Itgbl1 (integrin subunit beta like 1) - Rat Genome Database

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Gene: Itgbl1 (integrin subunit beta like 1) Rattus norvegicus
Analyze
Symbol: Itgbl1
Name: integrin subunit beta like 1
RGD ID: 1560635
Description: Predicted to enable integrin binding activity. Predicted to be involved in several processes, including cell adhesion mediated by integrin; cell-matrix adhesion; and integrin-mediated signaling pathway. Predicted to be located in extracellular region. Predicted to be part of integrin complex. Predicted to be active in cell surface and focal adhesion. Orthologous to human ITGBL1 (integrin subunit beta like 1); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 3-chloropropane-1,2-diol; aflatoxin B1.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: integrin beta-like protein 1; integrin, beta-like 1; LOC498564; similar to integrin, beta-like 1
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
GRCr815107,186,792 - 107,448,335 (+)NCBIGRCr8
mRatBN7.215100,780,184 - 101,041,734 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl15100,780,184 - 101,041,733 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx15104,725,109 - 104,995,329 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.015105,820,283 - 106,084,368 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.015102,747,527 - 103,011,619 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.015110,114,148 - 110,378,970 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl15110,114,148 - 110,378,969 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.015113,495,871 - 113,759,208 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.415108,785,509 - 109,051,028 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera1599,524,299 - 99,783,600 (+)NCBICelera
Cytogenetic Map15q25NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

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. GOA pipeline RGD automated data pipeline
3. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
4. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
5. 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.
Additional References at PubMed
PMID:24006456   PMID:37395147  


Genomics

Comparative Map Data
Itgbl1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr815107,186,792 - 107,448,335 (+)NCBIGRCr8
mRatBN7.215100,780,184 - 101,041,734 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl15100,780,184 - 101,041,733 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx15104,725,109 - 104,995,329 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.015105,820,283 - 106,084,368 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.015102,747,527 - 103,011,619 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.015110,114,148 - 110,378,970 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl15110,114,148 - 110,378,969 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.015113,495,871 - 113,759,208 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.415108,785,509 - 109,051,028 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera1599,524,299 - 99,783,600 (+)NCBICelera
Cytogenetic Map15q25NCBI
ITGBL1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh3813101,452,675 - 101,720,856 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl13101,452,593 - 101,720,856 (+)EnsemblGRCh38hg38GRCh38
GRCh3713102,105,026 - 102,373,206 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 3613100,902,967 - 101,166,795 (+)NCBINCBI36Build 36hg18NCBI36
Build 3413100,902,966 - 101,166,794NCBI
Celera1382,947,678 - 83,211,592 (+)NCBICelera
Cytogenetic Map13q33.1NCBI
HuRef1382,698,206 - 82,966,639 (+)NCBIHuRef
CHM1_113102,074,993 - 102,343,275 (+)NCBICHM1_1
T2T-CHM13v2.013100,667,841 - 100,936,857 (+)NCBIT2T-CHM13v2.0
Itgbl1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm3914123,897,331 - 124,215,173 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl14123,897,383 - 124,213,030 (+)EnsemblGRCm39 Ensembl
GRCm3814123,659,937 - 123,978,865 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl14123,659,971 - 123,975,618 (+)EnsemblGRCm38mm10GRCm38
MGSCv3714124,059,362 - 124,373,301 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv3614122,795,353 - 123,109,258 (+)NCBIMGSCv36mm8
Celera14123,117,270 - 123,428,005 (+)NCBICelera
Cytogenetic Map14E5NCBI
cM Map1466.1NCBI
Itgbl1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554049,332,169 - 9,546,245 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049554049,331,407 - 9,545,711 (-)NCBIChiLan1.0ChiLan1.0
ITGBL1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v214102,939,483 - 103,234,000 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan113101,606,927 - 101,899,428 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01382,609,493 - 82,877,474 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.113101,746,410 - 102,010,227 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl13101,747,760 - 102,014,605 (+)Ensemblpanpan1.1panPan2
ITGBL1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12251,157,789 - 51,377,441 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2251,158,169 - 51,380,430 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2250,937,978 - 51,157,393 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.02251,602,342 - 51,827,243 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl2251,602,571 - 51,827,217 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.12251,265,906 - 51,478,891 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.02251,275,078 - 51,487,305 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.02251,322,401 - 51,535,328 (+)NCBIUU_Cfam_GSD_1.0
Itgbl1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024404945186,499,221 - 186,718,026 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049364729,233,576 - 9,452,954 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049364729,227,795 - 9,452,936 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
ITGBL1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1170,042,232 - 70,246,968 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11170,042,051 - 70,246,974 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21177,341,847 - 77,451,340 (+)NCBISscrofa10.2Sscrofa10.2susScr3
ITGBL1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1380,045,404 - 80,303,978 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl380,045,577 - 80,302,006 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366604636,557,095 - 36,814,496 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Itgbl1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046247939,645,861 - 9,878,634 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046247939,645,076 - 9,878,788 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Itgbl1
1420 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:273
Count of miRNA genes:180
Interacting mature miRNAs:210
Transcripts:ENSRNOT00000006264
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
731177Uae26Urinary albumin excretion QTL 262.40.025urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)1567588667101769107Rat
1549844Bss7Bone structure and strength QTL 76.4femur strength trait (VT:0010010)femur midshaft polar moment of inertia (CMO:0001669)1575788062101769107Rat
70155Gcs1Gastric cancer susceptibility QTL13.8stomach morphology trait (VT:0000470)stomach tumor susceptibility score (CMO:0002043)1576306099101769107Rat
2317055Aia10Adjuvant induced arthritis QTL 103.41joint integrity trait (VT:0010548)left rear ankle joint diameter (CMO:0002149)1575788062101769107Rat
631655Bp126Blood pressure QTL 1264arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1558156477101769107Rat

