TRBV25-1 (T cell receptor beta variable 25-1) - 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: TRBV25-1 (T cell receptor beta variable 25-1) Homo sapiens
Analyze
Symbol: TRBV25-1
Name: T cell receptor beta variable 25-1
RGD ID: 1347072
HGNC Page HGNC:12205
Description: Predicted to be involved in cell surface receptor signaling pathway. Predicted to be located in membrane. Predicted to be part of T cell receptor complex. Predicted to be active in plasma membrane.
Type: gene (Ensembl: TR_V_gene)
RefSeq Status: VALIDATED
Previously known as: TCRBV11S1A1T; TCRBV25S1; TRBV251
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
GRCh387142,670,777 - 142,671,244 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl7142,670,740 - 142,671,244 (+)EnsemblGRCh38hg38GRCh38
GRCh377142,378,609 - 142,379,076 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 367142,058,172 - 142,058,639 (+)NCBINCBI36Build 36hg18NCBI36
Celera7137,185,360 - 137,185,827 (+)NCBICelera
Cytogenetic Map7q34NCBI
HuRef7136,707,094 - 136,707,561 (+)NCBIHuRef
CHM1_17142,304,749 - 142,305,216 (+)NCBICHM1_1
T2T-CHM13v2.07144,026,470 - 144,026,937 (+)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:8650574   PMID:21873635  


