TRAV25 (T cell receptor alpha variable 25) - 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: TRAV25 (T cell receptor alpha variable 25) Homo sapiens
Analyze
No known orthologs.
Symbol: TRAV25
Name: T cell receptor alpha variable 25
RGD ID: 1349708
HGNC Page HGNC:12122
Description: Predicted to be involved in response to bacterium. Predicted to be located in plasma membrane. Predicted to be part of T cell receptor complex.
Type: gene (Ensembl: TR_V_gene)
RefSeq Status: REVIEWED
Previously known as: TCRAV25S1; TCRAV32S1
RGD Orthologs
Alliance Genes
More Info homologs ...
Allele / Splice: See ClinVar data
Latest Assembly: GRCh38 - Human Genome Assembly GRCh38
NCBI Annotation Information: Annotation category: partial on reference assembly
Position:
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381422,112,423 - 22,113,031 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1422,112,347 - 22,113,031 (+)EnsemblGRCh38hg38GRCh38
GRCh371422,580,376 - 22,580,984 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361421,650,216 - 21,650,824 (+)NCBINCBI36Build 36hg18NCBI36
Celera142,443,935 - 2,444,543 (+)NCBICelera
Cytogenetic Map14q11.2NCBI
HuRef142,698,238 - 2,698,846 (+)NCBIHuRef
CHM1_11422,580,325 - 22,580,933 (+)NCBICHM1_1
T2T-CHM13v2.01416,310,255 - 16,310,863 (+)NCBIT2T-CHM13v2.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component

