Tmem39b Gene Detail

Summary

• Symbol
  Tmem39b
• Name
  transmembrane protein 39b
• Synonyms
  6330509E05Rik, MGC:59407

• Feature Type
  protein coding gene
• IDs
  MGI:2682939
  NCBI Gene: 230770
• Alliance
  gene page
• Transcription Start Sites
  5 TSS

Location &
Maps

• Sequence Map
  Chr4:129676355-129696838 bp, - strand
• From Ensembl annotation of GRCm38
  

  View this region in JBrowse
  
  

• Genome Browsers
  Ensembl | UCSC | NCBI

• Genetic Map
  Chromosome 4, 63.31 cM, cytoband D2.3
• Mapping Data
  2 experiments

Strain
Comparison

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

Strain	Gene Model ID	Feature Type	Coordinates
C57BL/6J	MGI_C57BL6J_2682939	protein coding gene	Chr4:129676355-129696846 (-)
129S1/SvImJ	MGP_129S1SvImJ_G0028837	protein coding gene	Chr4:131618547-131640030 (-)
A/J	MGP_AJ_G0028796	protein coding gene	Chr4:126356841-126378048 (-)
AKR/J	MGP_AKRJ_G0028749	protein coding gene	Chr4:129880797-129902955 (-)
BALB/cJ	MGP_BALBcJ_G0028819	protein coding gene	Chr4:126963310-126983996 (-)
C3H/HeJ	MGP_C3HHeJ_G0028533	protein coding gene	Chr4:129942755-129963445 (-)
C57BL/6NJ	MGP_C57BL6NJ_G0029261	protein coding gene	Chr4:136561669-136591511 (-)
CAROLI/EiJ	MGP_CAROLIEiJ_G0026533	protein coding gene	Chr4:119486909-119508926 (-)
CAST/EiJ	MGP_CASTEiJ_G0027965	protein coding gene	Chr4:128122648-128148210 (-)
CBA/J	MGP_CBAJ_G0028499	protein coding gene	Chr4:139984999-140012712 (-)
DBA/2J	MGP_DBA2J_G0028648	protein coding gene	Chr4:126792253-126812329 (-)
FVB/NJ	MGP_FVBNJ_G0028615	protein coding gene	Chr4:125549008-125569186 (-)
LP/J	MGP_LPJ_G0028749	protein coding gene	Chr4:131923395-131952200 (-)
NOD/ShiLtJ	MGP_NODShiLtJ_G0028641	protein coding gene	Chr4:144762775-144787237 (-)
NZO/HlLtJ	MGP_NZOHlLtJ_G0029299	protein coding gene	Chr4:130249445-130272307 (-)
PWK/PhJ	MGP_PWKPhJ_G0027687	protein coding gene	Chr4:123392637-123413456 (-)
SPRET/EiJ	MGP_SPRETEiJ_G0027513	protein coding gene	Chr4:126118832-126140697 (-)
WSB/EiJ	MGP_WSBEiJ_G0028046	protein coding gene	Chr4:130377564-130400041 (-)

Homology

• Human Ortholog
  TMEM39B, transmembrane protein 39B

• Vertebrate Orthologs
  10

• Human Ortholog
  TMEM39B, transmembrane protein 39B
  Orthology source: HomoloGene, HGNC
• Links
  HGNC:25510

  NCBI Gene ID: 55116

  neXtProt AC: NX_Q9GZU3

  UniProt: Q9GZU3

  
  
• Chr Location
  1p35.2; chr1:32072031-32102866 (+)  GRCh38.p7

---

• HomoloGene
  Vertebrate Homology Class 23069
  1 human;1 mouse;1 rat;1 chimpanzee;1 cattle;1 dog;1 chicken;1 zebrafish;1 frog, western clawed;1 macaque, rhesus
  
• HCOP
  human homology predictions: TMEM39B
• Gene Tree
  Tmem39b
  

Mutations,
Alleles, and
Phenotypes

• Phenotype Summary
  11 phenotype references
  

• All Mutations and Alleles
  8
• Chemically induced (other)
  2
• Gene trapped
  1
• Radiation induced
  1
• Targeted
  4
• Genomic Mutations
  4 involving Tmem39b
• Incidental Mutations
  Mutagenetix , APF
• Find Mice (IMSR)
  20 strains or lines available

Gene Ontology
(GO)
Classifications

• All GO Annotations
  2
• GO References
  1

• External Resources
  FuncBase

Expression

• cDNA Data
  31

• Other Mouse Links
  Allen Institute
  GEO
  Expression Atlas
• Other Vertebrate Links
  Xenbase tmem39b
  ZFIN tmem39b

Interactions

• Tmem39b interacts with 248 markers (Mir1a-1, Mir1a-2, Mir7-1, ...) View All

Sequences &
Gene Models

• All Sequences
  50
• RefSeq
  8
• UniProt
  4
• CCDS
  CCDS18702.1
• UniGene
  257157

• Ensembl
  ENSMUSG00000053730 (Evidence)
• NCBI Gene
  230770 (Evidence)

Representative Sequences			Length	Strain/Species
genomic	ENSMUSG00000053730	Ensembl Gene Model | MGI Sequence Detail	20484	C57BL/6J
transcript	ENSMUST00000102588	Ensembl | MGI Sequence Detail	1810	Not Applicable
polypeptide	ENSMUSP00000099648	Ensembl | MGI Sequence Detail	492	Not Applicable

Protein
Information

• UniProt
  4 Sequences
• Protein Ontology
  PR:000031382 transmembrane protein 39B
  (term hierarchy)
• InterPro Domains
  IPR019397 Uncharacterised protein family TMEM39

Molecular
Reagents

• All nucleic 31

  cDNA 31

  
  

  Microarray probesets 1

Other
Accession IDs

MGI:1923394

References

• Summaries
  All 29

  Gene Ontology 1

  Phenotypes 11
• Earliest
  J:93290 Araki K, et al., Exchangeable gene trap using the Cre/mutated lox system. Cell Mol Biol (Noisy-Le-Grand). 1999 Jul;45(5):737-50
• 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 Tmem39b:

(View these features in JBrowse)

Transcription Start Site	Location	Distance from Gene 5'-end
Tssr43560	Chr4:129696849-129696860 (-)	-17 bp
Tssr43559	Chr4:129696817-129696843 (-)	8 bp
Tssr43558	Chr4:129696758-129696804 (-)	57 bp
Tssr43557	Chr4:129696734-129696743 (-)	99 bp
Tssr43556	Chr4:129696579-129696602 (-)	247 bp