Traj39 Gene Detail

Summary

• Symbol
  Traj39
• Name
  T cell receptor alpha joining 39
• Synonyms
  Gm16669

• Feature Type
  gene segment
• IDs
  MGI:4439593
  NCBI Gene: 100124349
• Alliance
  gene page
• Transcription Start Sites
  3 TSS

Location &
Maps

• Sequence Map
  Chr14:54417419-54417481 bp, + strand

  From NCBI annotation of GRCm39
  

• View this region in JBrowse
  

• Genome Browsers
  Ensembl | UCSC | NCBI

• Genetic Map
  Chromosome 14, 27.68 cM
• Mapping Data
  1 experiment

Strain
Comparison

• SNPs within 2kb
  44 from dbSNP Build 142
• Strain Annotations
  18

Strain	Gene Model ID	Feature Type	Coordinates
C57BL/6J	MGI_C57BL6J_4439593	gene segment	Chr14:54417419-54417481 (+)
129S1/SvImJ	MGP_129S1SvImJ_G0002452	gene segment	Chr14:48108364-48108426 (+)
A/J	MGP_AJ_G0002426	gene segment	Chr14:47200253-47200315 (+)
AKR/J	MGP_AKRJ_G0002412	gene segment	Chr14:48907678-48907740 (+)
BALB/cJ	MGP_BALBcJ_G0002420	gene segment	Chr14:47168675-47168737 (+)
C3H/HeJ	MGP_C3HHeJ_G0002399	gene segment	Chr14:48589754-48589816 (+)
C57BL/6NJ	MGP_C57BL6NJ_G0002547	gene segment	Chr14:50573823-50573885 (+)
CAROLI/EiJ	MGP_CAROLIEiJ_G0002146	gene segment	Chr14:45613033-45613095 (+)
CAST/EiJ	MGP_CASTEiJ_G0002361	gene segment	Chr14:44821450-44821512 (+)
CBA/J	MGP_CBAJ_G0002390	gene segment	Chr14:52064449-52064511 (+)
DBA/2J	MGP_DBA2J_G0002395	gene segment	Chr14:46944000-46944062 (+)
FVB/NJ	MGP_FVBNJ_G0002409	gene segment	Chr14:46398755-46398817 (+)
LP/J	MGP_LPJ_G0002449	gene segment	Chr14:49133407-49133469 (+)
NOD/ShiLtJ	MGP_NODShiLtJ_G0002379	gene segment	Chr14:51508593-51508655 (+)
NZO/HlLtJ	MGP_NZOHlLtJ_G0002542	gene segment	Chr14:48091025-48091087 (+)
PWK/PhJ	MGP_PWKPhJ_G0002322	gene segment	Chr14:43467494-43467556 (+)
SPRET/EiJ	MGP_SPRETEiJ_G0002274	gene segment	Chr14:44066572-44066634 (+)
WSB/EiJ	MGP_WSBEiJ_G0002388	gene segment	Chr14:48380927-48380989 (+)

Homology

• Human Ortholog
  TRAJ39, T cell receptor alpha joining 39

• Vertebrate Orthologs
  1

Vertebrate Orthology Source

Alliance of Genome Resources

• Human Ortholog
  TRAJ39, T cell receptor alpha joining 39
  
• Links
  HGNC:12069

  NCBI Gene ID: 28716

  
  
• Chr Location
  14q11.2; chr14:22501601-22501663 (+)  GRCh38

---

• MGI Vertebrate Homology
  Traj39 stringent orthology
  1 human;1 mouse
  
• HCOP
  vertebrate homology predictions: TRAJ39
• Gene Tree
  Traj39
  

Mutations,
Alleles, and
Phenotypes

• Phenotype Summary
  2 phenotype references
  

• All Mutations and Alleles
  3
• Targeted
  3
• Genomic Mutations
  3 involving Traj39
• Find Mice (IMSR)
  1 strains or lines available

Expression

• Assay Results
  706

Tissue x Stage Matrix

• Other Mouse Links
  Expression Atlas

Sequences &
Gene Models

• All Sequences
  24
• RefSeq
  1
• UniProt
  1

• Ensembl
  ENSMUSG00000076891 (Evidence)
• NCBI Gene
  100124349

Representative Sequences			Length	Strain/Species
genomic	100124349	NCBI Gene Model | MGI Sequence Detail	63	C57BL/6J
polypeptide	A0A0G2JDX5	UniProt | EBI | MGI Sequence Detail	21	Not Applicable

Protein
Information

• UniProt
  1 Sequence

References

• Summaries
  All 7

  Phenotypes 2
• Earliest
  J:82395 Bassing CH, et al., T cell receptor (TCR) alpha/delta locus enhancer identity and position are critical for the assembly of TCR delta and alpha variable region genes. Proc Natl Acad Sci U S A. 2003 Mar 4;100(5):2598-603
• Latest
  J:164272 Giudicelli V, et al., IMGT/GENE-DB: a comprehensive database for human and mouse immunoglobulin and T cell receptor genes. Nucleic Acids Res. 2005 Jan 1;33(Database issue):D256-61

TSS for Traj39:

(View these features in JBrowse)

Transcription Start Site	Location	Distance from Gene 5'-end
Tssr125571	Chr14:54416981-54416987 (+)	-435 bp
Tssr125572	Chr14:54417104-54417117 (+)	-308 bp
Tssr125573	Chr14:54417169-54417179 (+)	-245 bp