References
Additional References at PubMed
PMID:8188290   PMID:21873635  


Genomics


Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
GRCh38/hg38 14q11.2(chr14:21919243-22511027)x1 copy number loss See cases [RCV000135132] Chr14:21919243..22511027 [GRCh38]
Chr14:22387418..22980010 [GRCh37]
Chr14:21457258..22049850 [NCBI36]
Chr14:14q11.2		 benign
GRCh38/hg38 14q11.2-32.33(chr14:20151149-106855263)x3 copy number gain See cases [RCV000135543] Chr14:20151149..106855263 [GRCh38]
Chr14:20619308..107263478 [GRCh37]
Chr14:19689148..106334523 [NCBI36]
Chr14:14q11.2-32.33		 pathogenic
GRCh38/hg38 14q11.2(chr14:21973760-22442515)x1 copy number loss See cases [RCV000135471] Chr14:21973760..22442515 [GRCh38]
Chr14:22441989..22911507 [GRCh37]
Chr14:21511829..21981347 [NCBI36]
Chr14:14q11.2		 benign
GRCh38/hg38 14q11.2(chr14:21854413-22495939)x1 copy number loss See cases [RCV000135900] Chr14:21854413..22495939 [GRCh38]
Chr14:22322590..22964922 [GRCh37]
Chr14:21392430..22034762 [NCBI36]
Chr14:14q11.2		 benign
GRCh38/hg38 14q11.2-12(chr14:20412587-25018120)x3 copy number gain See cases [RCV000137725] Chr14:20412587..25018120 [GRCh38]
Chr14:20880746..25487326 [GRCh37]
Chr14:19950586..24557166 [NCBI36]
Chr14:14q11.2-12		 likely pathogenic
GRCh38/hg38 14q11.2(chr14:22021665-22324997)x3 copy number gain See cases [RCV000138466] Chr14:22021665..22324997 [GRCh38]
Chr14:22489905..22793429 [GRCh37]
Chr14:21559745..21863269 [NCBI36]
Chr14:14q11.2		 benign|likely benign|conflicting data from submitters
GRCh38/hg38 14q11.2(chr14:21919182-22201679)x3 copy number gain See cases [RCV000139288] Chr14:21919182..22201679 [GRCh38]
Chr14:22387357..22669573 [GRCh37]
Chr14:21457197..21739413 [NCBI36]
Chr14:14q11.2		 likely benign
GRCh38/hg38 14q11.2(chr14:22021665-22428036)x3 copy number gain See cases [RCV000139203] Chr14:22021665..22428036 [GRCh38]
Chr14:22489905..22897028 [GRCh37]
Chr14:21559745..21966868 [NCBI36]
Chr14:14q11.2		 likely benign
GRCh38/hg38 14q11.2(chr14:21973759-22428036)x3 copy number gain See cases [RCV000139486] Chr14:21973759..22428036 [GRCh38]
Chr14:22441988..22897028 [GRCh37]
Chr14:21511828..21966868 [NCBI36]
Chr14:14q11.2		 benign
GRCh38/hg38 14q11.2(chr14:21919182-22398359)x3 copy number gain See cases [RCV000139614] Chr14:21919182..22398359 [GRCh38]
Chr14:22387357..22866762 [GRCh37]
Chr14:21457197..21936602 [NCBI36]
Chr14:14q11.2		 likely benign
GRCh38/hg38 14q11.2(chr14:21010790-22951814)x3 copy number gain See cases [RCV000140829] Chr14:21010790..22951814 [GRCh38]
Chr14:21478949..23421023 [GRCh37]
Chr14:20548789..22490863 [NCBI36]
Chr14:14q11.2		 uncertain significance
GRCh38/hg38 14q11.2(chr14:21830995-22324997)x3 copy number gain See cases [RCV000142945] Chr14:21830995..22324997 [GRCh38]
Chr14:22299151..22793429 [GRCh37]
Chr14:21368991..21863269 [NCBI36]
Chr14:14q11.2		 pathogenic|likely benign
GRCh38/hg38 14q11.2(chr14:22021665-22398359)x3 copy number gain See cases [RCV000142894] Chr14:22021665..22398359 [GRCh38]
Chr14:22489905..22866762 [GRCh37]
Chr14:21559745..21936602 [NCBI36]
Chr14:14q11.2		 likely benign
GRCh38/hg38 14q11.2(chr14:21973759-22398359)x3 copy number gain See cases [RCV000142826] Chr14:21973759..22398359 [GRCh38]
Chr14:22441988..22866762 [GRCh37]
Chr14:21511828..21936602 [NCBI36]
Chr14:14q11.2		 likely benign
GRCh38/hg38 14q11.2(chr14:21973759-22324997)x3 copy number gain See cases [RCV000142998] Chr14:21973759..22324997 [GRCh38]
Chr14:22441988..22793429 [GRCh37]
Chr14:21511828..21863269 [NCBI36]
Chr14:14q11.2		 pathogenic|likely benign
GRCh38/hg38 14q11.2-32.33(chr14:20043514-106877229)x3 copy number gain See cases [RCV000143373] Chr14:20043514..106877229 [GRCh38]
Chr14:20511673..107285437 [GRCh37]
Chr14:19581513..106356482 [NCBI36]
Chr14:14q11.2-32.33		 pathogenic
GRCh38/hg38 14q11.2-21.2(chr14:20022693-44093672)x3 copy number gain See cases [RCV000143186] Chr14:20022693..44093672 [GRCh38]
Chr14:20490852..44562875 [GRCh37]
Chr14:19560692..43632625 [NCBI36]
Chr14:14q11.2-21.2		 pathogenic
GRCh38/hg38 14q11.2-21.3(chr14:20043513-48642042)x3 copy number gain See cases [RCV000143748] Chr14:20043513..48642042 [GRCh38]
Chr14:20511672..49111245 [GRCh37]
Chr14:19581512..48180995 [NCBI36]
Chr14:14q11.2-21.3		 pathogenic
GRCh38/hg38 14q11.2(chr14:19755249-22741281)x1 copy number loss See cases [RCV000051483] Chr14:19755249..22741281 [GRCh38]
Chr14:20223408..23210490 [GRCh37]
Chr14:19293248..22280330 [NCBI36]
Chr14:14q11.2		 pathogenic
GRCh38/hg38 14q11.2-12(chr14:20151149-27723796)x1 copy number loss Developmental Delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000051484]|Developmental delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000051484]|See cases [RCV000051484] Chr14:20151149..27723796 [GRCh38]
Chr14:20619308..28193002 [GRCh37]
Chr14:19689148..27262842 [NCBI36]
Chr14:14q11.2-12		 pathogenic
GRCh38/hg38 14q11.2-21.2(chr14:20196945-45284802)x1 copy number loss See cases [RCV000051485] Chr14:20196945..45284802 [GRCh38]
Chr14:20665104..45754005 [GRCh37]
Chr14:19734944..44823755 [NCBI36]
Chr14:14q11.2-21.2		 pathogenic
GRCh38/hg38 14q11.2(chr14:21919243-22442515)x1 copy number loss See cases [RCV000051207] Chr14:21919243..22442515 [GRCh38]
Chr14:22387418..22911507 [GRCh37]
Chr14:21457258..21981347 [NCBI36]
Chr14:14q11.2		 benign
GRCh38/hg38 14q11.2(chr14:20151149-23442195)x3 copy number gain See cases [RCV000050914] Chr14:20151149..23442195 [GRCh38]
Chr14:20619308..23911404 [GRCh37]
Chr14:19689148..22981244 [NCBI36]
Chr14:14q11.2		 pathogenic
GRCh38/hg38 14q11.2(chr14:22021664-22592708)x1 copy number loss See cases [RCV000053682] Chr14:22021664..22592708 [GRCh38]
Chr14:22489904..23061615 [GRCh37]
Chr14:21559744..22131455 [NCBI36]
Chr14:14q11.2		 benign
GRCh38/hg38 14q11.2-21.1(chr14:20000611-38984415)x3 copy number gain See cases [RCV000053803] Chr14:20000611..38984415 [GRCh38]
Chr14:20468770..39453619 [GRCh37]
Chr14:19538610..38523370 [NCBI36]
Chr14:14q11.2-21.1		 pathogenic
GRCh38/hg38 14q11.2-21.1(chr14:20150949-39746154)x3 copy number gain Developmental Delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000053806]|Developmental delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000053806]|See cases [RCV000053806] Chr14:20150949..39746154 [GRCh38]
Chr14:20619108..40215358 [GRCh37]
Chr14:19688948..39285109 [NCBI36]
Chr14:14q11.2-21.1		 pathogenic
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:274
Count of miRNA genes:258
Interacting mature miRNAs:269
Transcripts:ENST00000390454
Prediction methods: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 sensory system adipose tissue appendage pharyngeal arch
High
Medium 1 27 3 51 1
Low 256 621 143 51 927 41 73 23 21 80 114 295 9 101 31 2
Below cutoff 708 516 390 165 294 107 831 288 523 92 269 464 60 437 453

