 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0524,256,110 - 24,283,037 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4519,822,440 - 19,849,223 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.1519,822,439 - 19,849,220 (+)NCBI
Celera518,790,757 - 18,817,395 (+)NCBICelera
Cytogenetic Map5q12NCBI
SDCBP
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38858,553,261 - 58,582,858 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl858,552,924 - 58,582,859 (+)EnsemblGRCh38hg38GRCh38
GRCh37859,465,820 - 59,495,417 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36859,628,282 - 59,657,973 (+)NCBINCBI36Build 36hg18NCBI36
Build 34859,628,281 - 59,657,972NCBI
Celera855,458,752 - 55,488,443 (+)NCBICelera
Cytogenetic Map8q12.1NCBI
HuRef854,952,903 - 54,982,593 (+)NCBIHuRef
CHM1_1859,517,611 - 59,547,302 (+)NCBICHM1_1
T2T-CHM13v2.0858,974,408 - 59,004,011 (+)NCBIT2T-CHM13v2.0
Sdcbp
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm3946,365,713 - 6,396,120 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl46,365,650 - 6,408,423 (+)EnsemblGRCm39 Ensembl
GRCm3846,365,680 - 6,396,122 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl46,365,650 - 6,408,423 (+)EnsemblGRCm38mm10GRCm38
MGSCv3746,292,827 - 6,323,269 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv3646,292,868 - 6,322,797 (+)NCBIMGSCv36mm8
Celera46,283,969 - 6,314,409 (+)NCBICelera
Cytogenetic Map4A1NCBI
cM Map42.91NCBI
Sdcbp
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495545417,089,232 - 17,113,484 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495545417,093,930 - 17,113,491 (+)NCBIChiLan1.0ChiLan1.0
SDCBP
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2774,231,999 - 74,264,164 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1849,885,857 - 49,918,036 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0854,992,627 - 55,022,560 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1856,643,962 - 56,673,834 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl856,643,962 - 56,673,833 (+)Ensemblpanpan1.1panPan2
SDCBP
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1299,331,876 - 9,370,489 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha299,644,617 - 9,683,238 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0299,417,267 - 9,455,907 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl299,417,305 - 9,455,885 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1299,415,389 - 9,453,988 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0299,541,083 - 9,579,672 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0299,820,349 - 9,859,247 (+)NCBIUU_Cfam_GSD_1.0
Sdcbp
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440530360,438,300 - 60,453,495 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_00493649614,331,662 - 14,347,197 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_00493649614,331,971 - 14,347,123 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SDCBP
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl474,295,922 - 74,341,085 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1474,295,941 - 74,357,720 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2481,090,105 - 81,122,727 (-)NCBISscrofa10.2Sscrofa10.2susScr3
SDCBP
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1854,536,286 - 54,565,884 (+)NCBIChlSab1.1ChlSab1.1chlSab2
Vero_WHO_p1.0NW_02366603987,157,660 - 87,187,388 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Sdcbp
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462474433,524,416 - 33,557,025 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462474433,524,045 - 33,558,963 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Sdcbp
190 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.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
2293666Bmd38Bone mineral density QTL 384.4femur size trait (VT:1000369)femoral neck cortical cross-sectional area (CMO:0001702)5894822853948228Rat
1576314Eutr1Estrogen induced uterine response QTL 1uterus integrity trait (VT:0010575)pyometritis severity score (CMO:0002009)52138965166875058Rat
70212Niddm25Non-insulin dependent diabetes mellitus QTL 253.54blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)51131345958Rat
1358353Srcrtb2Stress Responsive Cort Basal QTL 23.480.003blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)51887394774251464Rat
1300117Hrtrt8Heart rate QTL 83.49heart pumping trait (VT:2000009)heart rate (CMO:0000002)5384401847869213Rat
7394712Emca13Estrogen-induced mammary cancer QTL 13mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)5982326699753708Rat
634305Mamtr1Mammary tumor resistance QTL 10.0001mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)512789751113558310Rat
1331771Rf35Renal function QTL 354.36965kidney blood vessel physiology trait (VT:0100012)absolute change in renal blood flow rate (CMO:0001168)572947086724018Rat
2312562Pur18Proteinuria QTL 182.60.001urine total protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)5213896532656739Rat
8662454Vetf3Vascular elastic tissue fragility QTL 327.4artery integrity trait (VT:0010639)number of ruptures of the internal elastic lamina of the abdominal aorta and iliac arteries (CMO:0002562)5228222669540447Rat
61462Niddm10Non-insulin dependent diabetes mellitus QTL 103.90.001blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)5511215947171491Rat
1641903Alcrsp3Alcohol response QTL 3response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)51268928557689285Rat
1331756Rf34Renal function QTL 344.16275kidney blood vessel physiology trait (VT:0100012)absolute change in renal blood flow rate (CMO:0001168)5190450412Rat
2313085Bss59Bone structure and strength QTL 592.90.0001long bone metaphysis morphology trait (VT:0000133)tibia midshaft total cross-sectional area (CMO:0001715)5384401826141981Rat
1600358Mamtr5Mammary tumor resistance QTL 5mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)51887394763873947Rat

