Shcbp1 (SHC binding and spindle associated 1) - Rat Genome Database
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Gene: Shcbp1 (SHC binding and spindle associated 1) Rattus norvegicus
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Symbol: Shcbp1
Name: SHC binding and spindle associated 1
RGD ID: 1590844
Description: Predicted to have SH2 domain binding activity. Predicted to be involved in fibroblast growth factor receptor signaling pathway and regulation of neural precursor cell proliferation. Orthologous to human SHCBP1 (SHC binding and spindle associated 1); INTERACTS WITH 1-naphthyl isothiocyanate; 2,3,7,8-tetrachlorodibenzodioxine; 2-amino-2-deoxy-D-glucopyranose.
Type: protein-coding
RefSeq Status: MODEL
Also known as: LOC364648; SHC SH2 domain-binding protein 1; Shc SH2-domain binding protein 1; similar to Shc SH2-domain binding protein 1
Orthologs:
Homo sapiens (human) : SHCBP1 (SHC binding and spindle associated 1)  HGNC  Alliance
Mus musculus (house mouse) : Shcbp1 (Shc SH2-domain binding protein 1)  MGI  Alliance
Chinchilla lanigera (long-tailed chinchilla) : Shcbp1 (SHC binding and spindle associated 1)
Pan paniscus (bonobo/pygmy chimpanzee) : SHCBP1 (SHC binding and spindle associated 1)
Canis lupus familiaris (dog) : SHCBP1 (SHC binding and spindle associated 1)
Ictidomys tridecemlineatus (thirteen-lined ground squirrel) : Shcbp1 (SHC binding and spindle associated 1)
Sus scrofa (pig) : SHCBP1 (SHC binding and spindle associated 1)
Chlorocebus sabaeus (African green monkey) : SHCBP1 (SHC binding and spindle associated 1)
Heterocephalus glaber (naked mole-rat) : Shcbp1 (SHC binding and spindle associated 1)
more info ...
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rnor_6.01690,613,826 - 90,642,683 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1690,613,870 - 90,641,420 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01689,996,147 - 90,027,873 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41690,002,645 - 90,022,167 (-)NCBIRGSC3.4rn4RGSC3.4
Celera1682,361,107 - 82,392,376 (+)NCBICelera
Cytogenetic Map16q12.5NCBI
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
1,1-dichloroethene  (ISO)
1,2-dimethylhydrazine  (ISO)
1-naphthyl isothiocyanate  (EXP)
17alpha-ethynylestradiol  (ISO)
17beta-estradiol  (ISO)
2,2',4,4',5,5'-hexachlorobiphenyl  (ISO)
2,2',5,5'-tetrachlorobiphenyl  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,4-diaminotoluene  (ISO)
2-amino-2-deoxy-D-glucopyranose  (EXP)
3-isobutyl-1-methyl-7H-xanthine  (ISO)
3-methylcholanthrene  (ISO)
4,4'-diaminodiphenylmethane  (EXP,ISO)
6-propyl-2-thiouracil  (EXP)
aflatoxin B1  (ISO)
aldehydo-D-glucosamine  (EXP)
azathioprine  (ISO)
benzo[a]pyrene  (ISO)
benzo[a]pyrene diol epoxide I  (ISO)
benzo[b]fluoranthene  (ISO)
beta-D-glucosamine  (EXP)
bisphenol A  (EXP,ISO)
cadmium dichloride  (EXP)
calcitriol  (ISO)
carbon nanotube  (ISO)
chloropicrin  (ISO)
choline  (ISO)
cisplatin  (ISO)
cobalt dichloride  (ISO)
copper atom  (ISO)
copper(0)  (ISO)
copper(II) sulfate  (ISO)
coumestrol  (ISO)
cyclosporin A  (ISO)
DDT  (ISO)
deoxynivalenol  (ISO)
dexamethasone  (ISO)
dibenz[a,h]anthracene  (ISO)
dioxygen  (ISO)
Enterolactone  (ISO)
erythromycin estolate  (EXP)
folic acid  (ISO)
furan  (EXP)
hydrogen peroxide  (ISO)
indometacin  (ISO)
kojic acid  (ISO)
L-methionine  (ISO)
lucanthone  (ISO)
MeIQx  (ISO)
methamphetamine  (EXP,ISO)
methotrexate  (ISO)
methylparaben  (ISO)
N-nitrosodimethylamine  (EXP)
N-Nitrosopyrrolidine  (ISO)
ozone  (ISO)
paracetamol  (ISO)
phenethyl isothiocyanate  (ISO)
phenobarbital  (ISO)
phytoestrogen  (ISO)
pirinixic acid  (ISO)
piroxicam  (ISO)
pregnenolone 16alpha-carbonitrile  (ISO)
progesterone  (ISO)
propanal  (ISO)
resveratrol  (ISO)
silicon dioxide  (ISO)
sodium arsenite  (ISO)
sunitinib  (ISO)
tamoxifen  (ISO)
testosterone  (ISO)
tetrachloromethane  (ISO)
thioacetamide  (EXP)
titanium dioxide  (EXP,ISO)
trichloroethene  (ISO)
trimellitic anhydride  (ISO)
valproic acid  (ISO)
zaragozic acid A  (EXP,ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Molecular Function