Sequence


Reference Sequences
RefSeq Acc Id: ENST00000390454   ⟹   ENSP00000452100
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1422,112,347 - 22,113,031 (+)Ensembl
Protein Sequences
GenBank Protein A0A0B4J276 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSP00000452100.1
Reference Protein Sequences
RefSeq Acc Id: ENSP00000452100   ⟸   ENST00000390454
Protein Domains
Ig-like

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-A0A0B4J276-F1-model_v2 AlphaFold A0A0B4J276 1-109 view protein structure


Additional Information

Database Acc Id Source(s)
AGR Gene HGNC:12122 AgrOrtholog
COSMIC TRAV25 COSMIC
Ensembl Genes ENSG00000211806 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENST00000390454.2 UniProtKB/Swiss-Prot
Gene3D-CATH 2.60.40.10 UniProtKB/Swiss-Prot
GTEx ENSG00000211806 GTEx
HGNC ID HGNC:12122 ENTREZGENE
Human Proteome Map TRAV25 Human Proteome Map
InterPro Ig-like_dom UniProtKB/Swiss-Prot
  Ig-like_dom_sf UniProtKB/Swiss-Prot
  Ig-like_fold UniProtKB/Swiss-Prot
  Ig_V-set UniProtKB/Swiss-Prot
NCBI Gene TRAV25 ENTREZGENE
PANTHER T CELL RECEPTOR ALPHA VARIABLE 22 UniProtKB/Swiss-Prot
  T CELL RECEPTOR ALPHA VARIABLE 39 UniProtKB/Swiss-Prot
Pfam V-set UniProtKB/Swiss-Prot
PharmGKB PA36804 PharmGKB
PROSITE IG_LIKE UniProtKB/Swiss-Prot
SMART IGv UniProtKB/Swiss-Prot
Superfamily-SCOP SSF48726 UniProtKB/Swiss-Prot
UniProt A0A0B4J276 ENTREZGENE, UniProtKB/Swiss-Prot