Markers in Region
RH129294  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2519,516,940 - 19,517,131 (+)MAPPERmRatBN7.2
Rnor_6.0519,498,257 - 19,498,447NCBIRnor6.0
Rnor_5.0524,282,795 - 24,282,985UniSTSRnor5.0
RGSC_v3.4519,848,981 - 19,849,171UniSTSRGSC3.4
Celera518,817,153 - 18,817,343UniSTS
Cytogenetic Map5q12UniSTS


Expression

RNA-SEQ Expression

alimentary part of gastrointestinal system
appendage
circulatory system
ectoderm
endocrine system
endoderm
exocrine system
hemolymphoid system
hepatobiliary system
integumental system
mesenchyme
mesoderm
nervous system
renal system
reproductive system
respiratory system
9 11 49 113 91 90 59 25 59 6 218 97 93 45 60 31

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_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
  XM_063288487 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_063288488 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_063288489 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_063288490 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_063288491 (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
  JAXUCZ010000005 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Ensembl Acc Id: ENSRNOT00000013563   ⟹   ENSRNOP00000013563
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl519,489,967 - 19,517,187 (+)Ensembl
Rnor_6.0 Ensembl519,471,664 - 19,498,485 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000098340   ⟹   ENSRNOP00000079793
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl519,503,468 - 19,517,872 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000110124   ⟹   ENSRNOP00000084825
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl519,489,970 - 19,527,572 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000115856   ⟹   ENSRNOP00000081603
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl519,489,961 - 19,517,175 (+)Ensembl
RefSeq Acc Id: NM_031986   ⟹   NP_114192
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8524,287,499 - 24,314,712 (+)NCBI
mRatBN7.2519,489,977 - 19,517,188 (+)NCBI
Rnor_6.0519,471,664 - 19,498,499 (+)NCBI
Rnor_5.0524,256,110 - 24,283,037 (+)NCBI
RGSC_v3.4519,822,440 - 19,849,223 (+)RGD
Celera518,790,757 - 18,817,395 (+)RGD
Sequence:
RefSeq Acc Id: XM_039110855   ⟹   XP_038966783
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8524,287,497 - 24,314,707 (+)NCBI
mRatBN7.2519,489,960 - 19,517,188 (+)NCBI
RefSeq Acc Id: XM_039110857   ⟹   XP_038966785
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8524,245,297 - 24,314,707 (+)NCBI
mRatBN7.2519,473,640 - 19,517,188 (+)NCBI
RefSeq Acc Id: XM_039110858   ⟹   XP_038966786
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8524,287,515 - 24,314,707 (+)NCBI
mRatBN7.2519,489,970 - 19,517,188 (+)NCBI
RefSeq Acc Id: XM_039110859   ⟹   XP_038966787
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8524,291,353 - 24,314,707 (+)NCBI
mRatBN7.2519,493,819 - 19,517,188 (+)NCBI
RefSeq Acc Id: XM_039110860   ⟹   XP_038966788
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8524,287,517 - 24,314,707 (+)NCBI
mRatBN7.2519,490,182 - 19,517,188 (+)NCBI
RefSeq Acc Id: XM_039110861   ⟹   XP_038966789
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8524,287,718 - 24,314,707 (+)NCBI
mRatBN7.2519,490,386 - 19,517,188 (+)NCBI
RefSeq Acc Id: XM_039110862   ⟹   XP_038966790
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8524,287,454 - 24,314,707 (+)NCBI
mRatBN7.2519,489,906 - 19,517,188 (+)NCBI
RefSeq Acc Id: XM_039110863   ⟹   XP_038966791
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8524,287,524 - 24,314,707 (+)NCBI
mRatBN7.2519,489,960 - 19,517,188 (+)NCBI
RefSeq Acc Id: XM_039110864   ⟹   XP_038966792
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8524,291,341 - 24,314,707 (+)NCBI
mRatBN7.2519,493,808 - 19,517,188 (+)NCBI
RefSeq Acc Id: XM_063288487   ⟹   XP_063144557
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8524,245,335 - 24,314,707 (+)NCBI
RefSeq Acc Id: XM_063288488   ⟹   XP_063144558