Markers in Region
RH130155  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.215101,041,481 - 101,041,665 (+)MAPPERmRatBN7.2
Rnor_6.015110,378,718 - 110,378,901NCBIRnor6.0
Rnor_5.015113,758,956 - 113,759,139UniSTSRnor5.0
RGSC_v3.415109,050,776 - 109,050,959UniSTSRGSC3.4
Celera1599,783,348 - 99,783,531UniSTS
RH 3.4 Map15743.5UniSTS
Cytogenetic Map15q25UniSTS
AW528074  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.215101,036,347 - 101,036,475 (+)MAPPERmRatBN7.2
Rnor_6.015110,373,584 - 110,373,711NCBIRnor6.0
Rnor_5.015113,753,822 - 113,753,949UniSTSRnor5.0
RGSC_v3.415109,045,642 - 109,045,769UniSTSRGSC3.4
Celera1599,778,214 - 99,778,341UniSTS
RH 3.4 Map15692.39UniSTS
Cytogenetic Map15q25UniSTS
AU048864  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.215100,840,143 - 100,840,245 (+)MAPPERmRatBN7.2
Rnor_6.015110,174,576 - 110,174,677NCBIRnor6.0
Rnor_5.015113,556,299 - 113,556,400UniSTSRnor5.0
RGSC_v3.415108,845,866 - 108,845,967UniSTSRGSC3.4
Celera1599,584,043 - 99,584,144UniSTS
Cytogenetic Map15q25UniSTS
G46240  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.215100,824,198 - 100,824,383 (+)MAPPERmRatBN7.2
Rnor_6.015110,158,157 - 110,158,341NCBIRnor6.0
Rnor_5.015113,539,880 - 113,540,064UniSTSRnor5.0
RGSC_v3.415108,829,518 - 108,829,702UniSTSRGSC3.4
Celera1599,568,311 - 99,568,495UniSTS
Cytogenetic Map15q25UniSTS


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 21 8 6 8 11 14 8 6
Low 3 18 37 21 11 21 2 3 59 27 23 3 2
Below cutoff 4 16 16 16 4 8 4

Sequence


RefSeq Acc Id: ENSRNOT00000006264   ⟹   ENSRNOP00000006264
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl15100,780,184 - 101,041,733 (+)Ensembl
Rnor_6.0 Ensembl15110,114,148 - 110,378,969 (+)Ensembl
RefSeq Acc Id: NM_001017505   ⟹   NP_001017505
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr815107,186,792 - 107,448,335 (+)NCBI
mRatBN7.215100,780,184 - 101,041,734 (+)NCBI
Rnor_6.015110,114,148 - 110,378,970 (+)NCBI
Rnor_5.015113,495,871 - 113,759,208 (+)NCBI
RGSC_v3.415108,785,509 - 109,051,028 (+)RGD
Celera1599,524,299 - 99,783,600 (+)RGD
Sequence:
Protein Sequences
Protein RefSeqs NP_001017505 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAH87076 (Get FASTA)   NCBI Sequence Viewer  
  EDM02594 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000006264.3
  ENSRNOP00060004534
GenBank Protein Q5PQQ8 (Get FASTA)   NCBI Sequence Viewer  
RefSeq Acc Id: NP_001017505   ⟸   NM_001017505
- Peptide Label: precursor
- UniProtKB: Q5PQQ8 (UniProtKB/Swiss-Prot),   A6HUN1 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000006264   ⟸   ENSRNOT00000006264
Protein Domains
EGF-like

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q5PQQ8-F1-model_v2 AlphaFold Q5PQQ8 1-494 view protein structure

Transcriptome

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

Promoters
RGD ID:13699887
Promoter ID:EPDNEW_R10411
Type:initiation region
Name:Itgbl1_1
Description:integrin subunit beta like 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_6.015110,114,048 - 110,114,108EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1560635 AgrOrtholog
BioCyc Gene G2FUF-12331 BioCyc
Ensembl Genes ENSRNOG00000004516 Ensembl, UniProtKB/Swiss-Prot
  ENSRNOG00060003694 UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000006264.5 UniProtKB/Swiss-Prot
  ENSRNOT00060006121 UniProtKB/Swiss-Prot
Gene3D-CATH Laminin UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7134947 IMAGE-MGC_LOAD
InterPro EGF-like_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  EGF_extracell UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Integrin_bsu UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:498564 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
MGC_CLONE MGC:94470 IMAGE-MGC_LOAD
NCBI Gene 498564 ENTREZGENE
PANTHER INTEGRIN BETA SUBUNIT UniProtKB/TrEMBL
  INTEGRIN BETA-PS UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PTHR10082 UniProtKB/Swiss-Prot
Pfam EGF_2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Itgbl1 PhenoGen
PROSITE EGF_1 UniProtKB/Swiss-Prot
  EGF_2 UniProtKB/Swiss-Prot
  INTEGRIN_BETA UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
RatGTEx ENSRNOG00000004516 RatGTEx
  ENSRNOG00060003694 RatGTEx
SMART EGF UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP EGF/Laminin UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A6HUN1 ENTREZGENE, UniProtKB/TrEMBL
  ITGBL_RAT UniProtKB/Swiss-Prot, ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2015-12-23 Itgbl1  integrin subunit beta like 1  Itgbl1  integrin, beta-like 1  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-03-05 Itgbl1  integrin, beta-like 1  LOC498564  similar to integrin, beta-like 1  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-02-09 LOC498564  similar to integrin, beta-like 1      Symbol and Name status set to provisional 70820 PROVISIONAL