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: 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 ...
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2519,473,499 - 19,517,188 (+)NCBI
Rnor_6.0 Ensembl519,471,664 - 19,498,485 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0519,471,664 - 19,498,499 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0524,256,110 - 24,283,037 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4519,822,440 - 19,849,223 (+)NCBIRGSC3.4rn4RGSC3.4
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
Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Pathway Annotations     Click to see Annotation Detail View
References

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 AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2519,473,499 - 19,517,188 (+)NCBI
Rnor_6.0 Ensembl519,471,664 - 19,498,485 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0519,471,664 - 19,498,499 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0524,256,110 - 24,283,037 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4519,822,440 - 19,849,223 (+)NCBIRGSC3.4rn4RGSC3.4
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
GRCh38.p13 Ensembl858,552,924 - 58,582,859 (+)EnsemblGRCh38hg38GRCh38
GRCh38858,553,261 - 58,582,860 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh37859,465,820 - 59,495,417 (+)NCBIGRCh37GRCh37hg19GRCh37
GRCh37859,465,566 - 59,495,419 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36859,628,282 - 59,657,973 (+)NCBINCBI36hg18NCBI36
Build 34859,628,281 - 59,657,972NCBI
Celera855,458,752 - 55,488,443 (+)NCBI
Cytogenetic Map8q12.1NCBI
HuRef854,952,903 - 54,982,593 (+)NCBIHuRef
CHM1_1859,517,611 - 59,547,302 (+)NCBICHM1_1
Sdcbp
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm3946,365,654 - 6,396,122 (+)NCBIGRCm39mm39
GRCm3846,365,680 - 6,396,122 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl46,365,650 - 6,408,423 (+)EnsemblGRCm38mm10GRCm38
MGSCv3746,292,827 - 6,323,269 (+)NCBIGRCm37mm9NCBIm37
MGSCv3646,292,868 - 6,322,797 (+)NCBImm8
Celera46,283,969 - 6,314,409 (+)NCBICelera
Cytogenetic Map4A1NCBI
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
PanPan1.1856,643,962 - 56,673,834 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl856,643,962 - 56,673,833 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0854,992,627 - 55,022,560 (+)NCBIMhudiblu_PPA_v0panPan3
LOC482977
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1299,331,876 - 9,370,489 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Sdcbp
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
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
LOC103236850
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1854,536,286 - 54,565,884 (+)NCBI
Sdcbp
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462474433,524,045 - 33,558,963 (-)NCBI

Position Markers
RH129294  
Rat AssemblyChrPosition (strand)SourceJBrowse
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


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1331771Rf35Renal function QTL 354.36965kidney blood vessel physiology trait (VT:0100012)absolute change in renal blood flow rate (CMO:0001168)5189432042Rat
1331756Rf34Renal function QTL 344.16275kidney blood vessel physiology trait (VT:0100012)absolute change in renal blood flow rate (CMO:0001168)5193273395Rat
70212Niddm25Non-insulin dependent diabetes mellitus QTL 253.54blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)51136640934Rat
2312562Pur18Proteinuria QTL 182.60.001total urine protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)5152509833001026Rat
1576314Eutr1Estrogen induced uterine response QTL 1uterus integrity trait (VT:0010575)pyometritis severity score (CMO:0002009)5152509878720537Rat
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)5166658771552720Rat
2313085Bss59Bone structure and strength QTL 592.90.0001long bone metaphysis morphology trait (VT:0000133)tibia midshaft total cross-sectional area (CMO:0001715)5325132926252076Rat
1300117Hrtrt8Heart rate QTL 83.49heart pumping trait (VT:2000009)heart rate (CMO:0000002)5325132948722188Rat
61462Niddm10Non-insulin dependent diabetes mellitus QTL 103.90.001blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)5452573847978104Rat
2293666Bmd38Bone mineral density QTL 384.4femur size trait (VT:1000369)femoral neck cortical cross-sectional area (CMO:0001702)5863228553632285Rat
7394712Emca13Estrogen-induced mammary cancer QTL 13mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)59514842103580403Rat
634305Mamtr1Mammary tumor resistance QTL 10.0001mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)512651967117554267Rat
1641903Alcrsp3Alcohol response QTL 3response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)51328888858288888Rat
1600358Mamtr5Mammary tumor resistance QTL 5mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)51884791363847913Rat
1358353Srcrtb2Stress Responsive Cort Basal QTL 23.480.003blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)51884791376608178Rat

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

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 AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl519,471,664 - 19,498,485 (+)Ensembl
RefSeq Acc Id: NM_031986   ⟹   NP_114192
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
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
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2519,489,960 - 19,517,188 (+)NCBI
RefSeq Acc Id: XM_039110856   ⟹   XP_038966784
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2519,473,499 - 19,517,188 (+)NCBI
RefSeq Acc Id: XM_039110857   ⟹   XP_038966785
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2519,473,640 - 19,517,188 (+)NCBI
RefSeq Acc Id: XM_039110858   ⟹   XP_038966786
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2519,489,970 - 19,517,188 (+)NCBI
RefSeq Acc Id: XM_039110859   ⟹   XP_038966787
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2519,493,819 - 19,517,188 (+)NCBI
RefSeq Acc Id: XM_039110860   ⟹   XP_038966788
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2519,490,182 - 19,517,188 (+)NCBI
RefSeq Acc Id: XM_039110861   ⟹   XP_038966789
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2519,490,386 - 19,517,188 (+)NCBI
RefSeq Acc Id: XM_039110862   ⟹   XP_038966790
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2519,489,906 - 19,517,188 (+)NCBI
RefSeq Acc Id: XM_039110863   ⟹   XP_038966791
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2519,489,960 - 19,517,188 (+)NCBI
RefSeq Acc Id: XM_039110864   ⟹   XP_038966792
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2519,493,808 - 19,517,188 (+)NCBI
Reference Sequences
RefSeq Acc Id: NP_114192   ⟸   NM_031986
- UniProtKB: Q9JI92 (UniProtKB/Swiss-Prot)
- 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 AssemblyChrPosition (strand)Source
Rnor_6.0519,471,652 - 19,471,712EPDNEW

Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
ACI/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
ACI/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BBDP/Wor (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
BN/SsN (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
Buf/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
COP/CrCrl (MCW & UW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
University of Wisconsin (Dr. James Shull)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Charles River Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)
F344/NCrl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
F344/NRrrc (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
FHH/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHH/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FHL/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHL/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
GH/OmrMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
GK/Ox (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LE/Stm (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/Crl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/NCrlBR (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LH/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LL/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LN/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
M520/N (MCW)
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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

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