Tmem42 (transmembrane protein 42) - Rat Genome Database
Submit Data |  Help |  Video Tutorials |  News |  Publications |  FTP Download |  REST API |  Citing RGD |  Contact   
Gene: Tmem42 (transmembrane protein 42) Mus musculus
Analyze
Symbol: Tmem42
Name: transmembrane protein 42
RGD ID: 1615900
MGI Page MGI
Description: Predicted to localize to integral component of membrane. Orthologous to human TMEM42 (transmembrane protein 42); INTERACTS WITH 1,2-dichloroethane; 1,2-dimethylhydrazine; 2,3,7,8-tetrachlorodibenzodioxine.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: 0610027O18Rik; 4933429E06Rik; AV003444; D9Ertd662; D9Ertd662e; MGC29956
RGD Orthologs
Human
Rat
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: GRCm38 - Mouse Genome Assembly GRCm38
Position:
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm399122,850,072 - 122,852,556 (+)NCBIGRCm39mm39
GRCm389123,021,007 - 123,023,491 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl9123,021,326 - 123,023,705 (+)EnsemblGRCm38mm10GRCm38
MGSCv379122,930,444 - 122,932,609 (+)NCBIGRCm37mm9NCBIm37
MGSCv369122,870,024 - 122,872,181 (+)NCBImm8
Celera9123,474,978 - 123,477,288 (+)NCBICelera
Cytogenetic Map9F4NCBI
cM Map973.52NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component

Molecular Function

Phenotype Annotations     Click to see Annotation Detail View
References

References - curated
1. RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:8889548   PMID:10349636   PMID:10725249   PMID:10922068   PMID:11042159   PMID:11076861   PMID:11217851   PMID:12466851   PMID:12477932   PMID:16141072   PMID:16141073   PMID:21677750  


Genomics

Comparative Map Data
Tmem42
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm399122,850,072 - 122,852,556 (+)NCBIGRCm39mm39
GRCm389123,021,007 - 123,023,491 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl9123,021,326 - 123,023,705 (+)EnsemblGRCm38mm10GRCm38
MGSCv379122,930,444 - 122,932,609 (+)NCBIGRCm37mm9NCBIm37
MGSCv369122,870,024 - 122,872,181 (+)NCBImm8
Celera9123,474,978 - 123,477,288 (+)NCBICelera
Cytogenetic Map9F4NCBI
cM Map973.52NCBI
TMEM42
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl344,861,904 - 44,865,670 (+)EnsemblGRCh38hg38GRCh38
GRCh38344,861,912 - 44,865,664 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh37344,903,408 - 44,907,156 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36344,878,412 - 44,882,160 (+)NCBINCBI36hg18NCBI36
Build 34344,878,411 - 44,882,156NCBI
Celera344,841,374 - 44,845,122 (+)NCBI
Cytogenetic Map3p21.31NCBI
HuRef344,947,268 - 44,951,016 (+)NCBIHuRef
CHM1_1344,853,413 - 44,857,171 (+)NCBICHM1_1
Tmem42
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rnor_6.08132,105,965 - 132,108,462 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl8132,105,443 - 132,108,462 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.08131,260,785 - 131,263,282 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.48127,767,070 - 127,769,567 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.18127,786,495 - 127,789,190 (+)NCBI
Celera8121,789,143 - 121,791,640 (+)NCBICelera
Cytogenetic Map8q32NCBI
TMEM42
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1345,818,006 - 45,830,210 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl345,818,081 - 45,821,264 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0344,763,025 - 44,766,852 (+)NCBIMhudiblu_PPA_v0panPan3
TMEM42
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1 Ensembl2043,447,894 - 43,451,751 (-)EnsemblCanFam3.1canFam3CanFam3.1
CanFam3.12043,446,963 - 43,451,241 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Tmem42
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
SpeTri2.0NW_004936695853,246 - 857,485 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
TMEM42
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1328,045,397 - 28,054,920 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11328,045,370 - 28,054,628 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21330,938,202 - 30,956,826 (+)NCBISscrofa10.2Sscrofa10.2susScr3
TMEM42
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1226,334,659 - 6,338,493 (+)NCBI
ChlSab1.1 Ensembl226,334,700 - 6,338,592 (+)Ensembl
Tmem42
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462473075,622,212 - 75,625,426 (-)NCBI

