Trim42 Gene Detail

Summary

• Symbol
  Trim42
• Name
  tripartite motif-containing 42
• Synonyms
  4930486B16Rik

• Feature Type
  protein coding gene
• IDs
  MGI:1926161
  NCBI Gene: 78911
• Alliance
  gene page
• Transcription Start Sites
  1 TSS

Location &
Maps

• Sequence Map
  Chr9:97231615-97252011 bp, - strand

  From NCBI annotation of GRCm39
  

• View this region in JBrowse
  

• Genome Browsers
  Ensembl | UCSC | NCBI

• Genetic Map
  Chromosome 9, 51.06 cM, cytoband E4
• Mapping Data
  2 experiments

Strain
Comparison

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

Strain	Gene Model ID	Feature Type	Coordinates
C57BL/6J	MGI_C57BL6J_1926161	protein coding gene	Chr9:97231615-97252011 (-)
129S1/SvImJ	MGP_129S1SvImJ_G0035150	protein coding gene	Chr9:98604650-98626553 (-)
A/J	MGP_AJ_G0035132	protein coding gene	Chr9:95152766-95172864 (-)
AKR/J	MGP_AKRJ_G0035063	protein coding gene	Chr9:97451373-97471450 (-)
BALB/cJ	MGP_BALBcJ_G0035124	protein coding gene	Chr9:94830394-94851295 (-)
C3H/HeJ	MGP_C3HHeJ_G0034834	protein coding gene	Chr9:97873034-97900661 (-)
C57BL/6NJ	MGP_C57BL6NJ_G0035644	protein coding gene	Chr9:101419713-101443555 (-)
CAROLI/EiJ	MGP_CAROLIEiJ_G0032544	protein coding gene	Chr9:92948015-92968840 (-)
CAST/EiJ	MGP_CASTEiJ_G0034146	protein coding gene	Chr9:97662959-97683430 (-)
CBA/J	MGP_CBAJ_G0034802	protein coding gene	Chr9:104950144-104970627 (-)
DBA/2J	MGP_DBA2J_G0034964	protein coding gene	Chr9:94663370-94684147 (-)
FVB/NJ	MGP_FVBNJ_G0034912	protein coding gene	Chr9:93500092-93523263 (-)
LP/J	MGP_LPJ_G0035043	protein coding gene	Chr9:98866565-98893710 (-)
NOD/ShiLtJ	MGP_NODShiLtJ_G0034951	protein coding gene	Chr9:106915337-106938110 (-)
NZO/HlLtJ	MGP_NZOHlLtJ_G0035666	protein coding gene	Chr9:97704590-97731109 (-)
PWK/PhJ	MGP_PWKPhJ_G0033853	protein coding gene	Chr9:94855811-94877514 (-)
SPRET/EiJ	MGP_SPRETEiJ_G0033688	protein coding gene	Chr9:97746142-97770803 (-)
WSB/EiJ	MGP_WSBEiJ_G0034266	protein coding gene	Chr9:97567776-97589207 (-)

Homology

• Human Ortholog
  TRIM42, tripartite motif containing 42

• Vertebrate Orthologs
  2

Vertebrate Orthology Source

Alliance of Genome Resources

• Human Ortholog
  TRIM42, tripartite motif containing 42
  
• Synonyms
  PPP1R40, T4A1
• Links
  HGNC:19014

  NCBI Gene ID: 287015

  neXtProt AC: NX_Q8IWZ5

  UniProt: Q8IWZ5

  
  
• Chr Location
  3q23; chr3:140678064-140701150 (+)  GRCh38

---

• MGI Vertebrate Homology
  Trim42 stringent orthology
  1 human;1 mouse;1 rat
  
• HCOP
  vertebrate homology predictions: TRIM42
• Gene Tree
  Trim42
  

Mutations,
Alleles, and
Phenotypes

• Phenotype Summary
  7 phenotype references
  

• All Mutations and Alleles
  7
• Chemically induced (other)
  1
• Endonuclease-mediated
  2
• Gene trapped
  1
• Targeted
  3
• Genomic Mutations
  1 involving Trim42
• Incidental Mutations
  Mutagenetix , APF , CvDC
• Find Mice (IMSR)
  35 strains or lines available

Gene Ontology
(GO)
Classifications

• All GO Annotations
  1
• GO References
  1

Expression

• Assay Results
  730
• Tissues
  15
• cDNA Data
  6
• Literature Summary
  1

Images

Tissue x Stage Matrix

• Other Mouse Links
  Allen Institute
  GEO
  Expression Atlas

Sequences &
Gene Models

• All Sequences
  29
• RefSeq
  2
• UniProt
  2
• CCDS
  CCDS23422.1

• Ensembl
  ENSMUSG00000032451 (Evidence)
• NCBI Gene
  78911

Representative Sequences			Length	Strain/Species
genomic	78911	NCBI Gene Model | MGI Sequence Detail	20397	C57BL/6J
transcript	NM_030219	RefSeq | MGI Sequence Detail	2465	C57BL/6
polypeptide	Q9D2H5	UniProt | EBI | MGI Sequence Detail	723	Not Applicable

Protein
Information

• UniProt
  2 Sequences
• Protein Ontology
  PR:000030748 tripartite motif-containing protein 42
  (term hierarchy)
• InterPro Domains
  IPR000315 B-box-type zinc finger
  IPR017903 COS domain
  IPR051051 E3 ubiquitin-protein ligase TRIM/RNF
  IPR003961 Fibronectin type III
  IPR036116 Fibronectin type III superfamily
  IPR013783 Immunoglobulin-like fold
  IPR042765 TRIM42, RING-HC finger
  IPR001841 Zinc finger, RING-type
  IPR017907 Zinc finger, RING-type, conserved site

Molecular
Reagents

• All nucleic 6

  cDNA 6

  
  

  Microarray probesets 2

References

• Summaries
  All 25

  Developmental Gene Expression 1

  Gene Ontology 1

  Phenotypes 7
• Earliest
  J:65060 Kawai J, et al., Functional annotation of a full-length mouse cDNA collection. Nature. 2001 Feb 8;409(6821):685-90
• Latest
  J:173534 Skarnes WC, et al., A conditional knockout resource for the genome-wide study of mouse gene function. Nature. 2011 Jun 16;474(7351):337-42

TSS for Trim42:

(View these features in JBrowse)

Transcription Start Site	Location	Distance from Gene 5'-end
Tssr91023	Chr9:97252053-97252074 (-)	-53 bp