TRBV5-4 (T cell receptor beta variable 5-4) - Rat Genome Database

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Pathways
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Gene: TRBV5-4 (T cell receptor beta variable 5-4) Homo sapiens
Analyze
No known orthologs.
Symbol: TRBV5-4
Name: T cell receptor beta variable 5-4
RGD ID: 1345174
HGNC Page HGNC:12221
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: TCRBV5S4; TCRBV5S6A3N2T; TRBV54
RGD Orthologs
Alliance Orthologs
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
GRCh387142,463,117 - 142,463,581 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl7142,462,916 - 142,463,581 (+)EnsemblGRCh38hg38GRCh38
GRCh377142,168,380 - 142,168,844 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 367141,831,583 - 141,832,047 (+)NCBINCBI36Build 36hg18NCBI36
Celera7136,962,061 - 136,962,525 (+)NCBICelera
Cytogenetic Map7q34NCBI
HuRef7136,479,190 - 136,479,654 (+)NCBIHuRef
CHM1_17142,097,089 - 142,097,553 (+)NCBICHM1_1
T2T-CHM13v2.07143,799,854 - 143,800,318 (+)NCBIT2T-CHM13v2.0
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

Biological Process

Cellular Component

References

References - curated
# Reference Title Reference Citation
1. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
2. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:8020962   PMID:8650574   PMID:12477932   PMID:21873635  


Genomics

Variants

.
Variants in TRBV5-4
1 total Variants

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
NC_000007.14:g.142463468G>A single nucleotide variant Malignant melanoma [RCV000067693] Chr7:142463468 [GRCh38]
Chr7:142168493 [GRCh37]
Chr7:141831934 [NCBI36]
Chr7:7q34		 not provided
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 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(chr7:142355688-142553299)x1 copy number loss See cases [RCV000136726] Chr7:142355688..142553299 [GRCh38]
Chr7:141723794..141941891 [NCBI36]
Chr7:7q34		 benign
GRCh38/hg38 7q34(chr7:142355688-142605368)x1 copy number loss See cases [RCV000136743] Chr7:142355688..142605368 [GRCh38]
Chr7:141723794..141993871 [NCBI36]
Chr7:7q34		 benign
GRCh38/hg38 7q34(chr7:142416934-142605368)x1 copy number loss See cases [RCV000136745] Chr7:142416934..142605368 [GRCh38]
Chr7:141785397..141993871 [NCBI36]
Chr7:7q34		 benign
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 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 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 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 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 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 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 7q33-36.3(chr7:137463392-159345973)x3 copy number gain Neurodevelopmental disorder [RCV003327609] Chr7:137463392..159345973 [GRCh38]
Chr7:7q33-36.3		 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
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:258
Count of miRNA genes:247
Interacting mature miRNAs:258
Transcripts:ENST00000454561
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.

Markers in Region
SHGC-35337  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh377142,500,212 - 142,500,420UniSTSGRCh37
Cytogenetic Map7q34UniSTS
HuRef7136,838,519 - 136,838,727UniSTS
TNG Radiation Hybrid Map764382.0UniSTS
GeneMap99-GB4 RH Map7653.5UniSTS
Whitehead-RH Map7628.5UniSTS
GeneMap99-G3 RH Map75993.0UniSTS


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 9 97 8 2 153 2 27 6
Low 328 718 296 92 1104 83 258 22 108 110 221 550 9 218 109 1
Below cutoff 831 747 690 259 177 165 1675 430 1443 151 664 608 95 601 932

Sequence


Reference Sequences
RefSeq Acc Id: ENST00000454561   ⟹   ENSP00000413966
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl7142,462,916 - 142,463,581 (+)Ensembl
Protein Sequences
GenBank Protein A0A0C4DH59 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSP00000413966.2
  ENSP00000488374.1
Reference Protein Sequences
RefSeq Acc Id: ENSP00000413966   ⟸   ENST00000454561
Protein Domains
Ig-like

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-A0A0C4DH59-F1-model_v2 AlphaFold A0A0C4DH59 1-114 view protein structure


Additional Information

Database Acc Id Source(s)
COSMIC TRBV5-4 COSMIC
Ensembl Genes ENSG00000230099 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
  ENSG00000282466 UniProtKB/TrEMBL
Ensembl Transcript ENST00000454561.2 UniProtKB/Swiss-Prot
  ENST00000633696.1 UniProtKB/TrEMBL
Gene3D-CATH 2.60.40.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
GTEx ENSG00000230099 GTEx
  ENSG00000282466 GTEx
HGNC ID HGNC:12221 ENTREZGENE
Human Proteome Map TRBV5-4 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 TRBV5-4 ENTREZGENE
PANTHER T CELL RECEPTOR BETA VARIABLE 5-4 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  T-CELL RECEPTOR BETA CHAIN UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam V-set UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PharmGKB PA36901 PharmGKB
PROSITE IG_LIKE UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
SMART IGv UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF48726 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A0A0C4DH59 ENTREZGENE
  A0A0J9YXE9_HUMAN UniProtKB/TrEMBL
  TVB54_HUMAN UniProtKB/Swiss-Prot