Position Markers
AV003444  
Mouse AssemblyChrPosition (strand)SourceJBrowse
GRCm389123,023,319 - 123,023,461UniSTSGRCm38
MGSCv379122,932,437 - 122,932,579UniSTSGRCm37
Celera9123,477,116 - 123,477,258UniSTS
Cytogenetic Map9F4UniSTS
cM Map972.0UniSTS
Whitehead/MRC_RH91211.65UniSTS
UniSTS:236296  
Mouse AssemblyChrPosition (strand)SourceJBrowse
GRCm389123,019,963 - 123,020,167UniSTSGRCm38
MGSCv379122,929,081 - 122,929,285UniSTSGRCm37
Celera9123,473,615 - 123,473,819UniSTS
Cytogenetic Map9F4UniSTS
cM Map972.0UniSTS
AU015427  
Mouse AssemblyChrPosition (strand)SourceJBrowse
GRCm389123,019,931 - 123,020,051UniSTSGRCm38
MGSCv379122,929,049 - 122,929,169UniSTSGRCm37
Celera9123,473,583 - 123,473,703UniSTS
Cytogenetic Map9F4UniSTS
cM Map972.0UniSTS
cM Map972.0UniSTS
cM Map972.0UniSTS
Whitehead/MRC_RH91212.06UniSTS
AU015427  
Mouse AssemblyChrPosition (strand)SourceJBrowse
GRCm389123,019,910 - 123,020,153UniSTSGRCm38
MGSCv379122,929,028 - 122,929,271UniSTSGRCm37
Celera9123,473,562 - 123,473,805UniSTS
Cytogenetic Map9F4UniSTS
cM Map972.0UniSTS
Whitehead/MRC_RH91212.15UniSTS


QTLs in Region (GRCm38)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
10412242Alpq8_malcohol preference QTL 8 (mouse)Not determined989284925123284925Mouse
1301649Psl1_mpromotion susceptibility QTL 1 (mouse)Not determined989412277123412396Mouse
18182932Metl3_mmetabolite locus 3, N-acetylglutamate (mouse)989563342123563342Mouse
12910770Splic1_mspleen iron content 1 (mouse)991413879124595110Mouse
12910772Lvic6_mliver iron content 6 (mouse)991413879124595110Mouse
12910773Splic3_mspleen iron content 3 (mouse)991413879124595110Mouse
1558767Skmw11_mskeletal muscle weight 11 (mouse)Not determined991641084124595110Mouse
13463474Hbbcq5_mhemoglobin concentration QTL 5 (mouse)991641084124595110Mouse
13463475Hctq7_mhematocrit QTL 7 (mouse)991641084124595110Mouse
13463477Rbc9_mred blood cell count 9 (mouse)991641084124595110Mouse
13463478Mchq18_mmean corpuscular hemoglobin QTL 18 (mouse)991641084124595110Mouse
13463480Mchcq2_mmean corpuscular hemoglobin concentration QTL 2 (mouse)991641084124595110Mouse
12904937Edlmmq9_mextensor digitorum longus muscle mass QTL 9 (mouse)991683173124595110Mouse
12904947Tammq7_mtibialis anterior muscle mass QTL 7 (mouse)991683173124595110Mouse
12904961Gmmq7_mgastrocnemius muscle mass QTL 7 (mouse)991683173124595110Mouse
1302001Bdln5_mbody length 5 (mouse)Not determined993762590124595110Mouse
1301484Bwq6_mbody weight (mouse)Not determined993762590124595110Mouse
14746992Manh67_mmandible shape 67 (mouse)994036768124595110Mouse
11537364Cnes5_mC. neoformans susceptibility locus 5 (mouse)996917590124595110Mouse
1301297Lcho1_mliver cholesterol 1 (mouse)Not determined9101060861124595110Mouse
1357627Tgq2_mtriglyceride QTL 2 (mouse)Not determined9102000187124595110Mouse
1357648Obq18_mobesity QTL 18 (mouse)Not determined9102000187124595110Mouse
1301789Pbwg4_mpostnatal body weight growth 4 (mouse)Not determined9103289445124595110Mouse
10412290Pvacm1l_mplasma vascular cell adhesion molecule 1 levels (mouse)Not determined9103289445124595110Mouse
12879896Berr3_mberghei resistance locus 3 (mouse)9103289445124595110Mouse

