Itgb7 (integrin subunit beta 7) - Rat Genome Database

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Gene: Itgb7 (integrin subunit beta 7) Rattus norvegicus
Analyze
Symbol: Itgb7
Name: integrin subunit beta 7
RGD ID: 2929
Description: Predicted to enable integrin binding activity. Predicted to be involved in several processes, including integrin-mediated signaling pathway; leukocyte tethering or rolling; and substrate adhesion-dependent cell spreading. Predicted to act upstream of or within T cell migration. Predicted to be part of integrin alpha4-beta7 complex. Predicted to be active in cell surface and focal adhesion. Orthologous to human ITGB7 (integrin subunit beta 7); PARTICIPATES IN E-cadherin signaling pathway; integrin mediated signaling pathway; arrhythmogenic right ventricular cardiomyopathy pathway; INTERACTS WITH 17beta-estradiol; 17beta-estradiol 3-benzoate; 2,3,7,8-tetrachlorodibenzodioxine.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: integrin beta 7; integrin beta-7; integrin, beta 7
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
mRatBN7.27133,347,927 - 133,364,955 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl7133,347,960 - 133,364,876 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx7135,109,152 - 135,121,717 (-)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.07137,338,519 - 137,351,081 (-)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.07137,323,632 - 137,336,211 (-)NCBIRnor_WKY
Rnor_6.07143,820,236 - 143,837,802 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl7143,820,900 - 143,837,780 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.07141,617,387 - 141,634,902 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.47140,971,310 - 140,984,091 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.17141,047,752 - 141,057,691 (-)NCBI
Celera7129,781,783 - 129,794,228 (-)NCBICelera
RH 3.4 Map71054.0RGD
Cytogenetic Map7q36NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

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. High-density rat radiation hybrid maps containing over 24,000 SSLPs, genes, and ESTs provide a direct link to the rat genome sequence. Kwitek AE, etal., Genome Res. 2004 Apr;14(4):750-7
3. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
4. Electronic Transfer of LocusLink and RefSeq Data NCBI rat LocusLink and RefSeq merged data July 26, 2002
5. KEGG Annotation Import Pipeline Pipeline to import KEGG annotations from KEGG into RGD
6. PID Annotation Import Pipeline Pipeline to import Pathway Interaction Database annotations from NCI into RGD
7. GOA pipeline RGD automated data pipeline
8. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
9. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
10. The integrins. Takada Y, etal., Genome Biol. 2007;8(5):215.
11. Tentative Sequence Identification Numbers Tentative Sequence Data IDs. TIGR Gene Index, Rat Data
12. Structure-function analysis of the integrin beta 7 subunit: identification of domains involved in adhesion to MAdCAM-1. Tidswell M, etal., J Immunol 1997 Aug 1;159(3):1497-505.
Additional References at PubMed
PMID:12477932   PMID:15484189   PMID:18308860   PMID:19946888   PMID:20458337   PMID:23382219   PMID:23661644   PMID:23986478   PMID:35042191  


