Trav6-1 (T cell receptor alpha variable 6-1) - Rat Genome Database

Send us a Message
Submit Data |  Help |  Video Tutorials |  News |  Publications |  Download |  REST API |  Citing RGD |  Contact   
Search RGD Grant Resources Citing RGD About Us Contact Us
Genes Variants Community Projects QTLs Strains Markers Genome Information Ontologies Cell Lines References Download Submit Data
OntoMate (Literature Search) JBrowse (Genome Browser) Synteny Browser (VCMap) Variant Visualizer Multi-Ontology Enrichment (MOET) Gene-Ortholog Location Finder (GOLF) InterViewer (Protein-Protein Interactions) PhenoMiner (Quatitative Phenotypes) Gene Annotator OLGA (Gene List Generator) AllianceMine GViewer (Genome Viewer)
Aging & Age-Related Disease Cancer & Neoplastic Disease Cardiovascular Disease Coronavirus Disease Developmental Disease Diabetes Hematologic Disease Immune & Inflammatory Disease Infectious Disease Liver Disease Neurological Disease Obesity & Metabolic Syndrome Renal Disease Respiratory Disease Sensory Organ Disease
Find Models   new Genetic Models Autism Models Rat PhenoMiner (Quantitative Phenotypes) Chinchilla PhenoMiner Expected Ranges (Quantitative Phenotype) PhenoMiner Term Comparison Hybrid Rat Diversity Panel Phenotypes Phenotypes in Other Animal Models Animal Husbandry Strain Medical Records Phylogenetics Strain Availability Calendar Rats 101 Submissions Photo Archive
Pathways
Rat Community Forum Directory of Rat Laboratories Video Tutorials News RGD Publications RGD Presentations Archive Nomenclature Guidelines Resource Links Laboratory Resources Employment Resources
Gene: Trav6-1 (T cell receptor alpha variable 6-1) Rattus norvegicus
Analyze
Symbol: Trav6-1 (Ensembl: LOC100911980)
Name: T cell receptor alpha variable 6-1 (Ensembl:uncharacterized LOC100911980)
RGD ID: 6489577
Description: Predicted to be part of T cell receptor complex. Orthologous to human TRAV9-2 (T cell receptor alpha variable 9-2).
Type: gene (Ensembl: protein-coding)
RefSeq Status: MODEL
Previously known as: AABR07017610.1; LOC100911980; uncharacterized LOC100911980
RGD Orthologs
Human
Mouse
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81530,053,597 - 30,057,351 (+)NCBIGRCr8
mRatBN7.21526,712,279 - 26,713,004 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1526,712,109 - 26,712,910 (+)NCBImRatBN7.2 Ensembl
mRatBN7.2 Ensembl1526,712,109 - 26,712,910 (+)EnsemblmRatBN7.2 Ensembl
Rnor_6.01532,146,865 - 32,148,038 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1529,208,606 - 29,209,270 (+)NCBIRnor6.0rn6Rnor6.0
Rnor_5.01535,958,637 - 35,959,211 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
Cytogenetic Map15p13NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


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.

Genomics

Comparative Map Data
Trav6-1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81530,053,597 - 30,057,351 (+)NCBIGRCr8
mRatBN7.21526,712,279 - 26,713,004 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1526,712,109 - 26,712,910 (+)NCBImRatBN7.2 Ensembl
mRatBN7.2 Ensembl1526,712,109 - 26,712,910 (+)EnsemblmRatBN7.2 Ensembl
Rnor_6.01532,146,865 - 32,148,038 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1529,208,606 - 29,209,270 (+)NCBIRnor6.0rn6Rnor6.0
Rnor_5.01535,958,637 - 35,959,211 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
Cytogenetic Map15p13NCBI
TRAV9-2
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381421,941,184 - 21,941,657 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1421,941,128 - 21,941,657 (+)EnsemblGRCh38hg38GRCh38
GRCh371422,409,369 - 22,409,848 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361421,479,209 - 21,479,688 (+)NCBINCBI36Build 36hg18NCBI36
Celera142,272,942 - 2,273,420 (+)NCBICelera
Cytogenetic Map14q11.2NCBI
HuRef142,527,232 - 2,527,711 (+)NCBIHuRef
CHM1_11422,409,086 - 22,409,559 (+)NCBICHM1_1
T2T-CHM13v2.01416,138,817 - 16,139,290 (+)NCBIT2T-CHM13v2.0
Trav6-1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391452,875,972 - 52,876,419 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1452,875,972 - 52,876,419 (+)EnsemblGRCm39 Ensembl
GRCm381452,638,515 - 52,638,962 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1452,638,515 - 52,638,962 (+)EnsemblGRCm38mm10GRCm38
MGSCv371453,258,190 - 53,258,637 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361451,544,517 - 51,560,956 (+)NCBIMGSCv36mm8
Celera1449,616,214 - 49,616,732 (+)NCBICelera
Cytogenetic Map14C2NCBI
cM Map1427.03NCBI