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8524,287,523 - 24,314,707 (+)NCBI
RefSeq Acc Id: XM_063288489   ⟹   XP_063144559
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8524,245,279 - 24,314,707 (+)NCBI
RefSeq Acc Id: XM_063288490   ⟹   XP_063144560
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8524,287,666 - 24,314,707 (+)NCBI
RefSeq Acc Id: XM_063288491   ⟹   XP_063144561
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8524,287,735 - 24,314,707 (+)NCBI
RefSeq Acc Id: NP_114192   ⟸   NM_031986
- UniProtKB: Q9JI92 (UniProtKB/Swiss-Prot),   A0A8L2Q6V7 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000013563   ⟸   ENSRNOT00000013563
RefSeq Acc Id: XP_038966785   ⟸   XM_039110857
- Peptide Label: isoform X1
- UniProtKB: Q9JI92 (UniProtKB/Swiss-Prot),   A0A8L2Q6V7 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038966790   ⟸   XM_039110862
- Peptide Label: isoform X2
- UniProtKB: A0A8L2Q6V7 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038966783   ⟸   XM_039110855
- Peptide Label: isoform X1
- UniProtKB: Q9JI92 (UniProtKB/Swiss-Prot),   A0A8L2Q6V7 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038966791   ⟸   XM_039110863
- Peptide Label: isoform X2
- UniProtKB: A0A8L2Q6V7 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038966786   ⟸   XM_039110858
- Peptide Label: isoform X1
- UniProtKB: Q9JI92 (UniProtKB/Swiss-Prot),   A0A8L2Q6V7 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038966788   ⟸   XM_039110860
- Peptide Label: isoform X1
- UniProtKB: Q9JI92 (UniProtKB/Swiss-Prot),   A0A8L2Q6V7 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038966789   ⟸   XM_039110861
- Peptide Label: isoform X1
- UniProtKB: Q9JI92 (UniProtKB/Swiss-Prot),   A0A8L2Q6V7 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038966792   ⟸   XM_039110864
- Peptide Label: isoform X2
- UniProtKB: A0A8L2Q6V7 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038966787   ⟸   XM_039110859
- Peptide Label: isoform X1
- UniProtKB: Q9JI92 (UniProtKB/Swiss-Prot),   A0A8L2Q6V7 (UniProtKB/TrEMBL)
Ensembl Acc Id: ENSRNOP00000079793   ⟸   ENSRNOT00000098340
Ensembl Acc Id: ENSRNOP00000084825   ⟸   ENSRNOT00000110124
Ensembl Acc Id: ENSRNOP00000081603   ⟸   ENSRNOT00000115856
RefSeq Acc Id: XP_063144559   ⟸   XM_063288489
- Peptide Label: isoform X2
RefSeq Acc Id: XP_063144557   ⟸   XM_063288487
- Peptide Label: isoform X1
- UniProtKB: Q9JI92 (UniProtKB/Swiss-Prot)
RefSeq Acc Id: XP_063144558   ⟸   XM_063288488
- Peptide Label: isoform X2
RefSeq Acc Id: XP_063144560   ⟸   XM_063288490
- Peptide Label: isoform X2
RefSeq Acc Id: XP_063144561   ⟸   XM_063288491
- Peptide Label: isoform X2
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 AssemblyChrPosition (strand)Source
Rnor_6.0519,471,652 - 19,471,712EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:621497 AgrOrtholog
BioCyc Gene G2FUF-42071 BioCyc
Ensembl Genes ENSRNOG00000009683 Ensembl, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000013563.8 UniProtKB/TrEMBL
  ENSRNOT00000098340.1 UniProtKB/TrEMBL
  ENSRNOT00000110124.1 UniProtKB/TrEMBL
  ENSRNOT00000115856.1 UniProtKB/Swiss-Prot
Gene3D-CATH 2.30.42.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:5598152 IMAGE-MGC_LOAD
InterPro APP-Binding UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PDZ UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PDZ_sf 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
  SYNTENIN RELATED UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam PDZ UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Sdcbp PhenoGen
PROSITE PDZ UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
RatGTEx ENSRNOG00000009683 RatGTEx
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 ENTREZGENE, UniProtKB/TrEMBL
  A6JFP0_RAT UniProtKB/TrEMBL
  A6JFP1_RAT UniProtKB/TrEMBL
  A6JFP2_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 from RGD:11372204 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