Genomics


Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
GRCh38/hg38 7q34-35(chr7:141126407-145652221)x3 copy number gain See cases [RCV000133645] Chr7:141126407..145652221 [GRCh38]
Chr7:140826207..145349314 [GRCh37]
Chr7:140472676..144980247 [NCBI36]
Chr7:7q34-35		 pathogenic
GRCh38/hg38 7p22.3-q36.3(chr7:54185-159282390)x1 copy number loss See cases [RCV000135401] Chr7:54185..159282390 [GRCh38]
Chr7:54185..159075079 [GRCh37]
Chr7:149268..158767840 [NCBI36]
Chr7:7p22.3-q36.3		 pathogenic
GRCh38/hg38 7q34(chr7:142620494-142732123)x1 copy number loss See cases [RCV000135131] Chr7:142620494..142732123 [GRCh38]
Chr7:142328008..142455543 [GRCh37]
Chr7:142009000..142135117 [NCBI36]
Chr7:7q34		 benign
GRCh38/hg38 7q33-36.2(chr7:137751200-154815582)x3 copy number gain See cases [RCV000136592] Chr7:137751200..154815582 [GRCh38]
Chr7:137435946..154607292 [GRCh37]
Chr7:137086486..154238225 [NCBI36]
Chr7:7q33-36.2		 pathogenic
GRCh38/hg38 7q21.3-36.3(chr7:97419852-158923762)x3 copy number gain See cases [RCV000136717] Chr7:97419852..158923762 [GRCh38]
Chr7:97049164..158716453 [GRCh37]
Chr7:96887100..158409214 [NCBI36]
Chr7:7q21.3-36.3		 pathogenic
GRCh38/hg38 7q34(chr7:142237788-142779344)x3 copy number gain See cases [RCV000137716] Chr7:142237788..142779344 [GRCh38]
Chr7:141584064..142187156 [NCBI36]
Chr7:7q34		 likely benign
GRCh38/hg38 7q34-36.3(chr7:141960861-159335866)x1 copy number loss See cases [RCV000137256] Chr7:141960861..159335866 [GRCh38]
Chr7:142528609..159128556 [GRCh37]
Chr7:141307130..158821317 [NCBI36]
Chr7:7q34-36.3		 pathogenic
GRCh38/hg38 7q33-36.3(chr7:134666829-158591882)x1 copy number loss See cases [RCV000138120] Chr7:134666829..158591882 [GRCh38]
Chr7:134351581..158384574 [GRCh37]
Chr7:134002121..158077335 [NCBI36]
Chr7:7q33-36.3		 pathogenic
GRCh38/hg38 7q34(chr7:142620632-142753000)x1 copy number loss See cases [RCV000138687] Chr7:142620632..142753000 [GRCh38]
Chr7:142009138..142140425 [NCBI36]
Chr7:7q34		 likely benign
GRCh38/hg38 7q31.32-36.3(chr7:121863759-159335865)x3 copy number gain See cases [RCV000138847] Chr7:121863759..159335865 [GRCh38]
Chr7:121503813..159128555 [GRCh37]
Chr7:121291049..158821316 [NCBI36]
Chr7:7q31.32-36.3		 pathogenic
GRCh38/hg38 7q34(chr7:142578930-142753745)x1 copy number loss See cases [RCV000138582] Chr7:142578930..142753745 [GRCh38]
Chr7:141967536..142141170 [NCBI36]
Chr7:7q34		 likely benign
GRCh38/hg38 7q34(chr7:142503036-142753076)x1 copy number loss See cases [RCV000139181] Chr7:142503036..142753076 [GRCh38]
Chr7:141871507..142140501 [NCBI36]
Chr7:7q34		 likely benign
GRCh38/hg38 7q33-36.1(chr7:135017687-148807400)x1 copy number loss See cases [RCV000138903] Chr7:135017687..148807400 [GRCh38]
Chr7:134702438..148504492 [GRCh37]
Chr7:134352978..148135425 [NCBI36]
Chr7:7q33-36.1		 pathogenic
GRCh38/hg38 7q34(chr7:142578930-142752607)x3 copy number gain See cases [RCV000139475] Chr7:142578930..142752607 [GRCh38]
Chr7:141967536..142140032 [NCBI36]
Chr7:7q34		 likely benign
GRCh38/hg38 7q32.3-36.3(chr7:132444095-159335866)x3 copy number gain See cases [RCV000139654] Chr7:132444095..159335866 [GRCh38]
Chr7:132128854..159128556 [GRCh37]
Chr7:131779394..158821317 [NCBI36]
Chr7:7q32.3-36.3		 pathogenic
GRCh38/hg38 7q34(chr7:142620632-142753076)x1 copy number loss See cases [RCV000139708] Chr7:142620632..142753076 [GRCh38]
Chr7:142009138..142140501 [NCBI36]
Chr7:7q34		 likely benign
GRCh38/hg38 7q31.2-36.3(chr7:115459015-159325817)x3 copy number gain See cases [RCV000141413] Chr7:115459015..159325817 [GRCh38]
Chr7:115099069..159118507 [GRCh37]
Chr7:114886305..158811268 [NCBI36]
Chr7:7q31.2-36.3		 pathogenic
GRCh38/hg38 7q34(chr7:142503036-142753745)x1 copy number loss See cases [RCV000142812] Chr7:142503036..142753745 [GRCh38]
Chr7:141871507..142141170 [NCBI36]
Chr7:7q34		 likely benign
GRCh38/hg38 7q32.3-36.3(chr7:131228764-159335866)x3 copy number gain See cases [RCV000142802] Chr7:131228764..159335866 [GRCh38]
Chr7:130913523..159128556 [GRCh37]
Chr7:130564063..158821317 [NCBI36]
Chr7:7q32.3-36.3		 pathogenic
GRCh38/hg38 7q32.3-36.3(chr7:131171478-159327017)x3 copy number gain See cases [RCV000143754] Chr7:131171478..159327017 [GRCh38]
Chr7:130856237..159119707 [GRCh37]
Chr7:130506777..158812468 [NCBI36]
Chr7:7q32.3-36.3		 pathogenic
GRCh38/hg38 7q34-35(chr7:140061285-144622893)x3 copy number gain See cases [RCV000143724] Chr7:140061285..144622893 [GRCh38]
Chr7:139761085..144319986 [GRCh37]
Chr7:139407554..143950919 [NCBI36]
Chr7:7q34-35		 uncertain significance
GRCh37/hg19 7q34(chr7:141937588-142486548)x3 copy number gain See cases [RCV000143759] Chr7:141937588..142486548 [GRCh37]
Chr7:141584062..142186550 [NCBI36]
Chr7:7q34		 uncertain significance
GRCh38/hg38 7q32.3-36.3(chr7:132438072-159327017)x3 copy number gain See cases [RCV000143707] Chr7:132438072..159327017 [GRCh38]
Chr7:132122831..159119707 [GRCh37]
Chr7:131773371..158812468 [NCBI36]
Chr7:7q32.3-36.3		 pathogenic
GRCh38/hg38 7q32.1-36.3(chr7:129310166-159282390)x3 copy number gain See cases [RCV000050876] Chr7:129310166..159282390 [GRCh38]
Chr7:128950007..159075079 [GRCh37]
Chr7:128737243..158767840 [NCBI36]
Chr7:7q32.1-36.3		 pathogenic
GRCh38/hg38 7q34-35(chr7:142578948-144254897)x1 copy number loss See cases [RCV000050639] Chr7:142578948..144254897 [GRCh38]
Chr7:142528609..143951990 [GRCh37]
Chr7:141967554..143582923 [NCBI36]
Chr7:7q34-35		 pathogenic
GRCh38/hg38 7q32.3-36.3(chr7:132850196-159325876)x3 copy number gain See cases [RCV000051101] Chr7:132850196..159325876 [GRCh38]
Chr7:132534956..159118566 [GRCh37]
Chr7:132185496..158811327 [NCBI36]
Chr7:7q32.3-36.3		 pathogenic
GRCh38/hg38 7p22.3-q36.3(chr7:53985-159282531)x1 copy number loss See cases [RCV000052250] Chr7:53985..159282531 [GRCh38]
Chr7:53985..159075220 [GRCh37]
Chr7:149068..158767981 [NCBI36]
Chr7:7p22.3-q36.3		 pathogenic
GRCh38/hg38 7q33-36.3(chr7:136309982-159307523)x3 copy number gain See cases [RCV000053576] Chr7:136309982..159307523 [GRCh38]
Chr7:135994730..159100212 [GRCh37]
Chr7:135645270..158792973 [NCBI36]
Chr7:7q33-36.3		 pathogenic
GRCh38/hg38 7q34-36.3(chr7:142021716-159325876)x3 copy number gain Developmental Delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000053577]|Developmental delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000053577]|See cases [RCV000053577] Chr7:142021716..159325876 [GRCh38]
Chr7:142528609..159118566 [GRCh37]
Chr7:141367985..158811327 [NCBI36]
Chr7:7q34-36.3		 pathogenic
GRCh38/hg38 7q32.3-36.1(chr7:132023155-149309794)x1 copy number loss Developmental Delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000054172]|Developmental delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000054172]|See cases [RCV000054172] Chr7:132023155..149309794 [GRCh38]
Chr7:131707914..149006885 [GRCh37]
Chr7:131358454..148637818 [NCBI36]
Chr7:7q32.3-36.1		 pathogenic
GRCh38/hg38 7q33-35(chr7:135414108-144140219)x1 copy number loss See cases [RCV000054173] Chr7:135414108..144140219 [GRCh38]
Chr7:135098857..143837312 [GRCh37]
Chr7:134749397..143468245 [NCBI36]
Chr7:7q33-35		 pathogenic
GRCh38/hg38 7q34-36.3(chr7:139365967-159282531)x1 copy number loss Developmental Delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000054175]|Developmental delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000054175]|See cases [RCV000054175] Chr7:139365967..159282531 [GRCh38]
Chr7:139050713..159075220 [GRCh37]
Chr7:138701253..158767981 [NCBI36]
Chr7:7q34-36.3		 pathogenic
GRCh38/hg38 7q34-36.3(chr7:140754198-159307523)x1 copy number loss See cases [RCV000054176] Chr7:140754198..159307523 [GRCh38]
Chr7:140453998..159100212 [GRCh37]
Chr7:140100467..158792973 [NCBI36]
Chr7:7q34-36.3		 pathogenic
GRCh38/hg38 7q34-36.3(chr7:142358524-159282531)x1 copy number loss See cases [RCV000054177] Chr7:142358524..159282531 [GRCh38]
Chr7:142528609..159075220 [GRCh37]
Chr7:141726947..158767981 [NCBI36]
Chr7:7q34-36.3		 pathogenic
GRCh38/hg38 7q34-36.3(chr7:138620939-159233475)x3 copy number gain Neurodevelopmental disorder [RCV003327610] Chr7:138620939..159233475 [GRCh38]
Chr7:7q34-36.3		 likely pathogenic
GRCh38/hg38 7q33-36.3(chr7:137463392-159345973)x3 copy number gain Neurodevelopmental disorder [RCV003327609] Chr7:137463392..159345973 [GRCh38]
Chr7:7q33-36.3		 pathogenic
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:193
Count of miRNA genes:169
Interacting mature miRNAs:172
Transcripts:ENST00000390398
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.