Variants

.
Variants in Trav6-1
28 total Variants

QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1354657Despr13Despair related QTL 130.0022locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)15129912054Rat
8552920Pigfal8Plasma insulin-like growth factor 1 level QTL 83blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)15134723002Rat
8694361Abfw6Abdominal fat weight QTL 610.20.001visceral adipose mass (VT:0010063)abdominal fat pad weight to body weight ratio (CMO:0000095)15134723002Rat
9589149Insul29Insulin level QTL 299.060.001blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)15134723002Rat
731170Pur3Proteinuria QTL 32.30.0005urine protein amount (VT:0005160)urine protein excretion rate (CMO:0000759)15141686771Rat
1641887Alcrsp14Alcohol response QTL 14response to alcohol trait (VT:0010489)brain neurotensin receptor 1 density (CMO:0002068)15142356671Rat
2298549Neuinf12Neuroinflammation QTL 123.5nervous system integrity trait (VT:0010566)spinal cord beta-2 microglobulin mRNA level (CMO:0002125)15155302115Rat
10401805Kidm51Kidney mass QTL 51kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)1530632945306329Rat
738017Hcas7Hepatocarcinoma susceptibility QTL 72.91liver integrity trait (VT:0010547)liver nonremodeling tumorous lesion volume to total liver volume ratio (CMO:0001464)15226636846921453Rat
1582251Gluco24Glucose level QTL 243.20.0008blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)15553075650530756Rat
631273Lecl2Lens clarity QTL 20.001lens clarity trait (VT:0001304)age of onset/diagnosis of cataract (CMO:0001584)151059608955596089Rat
2300167Bmd63Bone mineral density QTL 635.90.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)151111114256111142Rat
2300173Bmd62Bone mineral density QTL 6212.80.0001lumbar vertebra mineral mass (VT:0010511)volumetric bone mineral density (CMO:0001553)151111114256111142Rat
2293688Bss29Bone structure and strength QTL 295.310.0001femur morphology trait (VT:0000559)femur midshaft cortical cross-sectional area (CMO:0001663)151111114256111142Rat
2317750Glom26Glomerulus QTL 264.3urine protein amount (VT:0005160)urine protein level (CMO:0000591)151249614165205939Rat
5685002Bss103Bone structure and strength QTL 1032.8tibia strength trait (VT:1000284)tibia total energy absorbed before break (CMO:0001736)151448116528469888Rat
61424Scl1Serum cholesterol level QTL 17.70.001blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)151672552880672115Rat
1331729Rf42Renal function QTL 423.071kidney blood vessel physiology trait (VT:0100012)absolute change in renal blood flow rate (CMO:0001168)151736289773690657Rat
631550Bw7Body weight QTL 73.6body mass (VT:0001259)body weight (CMO:0000012)151985656634924750Rat
2324620Coatc3Coat color QTL 3coat/hair pigmentation trait (VT:0010463)pigmented coat/hair area to total coat/hair area ratio (CMO:0001810)151985656646187442Rat
10054130Srcrt8Stress Responsive Cort QTL 82.180.0085blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)152211793367117933Rat
1578646Bmd18Bone mineral density QTL 185.2femur mineral mass (VT:0010011)trabecular volumetric bone mineral density (CMO:0001729)152280624098288169Rat
1578647Bmd17Bone mineral density QTL 174femur mineral mass (VT:0010011)total volumetric bone mineral density (CMO:0001728)152280624098288169Rat
1578660Bss19Bone structure and strength QTL 194.3femur morphology trait (VT:0000559)bone trabecular cross-sectional area (CMO:0002311)152280624098288169Rat


Expression


Sequence

Nucleotide Sequences
RefSeq Transcripts XM_003751475 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide JAXUCZ010000015 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000073722   ⟹   ENSRNOP00000065505
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1526,712,109 - 26,712,910 (+)Ensembl
RefSeq Acc Id: XM_003751475   ⟹   XP_003751523
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_5.01535,958,694 - 35,962,624 (+)NCBI
Protein Sequences
Ensembl Protein ENSRNOP00000065505.3
Reference Protein Sequences
RefSeq Acc Id: XP_003751523   ⟸   XM_003751475
RefSeq Acc Id: ENSRNOP00000065505   ⟸   ENSRNOT00000073722
Protein Domains
Ig-like

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-M0R7S3-F1-model_v2 AlphaFold M0R7S3 1-138 view protein structure

Transcriptome

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


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:6489577 AgrOrtholog
BioCyc Gene G2FUF-13863 BioCyc
Ensembl Genes ENSRNOG00000045632 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000073722.3 UniProtKB/TrEMBL
Gene3D-CATH 2.60.40.10 UniProtKB/TrEMBL
InterPro Ig-like_dom UniProtKB/TrEMBL
  Ig-like_dom_sf UniProtKB/TrEMBL
  Ig-like_fold UniProtKB/TrEMBL
  Ig_sub UniProtKB/TrEMBL
  Ig_V-set UniProtKB/TrEMBL
NCBI Gene LOC100911980 ENTREZGENE
PANTHER T CELL RECEPTOR ALPHA VARIABLE 6N-6 UniProtKB/TrEMBL
  T-CELL RECEPTOR ALPHA CHAIN V REGION UniProtKB/TrEMBL
Pfam V-set UniProtKB/TrEMBL
PhenoGen Trav6-1 PhenoGen
PROSITE IG_LIKE UniProtKB/TrEMBL
RatGTEx ENSRNOG00000045632 RatGTEx
SMART IGv UniProtKB/TrEMBL
  SM00409 UniProtKB/TrEMBL
Superfamily-SCOP SSF48726 UniProtKB/TrEMBL
UniProt M0R7S3_RAT UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2023-09-19 Trav6-1  T cell receptor alpha variable 6-1  LOC100911980  uncharacterized LOC100911980  Symbol and Name Changed 1299863 APPROVED
2022-06-02 LOC100911980  uncharacterized LOC100911980  AABR07017610.1    Data merged from RGD:15004861 737654 PROVISIONAL
2019-11-08 AABR07017610.1        Symbol and Name status set to provisional 45752 PROVISIONAL
2012-07-05 LOC100911980  uncharacterized LOC100911980      Symbol and Name status set to provisional 70820 PROVISIONAL