TRAJ25 (T cell receptor alpha joining 25 (non-functional)) - Rat Genome Database

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Gene: TRAJ25 (T cell receptor alpha joining 25 (non-functional)) Homo sapiens
Analyze
Symbol: TRAJ25
Name: T cell receptor alpha joining 25 (non-functional)
RGD ID: 1346970
HGNC Page HGNC:12054
Description: T cell receptors recognize foreign antigens which have been processed as small peptides and bound to major histocompatibility complex (MHC) molecules at the surface of antigen presenting cells (APC). Each T cell receptor is a dimer consisting of one alpha and one beta chain or one delta and one gamma chain. In a single cell, the T cell receptor loci are rearranged and expressed in the order delta, gamma, beta, and alpha. If both delta and gamma rearrangements produce functional chains, the cell expresses delta and gamma. If not, the cell proceeds to rearrange the beta and alpha loci. This region represents the germline organization of the T cell receptor alpha and delta loci. Both the alpha and delta loci include V (variable), J (joining), and C (constant) segments and the delta locus also includes diversity (D) segments. The delta locus is situated within the alpha locus, between the alpha V and J segments. During T cell development, the delta chain is synthesized by a recombination event at the DNA level joining a D segment with a J segment; a V segment is then joined to the D-J gene. The alpha chain is synthesized by recombination joining a single V segment with a J segment. For both chains, the C segment is later joined by splicing at the RNA level. Recombination of many different V segments with several J segments provides a wide range of antigen recognition. Additional diversity is attained by junctional diversity, resulting from the random additional of nucleotides by terminal deoxynucleotidyltransferase. Five variable segments can be used in either alpha or delta chains and are described by TRAV/DV symbols. Several V and J segments of the alpha locus are known to be incapable of encoding a protein and are considered pseudogenes. [provided by RefSeq, Aug 2016]
Type: gene (Ensembl: TR_J_gene)
RefSeq Status: REVIEWED
Previously known as: T cell receptor alpha joining 25
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
GRCh381422,518,812 - 22,518,871 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1422,518,812 - 22,518,871 (+)EnsemblGRCh38hg38GRCh38
GRCh371422,987,790 - 22,987,849 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361422,057,630 - 22,057,689 (+)NCBINCBI36Build 36hg18NCBI36
Celera142,850,773 - 2,850,832 (+)NCBICelera
Cytogenetic Map14q11.2NCBI
HuRef143,105,981 - 3,106,040 (+)NCBIHuRef
CHM1_11422,986,714 - 22,986,773 (+)NCBICHM1_1
T2T-CHM13v2.01416,716,563 - 16,716,622 (+)NCBIT2T-CHM13v2.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


References
Additional References at PubMed
PMID:2993909   PMID:8188290  


Genomics


Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
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 14q11.2-12(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(chr14:21010790-22951814)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 14q11.2-32.33(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(chr14:20151149-23442195)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:201
Count of miRNA genes:191
Interacting mature miRNAs:198
Transcripts:ENST00000390512
Prediction methods: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.


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 6 4 17 1
Low 26 7 22 15 169 15 17 16 6 19 19 19 1 4 10
Below cutoff 2 5 1 8 5 11 2 1 1 1 5

Sequence


Reference Sequences
RefSeq Acc Id: ENST00000390512   ⟹   ENSP00000452115
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1422,518,812 - 22,518,871 (+)Ensembl
Protein Sequences
GenBank Protein AAB86771 (Get FASTA)   NCBI Sequence Viewer  
  EAW66279 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSP00000452115.1
Reference Protein Sequences
RefSeq Acc Id: ENSP00000452115   ⟸   ENST00000390512


Additional Information

Database Acc Id Source(s)
COSMIC TRAJ25 COSMIC
Ensembl Genes ENSG00000211864 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENST00000390512.2 UniProtKB/TrEMBL
GTEx ENSG00000211864 GTEx
HGNC ID HGNC:12054 ENTREZGENE
Human Proteome Map TRAJ25 Human Proteome Map
NCBI Gene TRAJ25 ENTREZGENE
PharmGKB PA36731 PharmGKB
UniProt A0A075B6Z8_HUMAN UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-04-12 TRAJ25  T cell receptor alpha joining 25 (non-functional)    T cell receptor alpha joining 25  Symbol and/or name change 5135510 APPROVED