Markers in Region
TCRB  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh377142,378,624 - 142,379,001UniSTSGRCh37
Build 367142,058,187 - 142,058,564RGDNCBI36
Celera7137,185,375 - 137,185,752RGD
Cytogenetic Map7q34UniSTS
HuRef7136,707,109 - 136,707,486UniSTS
CRA_TCAGchr7v27141,749,917 - 141,750,294UniSTS


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
High
Medium 42 42 1
Low 182 638 134 14 857 7 714 294 733 9 287 276 7 143 654
Below cutoff 517 533 426 128 214 65 1063 457 978 27 294 414 63 431 709

Sequence


Reference Sequences
RefSeq Acc Id: ENST00000390398   ⟹   ENSP00000374921
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl7142,670,740 - 142,671,244 (+)Ensembl
Protein Sequences
GenBank Protein A0A075B6N4 (Get FASTA)   NCBI Sequence Viewer  
  AAA51031 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSP00000374921.3
  ENSP00000479511.2
Reference Protein Sequences
RefSeq Acc Id: ENSP00000374921   ⟸   ENST00000390398
Protein Domains
Ig-like

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-A0A075B6N4-F1-model_v2 AlphaFold A0A075B6N4 1-114 view protein structure


Additional Information

Database Acc Id Source(s)
COSMIC TRBV25-1 COSMIC
Ensembl Genes ENSG00000281963 UniProtKB/TrEMBL
  ENSG00000282499 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENST00000390398.3 UniProtKB/Swiss-Prot
  ENST00000610439.4 UniProtKB/TrEMBL
Gene3D-CATH 2.60.40.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
GTEx ENSG00000281963 GTEx
  ENSG00000282499 GTEx
HGNC ID HGNC:12205 ENTREZGENE
Human Proteome Map TRBV25-1 Human Proteome Map
InterPro Ig-like_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Ig-like_dom_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Ig-like_fold UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Ig_V-set UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
NCBI Gene TRBV25-1 ENTREZGENE
PANTHER T CELL RECEPTOR BETA CHAIN MC.7.G5-RELATED UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  T-CELL RECEPTOR BETA CHAIN UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam V-set UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PharmGKB PA36885 PharmGKB
PROSITE IG_LIKE UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF48726 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A0A075B6N4 ENTREZGENE
  A0A5C2_HUMAN UniProtKB/TrEMBL
  TVBY1_HUMAN UniProtKB/Swiss-Prot
UniProt Secondary A0A0G2JML5 UniProtKB/TrEMBL