Genomics

Comparative Map Data
Itgb7
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.27133,347,927 - 133,364,955 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl7133,347,960 - 133,364,876 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx7135,109,152 - 135,121,717 (-)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.07137,338,519 - 137,351,081 (-)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.07137,323,632 - 137,336,211 (-)NCBIRnor_WKY
Rnor_6.07143,820,236 - 143,837,802 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl7143,820,900 - 143,837,780 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.07141,617,387 - 141,634,902 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.47140,971,310 - 140,984,091 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.17141,047,752 - 141,057,691 (-)NCBI
Celera7129,781,783 - 129,794,228 (-)NCBICelera
RH 3.4 Map71054.0RGD
Cytogenetic Map7q36NCBI
ITGB7
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381253,191,323 - 53,207,251 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p13 Ensembl1253,191,323 - 53,207,282 (-)EnsemblGRCh38hg38GRCh38
GRCh371253,585,107 - 53,601,035 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361251,871,374 - 51,887,267 (-)NCBINCBI36Build 36hg18NCBI36
Build 341251,871,374 - 51,887,267NCBI
Celera1253,233,710 - 53,249,603 (-)NCBICelera
Cytogenetic Map12q13.13NCBI
HuRef1250,627,678 - 50,643,108 (-)NCBIHuRef
CHM1_11253,551,540 - 53,567,435 (-)NCBICHM1_1
T2T-CHM13v2.01253,156,921 - 53,172,850 (-)NCBIT2T-CHM13v2.0
Itgb7
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm3915102,124,429 - 102,141,840 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl15102,124,430 - 102,140,379 (-)EnsemblGRCm39 Ensembl
GRCm3815102,215,994 - 102,233,405 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl15102,215,995 - 102,231,944 (-)EnsemblGRCm38mm10GRCm38
MGSCv3715102,046,426 - 102,062,366 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv3615102,044,031 - 102,059,920 (-)NCBIMGSCv36mm8
Celera15104,372,957 - 104,388,896 (-)NCBICelera
Cytogenetic Map15F2NCBI
cM Map1557.39NCBI
Itgb7
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_004955458460,651 - 470,145 (-)EnsemblChiLan1.0
ChiLan1.0NW_004955458460,619 - 478,361 (-)NCBIChiLan1.0ChiLan1.0
ITGB7
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11236,328,355 - 36,344,616 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1236,328,355 - 36,344,616 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01235,546,107 - 35,562,641 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
ITGB7
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1271,989,402 - 1,994,654 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl271,985,782 - 1,994,651 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2744,255,197 - 44,270,311 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0271,983,495 - 1,998,639 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl271,989,625 - 1,999,208 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1272,001,705 - 2,016,793 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0271,986,671 - 2,001,734 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.02744,655,870 - 44,670,990 (-)NCBIUU_Cfam_GSD_1.0
Itgb7
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440494562,662,036 - 62,686,110 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_00493651210,484,838 - 10,494,506 (-)EnsemblSpeTri2.0
SpeTri2.0NW_00493651210,484,336 - 10,501,527 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
ITGB7
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl518,419,436 - 18,434,610 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1518,419,432 - 18,434,376 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2518,846,939 - 18,857,904 (-)NCBISscrofa10.2Sscrofa10.2susScr3
ITGB7
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11149,297,849 - 49,315,627 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl1149,297,458 - 49,315,716 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_023666037196,744,063 - 196,762,485 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Itgb7
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046249041,238,785 - 1,247,622 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046249041,238,524 - 1,253,575 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Itgb7
56 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:113
Count of miRNA genes:85
Interacting mature miRNAs:97
Transcripts:ENSRNOT00000016642
Prediction methods:Microtar, Miranda, Rnahybrid, Targetscan
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
1300179Kidm5Kidney mass QTL 53.51kidney mass (VT:0002707)left kidney wet weight (CMO:0000083)743747012135012528Rat
70173Niddm19Non-insulin dependent diabetes mellitus QTL 194.330.00005blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)764002457135012528Rat
1358891Bp265Blood pressure QTL 2652.21arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)783591953134666232Rat
1358914Bp266Blood pressure QTL 266arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)783591953134666232Rat
1549899Stresp8Stress response QTL 84.370.0008stress-related behavior trait (VT:0010451)defensive burying duration (CMO:0001961)790482196135012528Rat
2299163Iddm34Insulin dependent diabetes mellitus QTL 342.71blood glucose amount (VT:0000188)age at onset/diagnosis of type 1 diabetes mellitus (CMO:0001140)791281130135012528Rat
731176Glom5Glomerulus QTL 52.50.0035kidney glomerulus morphology trait (VT:0005325)count of superficial glomeruli not directly contacting the kidney surface (CMO:0001002)796670164135012528Rat
1331731Bp216Blood pressure QTL 2162.851arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)7102297359133492884Rat
731174Uae23Urinary albumin excretion QTL 232.40.0042urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)7104603555135012528Rat
2306821Bp335Blood pressure QTL 3350.001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)7106571501135012528Rat
631663Bw6Body weight QTL 63.4body mass (VT:0001259)body weight (CMO:0000012)7111075573134976056Rat
1300112Bp183Blood pressure QTL 1833.51arterial blood pressure trait (VT:2000000)blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)7111182207135012528Rat
1331748Bp215Blood pressure QTL 2154.043arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)7112308254133492884Rat
1357339Stl14Serum triglyceride level QTL 143.450.0001blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)7112729683133492707Rat
1354582Stl11Serum triglyceride level QTL 113.42blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)7119513385135012528Rat

Markers in Region
D7Ztm1  
Rat AssemblyChrPosition (strand)SourceJBrowse
Cytogenetic Map7q36UniSTS
RH94429  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.27133,347,955 - 133,348,119 (+)MAPPERmRatBN7.2
Rnor_6.07143,820,895 - 143,821,058NCBIRnor6.0
Rnor_5.07141,618,047 - 141,618,210UniSTSRnor5.0
RGSC_v3.47140,971,337 - 140,971,500UniSTSRGSC3.4
Celera7129,781,810 - 129,781,973UniSTS
RH 3.4 Map71054.0UniSTS
Cytogenetic Map7q36UniSTS


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 8 19 6
Low 1 25 47 39 39 7 10 5 26 21 5 7
Below cutoff 18 2 2 2 1 1 53 9 20 1

