Shcbp1 (SHC binding and spindle associated 1) - Rat Genome Database

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Gene: Shcbp1 (SHC binding and spindle associated 1) Rattus norvegicus
Analyze
Symbol: Shcbp1
Name: SHC binding and spindle associated 1
RGD ID: 1590844
Description: Predicted to enable SH2 domain binding activity. Predicted to be involved in fibroblast growth factor receptor signaling pathway and regulation of neural precursor cell proliferation. Predicted to be located in cytoplasm and spindle. Orthologous to human SHCBP1 (SHC binding and spindle associated 1); INTERACTS WITH 1-naphthyl isothiocyanate; 17beta-estradiol; 17beta-estradiol 3-benzoate.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: LOC364648; SHC SH2 domain-binding protein 1; Shc SH2-domain binding protein 1; similar to Shc SH2-domain binding protein 1
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21684,672,276 - 84,703,839 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1684,672,321 - 84,703,844 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1689,951,043 - 89,989,091 (+)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.01693,403,611 - 93,441,659 (+)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.01688,677,422 - 88,715,471 (+)NCBIRnor_WKY
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 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
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  (EXP,ISO)
17beta-estradiol 3-benzoate  (EXP)
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)
all-trans-retinoic acid  (ISO)
antimycin A  (ISO)
aristolochic acid A  (ISO)
arsenite(3-)  (ISO)
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)
CGP 52608  (ISO)
chloropicrin  (ISO)
choline  (ISO)
cisplatin  (ISO)
cobalt dichloride  (ISO)
copper atom  (ISO)
copper(0)  (ISO)
copper(II) sulfate  (ISO)
coumestrol  (ISO)
Cuprizon  (EXP)
cyclosporin A  (ISO)
DDT  (ISO)
deoxynivalenol  (ISO)
dexamethasone  (ISO)
dibenz[a,h]anthracene  (ISO)
dioxygen  (EXP,ISO)
Enterolactone  (ISO)
erythromycin estolate  (EXP)
fenpyroximate  (ISO)
folic acid  (ISO)
furan  (EXP)
hydrogen peroxide  (ISO)
indometacin  (ISO)
ivermectin  (ISO)
kojic acid  (ISO)
L-methionine  (ISO)
lidocaine  (EXP)
lucanthone  (ISO)
MeIQx  (ISO)
methamphetamine  (EXP,ISO)
methotrexate  (ISO)
methylparaben  (ISO)
N-nitrosodimethylamine  (EXP)
N-Nitrosopyrrolidine  (ISO)
ozone  (ISO)
paracetamol  (ISO)
PCB138  (ISO)
perfluorooctanoic acid  (ISO)
phenethyl isothiocyanate  (ISO)
phenobarbital  (ISO)
phytoestrogen  (ISO)
pirinixic acid  (ISO)
piroxicam  (ISO)
pregnenolone 16alpha-carbonitrile  (ISO)
progesterone  (ISO)
propanal  (ISO)
resveratrol  (ISO)
rotenone  (ISO)
silicon dioxide  (ISO)
sodium arsenite  (ISO)
sunitinib  (ISO)
tamoxifen  (ISO)
tebufenpyrad  (ISO)
testosterone  (EXP,ISO)
tetrachloromethane  (ISO)
thioacetamide  (EXP)
titanium dioxide  (EXP,ISO)
trichloroethene  (ISO)
trimellitic anhydride  (ISO)
trovafloxacin  (ISO)
valproic acid  (ISO)
zaragozic acid A  (EXP,ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component
cytoplasm  (IEA)
spindle  (IEA)

Molecular Function

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. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
3. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:10086341   PMID:22508726  


Genomics

Comparative Map Data
Shcbp1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21684,672,276 - 84,703,839 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1684,672,321 - 84,703,844 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1689,951,043 - 89,989,091 (+)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.01693,403,611 - 93,441,659 (+)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.01688,677,422 - 88,715,471 (+)NCBIRnor_WKY
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 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera1682,361,107 - 82,392,376 (+)NCBICelera
Cytogenetic Map16q12.5NCBI
SHCBP1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381646,578,591 - 46,621,379 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p13 Ensembl1646,578,591 - 46,621,379 (-)EnsemblGRCh38hg38GRCh38
GRCh371646,612,503 - 46,655,291 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361645,171,968 - 45,212,785 (-)NCBINCBI36Build 36hg18NCBI36
Build 341645,171,967 - 45,212,785NCBI
Celera1631,122,631 - 31,163,484 (-)NCBICelera
Cytogenetic Map16q11.2NCBI
HuRef1632,503,090 - 32,544,039 (-)NCBIHuRef
CHM1_11648,021,380 - 48,062,245 (-)NCBICHM1_1
T2T-CHM13v2.01652,375,421 - 52,418,229 (-)NCBIT2T-CHM13v2.0
Shcbp1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm3984,785,976 - 4,829,567 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl84,785,976 - 4,829,567 (-)EnsemblGRCm39 Ensembl
GRCm3884,735,976 - 4,779,567 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl84,735,976 - 4,779,567 (-)EnsemblGRCm38mm10GRCm38
MGSCv3784,735,980 - 4,779,534 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv3684,735,980 - 4,779,534 (-)NCBIMGSCv36mm8
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_v0Mhudiblu_PPA_v0panPan3
SHCBP1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1158,465,366 - 8,491,085 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl158,465,409 - 8,490,214 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha158,619,202 - 8,644,900 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0158,581,757 - 8,607,467 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl158,581,788 - 8,607,462 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1158,410,759 - 8,436,448 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0158,491,552 - 8,517,342 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0158,507,310 - 8,533,000 (+)NCBIUU_Cfam_GSD_1.0
LOC101957263
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024407213121,415,130 - 121,418,030 (+)NCBIHiC_Itri_2
SpeTri2.0NW_004936597440,126 - 442,842 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SHCBP1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl638,029,864 - 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 - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1532,438,918 - 32,480,410 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl532,438,361 - 32,480,284 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366604744,123,360 - 44,164,876 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Shcbp1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462491439,197 - 107,922 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Shcbp1
430 total Variants
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.