References

Additional References at PubMed
PMID:10086341   PMID:22508726  


Genomics

Comparative Map Data
Shcbp1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rnor_6.01690,613,826 - 90,642,683 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1690,613,870 - 90,641,420 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01689,996,147 - 90,027,873 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41690,002,645 - 90,022,167 (-)NCBIRGSC3.4rn4RGSC3.4
Celera1682,361,107 - 82,392,376 (+)NCBICelera
Cytogenetic Map16q12.5NCBI
SHCBP1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1646,578,591 - 46,621,379 (-)EnsemblGRCh38hg38GRCh38
GRCh381646,578,591 - 46,621,379 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh371646,614,466 - 46,655,311 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361645,171,968 - 45,212,785 (-)NCBINCBI36hg18NCBI36
Build 341645,171,967 - 45,212,785NCBI
Celera1631,122,631 - 31,163,484 (-)NCBI
Cytogenetic Map16q11.2NCBI
HuRef1632,503,090 - 32,544,039 (-)NCBIHuRef
CHM1_11648,019,417 - 48,062,248 (-)NCBICHM1_1
Shcbp1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm3984,785,976 - 4,829,567 (-)NCBI
GRCm3884,735,976 - 4,779,567 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl84,735,976 - 4,779,567 (-)EnsemblGRCm38mm10GRCm38
MGSCv3784,735,980 - 4,779,534 (-)NCBIGRCm37mm9NCBIm37
MGSCv3684,735,980 - 4,779,534 (-)NCBImm8
Celera84,929,794 - 4,973,513 (-)NCBICelera
Cytogenetic Map8A1.1NCBI
Shcbp1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495544872,191 - 141,588 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495544874,969 - 141,627 (-)NCBIChiLan1.0ChiLan1.0
SHCBP1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11645,741,706 - 45,783,226 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1645,741,101 - 45,783,632 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01626,847,164 - 26,890,762 (-)NCBIMhudiblu_PPA_v0panPan3
SHCBP1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1 Ensembl158,465,409 - 8,490,214 (+)EnsemblCanFam3.1canFam3CanFam3.1
CanFam3.1158,465,366 - 8,491,085 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Shcbp1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
SpeTri2.0NW_004936597440,126 - 442,842 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SHCBP1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl638,029,572 - 38,063,859 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1638,029,869 - 38,063,773 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2633,218,790 - 33,224,681 (+)NCBISscrofa10.2Sscrofa10.2susScr3
SHCBP1
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1 Ensembl532,438,361 - 32,480,284 (-)Ensembl
ChlSab1.1532,438,918 - 32,480,410 (-)NCBI
Shcbp1
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462491439,197 - 107,922 (-)NCBI