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000016642   ⟹   ENSRNOP00000016642
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl7133,347,960 - 133,364,876 (-)Ensembl
Rnor_6.0 Ensembl7143,820,900 - 143,837,780 (-)Ensembl
RefSeq Acc Id: NM_013171   ⟹   NP_037303
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.27133,347,929 - 133,360,477 (-)NCBI
Rnor_6.07143,820,868 - 143,833,383 (-)NCBI
Rnor_5.07141,617,387 - 141,634,902 (-)NCBI
RGSC_v3.47140,971,310 - 140,984,091 (-)RGD
Celera7129,781,783 - 129,794,228 (-)RGD
Sequence:
RefSeq Acc Id: XM_006242383   ⟹   XP_006242445
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.27133,347,927 - 133,364,955 (-)NCBI
Rnor_6.07143,820,236 - 143,837,802 (-)NCBI
Rnor_5.07141,617,387 - 141,634,902 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039078494   ⟹   XP_038934422
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.27133,347,927 - 133,359,164 (-)NCBI
Protein Sequences
Protein RefSeqs NP_037303 (Get FASTA)   NCBI Sequence Viewer  
  XP_006242445 (Get FASTA)   NCBI Sequence Viewer  
  XP_038934422 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAB61241 (Get FASTA)   NCBI Sequence Viewer  
  AAH98806 (Get FASTA)   NCBI Sequence Viewer  
  EDL86853 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_037303   ⟸   NM_013171
- Peptide Label: precursor
- UniProtKB: G3V7M2 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006242445   ⟸   XM_006242383
- Peptide Label: isoform X1
- UniProtKB: G3V7M2 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000016642   ⟸   ENSRNOT00000016642
RefSeq Acc Id: XP_038934422   ⟸   XM_039078494
- Peptide Label: isoform X2
Protein Domains
INB   Integrin_b_cyt   Integrin_B_tail   PSI

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-G3V7M2-F1-model_v2 AlphaFold G3V7M2 1-807 view protein structure

Transcriptome

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

Promoters
RGD ID:13695693
Promoter ID:EPDNEW_R6218
Type:multiple initiation site
Name:Itgb7_1
Description:integrin subunit beta 7
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_6.07143,837,769 - 143,837,829EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:2929 AgrOrtholog
BioCyc Gene G2FUF-31945 BioCyc
Ensembl Genes ENSRNOG00000012208 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000016642 ENTREZGENE
  ENSRNOP00000016642.4 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000016642 ENTREZGENE
  ENSRNOT00000016642.7 UniProtKB/TrEMBL
Gene3D-CATH 3.40.50.410 UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7376553 IMAGE-MGC_LOAD
InterPro EGF_extracell UniProtKB/TrEMBL
  I-EGF_1 UniProtKB/TrEMBL
  Integin_beta_N UniProtKB/TrEMBL
  Integrin_bsu UniProtKB/TrEMBL
  Integrin_bsu-7 UniProtKB/TrEMBL
  Integrin_bsu_cyt UniProtKB/TrEMBL
  Integrin_bsu_N UniProtKB/TrEMBL
  Integrin_bsu_tail UniProtKB/TrEMBL
  Integrin_bsu_tail_dom_sf UniProtKB/TrEMBL
  Integrin_dom UniProtKB/TrEMBL
  Plexin-like_fold UniProtKB/TrEMBL
  vWFA_dom_sf UniProtKB/TrEMBL
KEGG Report rno:25713 UniProtKB/TrEMBL
MGC_CLONE MGC:112849 IMAGE-MGC_LOAD
NCBI Gene 25713 ENTREZGENE
PANTHER Integrin_beta_C UniProtKB/TrEMBL
  PTHR10082:SF36 UniProtKB/TrEMBL
Pfam EGF_2 UniProtKB/TrEMBL
  I-EGF_1 UniProtKB/TrEMBL
  Integrin_b_cyt UniProtKB/TrEMBL
  Integrin_beta UniProtKB/TrEMBL
  PSI_integrin UniProtKB/TrEMBL
PhenoGen Itgb7 PhenoGen
PIRSF Integrin_B UniProtKB/TrEMBL
PRINTS INTEGRINB UniProtKB/TrEMBL
PROSITE INTEGRIN_BETA UniProtKB/TrEMBL
SMART INB UniProtKB/TrEMBL
  Integrin_b_cyt UniProtKB/TrEMBL
  Integrin_B_tail UniProtKB/TrEMBL
  PSI UniProtKB/TrEMBL
Superfamily-SCOP Integrin_bsu_tail UniProtKB/TrEMBL
  SSF53300 UniProtKB/TrEMBL
  SSF69179 UniProtKB/TrEMBL
TIGR TC236197
UniProt G3V7M2 ENTREZGENE, UniProtKB/TrEMBL
  Q4G029_RAT UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2015-12-23 Itgb7  integrin subunit beta 7  Itgb7  integrin, beta 7  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2004-09-10 Itgb7  integrin, beta 7    integrin beta 7  Name updated 1299863 APPROVED
2002-06-10 Itgb7  Integrin beta 7      Symbol and Name status set to approved 70586 APPROVED

RGD Curation Notes
Note Type Note Reference
gene_domains has a metal ion-dependent adhesion site (MIDAS) domain 633040