QTLs in Region (mRatBN7.2)
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)164239634584729064Rat
8694429Bw164Body weight QTL 16450.001body lean mass (VT:0010483)lean tissue morphological measurement (CMO:0002184)165272646484729064Rat
8694364Abfw7Abdominal fat weight QTL 712.220.001visceral adipose mass (VT:0010063)abdominal fat pad weight to body weight ratio (CMO:0000095)165272646484729064Rat
7411648Foco22Food consumption QTL 22150.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)165272646484729064Rat

Markers in Region
AI502109  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21684,702,353 - 84,702,555 (+)MAPPERmRatBN7.2
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
mRatBN7.21684,702,999 - 84,703,160 (+)MAPPERmRatBN7.2
Rnor_6.01690,641,840 - 90,642,000NCBIRnor6.0
Rnor_5.01690,027,030 - 90,027,190UniSTSRnor5.0
Celera1682,391,533 - 82,391,693UniSTS
RH 3.4 Map16794.8UniSTS
Cytogenetic Map16q12.5UniSTS


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
mRatBN7.2 Ensembl1684,672,321 - 84,703,844 (+)Ensembl
Rnor_6.0 Ensembl1690,613,870 - 90,641,420 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000094192   ⟹   ENSRNOP00000083446
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1684,672,321 - 84,703,844 (+)Ensembl
RefSeq Acc Id: XM_039095270   ⟹   XP_038951198
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21684,672,276 - 84,703,839 (+)NCBI
RefSeq Acc Id: XM_039095271   ⟹   XP_038951199
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21684,672,278 - 84,703,839 (+)NCBI
RefSeq Acc Id: XR_005495150
RefSeq Status:
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21684,672,277 - 84,699,547 (+)NCBI
Protein Sequences
Protein RefSeqs NP_001386144 (Get FASTA)   NCBI Sequence Viewer  
  XP_038951198 (Get FASTA)   NCBI Sequence Viewer  
  XP_038951199 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: ENSRNOP00000072261   ⟸   ENSRNOT00000079334
RefSeq Acc Id: XP_038951198   ⟸   XM_039095270
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038951199   ⟸   XM_039095271
- Peptide Label: isoform X2
- UniProtKB: A0A8I5ZZD8 (UniProtKB/TrEMBL)
RefSeq Acc Id: ENSRNOP00000083446   ⟸   ENSRNOT00000094192
Protein Domains
Beta_helix

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-A0A0G2K2J0-F1-model_v2 AlphaFold A0A0G2K2J0 1-661 view protein structure

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

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1590844 AgrOrtholog
BioCyc Gene G2FUF-10566 BioCyc
Ensembl Genes ENSRNOG00000053026 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000072261 ENTREZGENE
  ENSRNOP00000072261.2 UniProtKB/TrEMBL
  ENSRNOP00000083446 ENTREZGENE
  ENSRNOP00000083446.1 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000079334 ENTREZGENE
  ENSRNOT00000079334.2 UniProtKB/TrEMBL
  ENSRNOT00000094192 ENTREZGENE
  ENSRNOT00000094192.1 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
  SHCBP1-like UniProtKB/TrEMBL
NCBI Gene 364648 ENTREZGENE
PANTHER PTHR14695 UniProtKB/TrEMBL
Pfam Beta_helix UniProtKB/TrEMBL
PhenoGen Shcbp1 PhenoGen
SMART PbH1 UniProtKB/TrEMBL
Superfamily-SCOP Pectin_lyas_like UniProtKB/TrEMBL
UniProt A0A0G2K2J0 ENTREZGENE, UniProtKB/TrEMBL
  A0A8I5ZZD8 ENTREZGENE, 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