Position Markers
AI502109  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01690,641,194 - 90,641,395NCBIRnor6.0
Rnor_5.01690,026,384 - 90,026,585UniSTSRnor5.0
Celera1682,390,886 - 82,391,087UniSTS
Cytogenetic Map16q12.5UniSTS
AW534701  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01690,641,840 - 90,642,000NCBIRnor6.0
Rnor_5.01690,027,030 - 90,027,190UniSTSRnor5.0
Celera1682,391,533 - 82,391,693UniSTS
Cytogenetic Map16q12.5UniSTS
RH 3.4 Map16794.8UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
7205510Activ5Activity QTL 53.780.00028locomotor behavior trait (VT:0001392)number of entries into a discrete space in an experimental apparatus (CMO:0000960)164655818890668790Rat
7411648Foco22Food consumption QTL 22150.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)165781635790668790Rat
8694429Bw164Body weight QTL 16450.001body lean mass (VT:0010483)lean tissue morphological measurement (CMO:0002184)165781635790668790Rat
8694364Abfw7Abdominal fat weight QTL 712.220.001visceral adipose mass (VT:0010063)abdominal fat pad weight to body weight ratio (CMO:0000095)165781635790668790Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:79
Count of miRNA genes:65
Interacting mature miRNAs:67
Transcripts:ENSRNOT00000071993
Prediction methods:Microtar, Miranda, Rnahybrid
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 2 26 26 20 14 20 30 18 35
Low 1 12 24 15 5 15 4 4 44 12 6 11 4
Below cutoff 5 7 6 6 4 7 5 4

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000079334   ⟹   ENSRNOP00000072261
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1690,613,870 - 90,641,420 (+)Ensembl
RefSeq Acc Id: XM_008773569   ⟹   XP_008771791
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Celera1682,361,107 - 82,392,376 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017600413   ⟹   XP_017455902
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01690,613,826 - 90,642,683 (+)NCBI
Sequence:
Protein Sequences
Protein RefSeqs XP_008771791 (Get FASTA)   NCBI Sequence Viewer  
  XP_017455902 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: XP_008771791   ⟸   XM_008773569
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: XP_017455902   ⟸   XM_017600413
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: ENSRNOP00000072261   ⟸   ENSRNOT00000079334
Protein Domains
Beta_helix

Transcriptome

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

Promoters
RGD ID:13700268
Promoter ID:EPDNEW_R10778
Type:multiple initiation site
Name:Shcbp1_1
Description:SHC binding and spindle associated 1
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_6.01690,613,846 - 90,613,906EPDNEW

Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
ACI/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
ACI/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BBDP/Wor (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
BN/SsN (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
Buf/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
COP/CrCrl (MCW & UW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
University of Wisconsin (Dr. James Shull)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Charles River Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)
F344/NCrl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
F344/NRrrc (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
FHH/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHH/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FHL/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHL/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
GH/OmrMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
GK/Ox (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LE/Stm (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/Crl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/NCrlBR (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LH/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LL/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LN/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
M520/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
MHS/Gib (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MNS/Gib (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MR/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
SBH/Ygl (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBH/Ygl sequenced by MCW
SBH/Ygl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SBN/Ygl (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBN/Ygl sequenced by MCW
SBN/Ygl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/NHsd (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHRSP/Gcrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SR/JrHsd (MCW)
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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: Rnor_6.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
16 90626141 90626142 T C snv WKY/N (MCW)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1590844 AgrOrtholog
Ensembl Genes ENSRNOG00000053026 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000072261 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000079334 ENTREZGENE, UniProtKB/TrEMBL
Gene3D-CATH 2.160.20.10 UniProtKB/TrEMBL
InterPro Beta_helix UniProtKB/TrEMBL
  PbH1 UniProtKB/TrEMBL
  Pectin_lyas_fold UniProtKB/TrEMBL
  Pectin_lyase_fold/virulence UniProtKB/TrEMBL
NCBI Gene 364648 ENTREZGENE
Pfam Beta_helix UniProtKB/TrEMBL
PhenoGen Shcbp1 PhenoGen
SMART PbH1 UniProtKB/TrEMBL
Superfamily-SCOP Pectin_lyas_like UniProtKB/TrEMBL
UniProt A0A0G2K2J0_RAT UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-04-27 Shcbp1  SHC binding and spindle associated 1  Shcbp1  Shc SH2-domain binding protein 1  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2013-05-24 Shcbp1  Shc SH2-domain binding protein 1  LOC687121  similar to Shc SH2-domain binding protein 1  Data Merged 1643240 APPROVED
2008-03-05 Shcbp1  Shc SH2-domain binding protein 1  LOC364648  similar to Shc SH2-domain binding protein 1  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-11-20 LOC364648  similar to Shc SH2-domain binding protein 1      Symbol and Name status set to provisional 70820 PROVISIONAL
2006-11-19 LOC687121  similar to Shc SH2-domain binding protein 1      Symbol and Name status set to provisional 70820 PROVISIONAL