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:173
Count of miRNA genes:148
Interacting mature miRNAs:165
Transcripts:ENSMUST00000084733
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


Sequence


Reference Sequences
RefSeq Acc Id: ENSMUST00000084733   ⟹   ENSMUSP00000081784
RefSeq Status:
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm38.p6 Ensembl9123,021,326 - 123,023,487 (+)Ensembl
RefSeq Acc Id: ENSMUST00000213514   ⟹   ENSMUSP00000149571
RefSeq Status:
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm38.p6 Ensembl9123,021,375 - 123,023,705 (+)Ensembl
RefSeq Acc Id: ENSMUST00000214077
RefSeq Status:
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm38.p6 Ensembl9123,021,418 - 123,022,120 (+)Ensembl
RefSeq Acc Id: ENSMUST00000214785   ⟹   ENSMUSP00000149811
RefSeq Status:
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm38.p6 Ensembl9123,021,418 - 123,022,249 (+)Ensembl
RefSeq Acc Id: NM_001164823   ⟹   NP_001158295
RefSeq Status: VALIDATED
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm399122,850,391 - 122,852,556 (+)NCBI
GRCm389123,021,326 - 123,023,491 (+)NCBI
MGSCv379122,930,444 - 122,932,609 (+)RGD
Celera9123,474,978 - 123,477,288 (+)RGD
cM Map9 ENTREZGENE
Sequence:
RefSeq Acc Id: NM_025339   ⟹   NP_079615
RefSeq Status: VALIDATED
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm399122,850,391 - 122,852,556 (+)NCBI
GRCm389123,021,326 - 123,023,491 (+)NCBI
MGSCv379122,930,444 - 122,932,609 (+)RGD
Celera9123,474,978 - 123,477,288 (+)RGD
cM Map9 ENTREZGENE
Sequence:
RefSeq Acc Id: XM_006512205   ⟹   XP_006512268
RefSeq Status:
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm399122,850,137 - 122,852,556 (+)NCBI
GRCm389123,021,070 - 123,023,491 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006512206   ⟹   XP_006512269
RefSeq Status:
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm399122,850,072 - 122,852,556 (+)NCBI
GRCm389123,021,007 - 123,023,491 (+)NCBI
Sequence:
Reference Sequences
RefSeq Acc Id: NP_079615   ⟸   NM_025339
- Peptide Label: isoform 1
- UniProtKB: Q9CR22 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: NP_001158295   ⟸   NM_001164823
- Peptide Label: isoform 2
- UniProtKB: Q9CR22 (UniProtKB/Swiss-Prot),   A0A1L1SRQ7 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006512269   ⟸   XM_006512206
- Peptide Label: isoform X1
- UniProtKB: Q9CR22 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_006512268   ⟸   XM_006512205
- Peptide Label: isoform X1
- UniProtKB: Q9CR22 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSMUSP00000081784   ⟸   ENSMUST00000084733
RefSeq Acc Id: ENSMUSP00000149571   ⟸   ENSMUST00000213514
RefSeq Acc Id: ENSMUSP00000149811   ⟸   ENSMUST00000214785

Promoters
RGD ID:6845259
Promoter ID:MM_KWN:59258
Type:CpG-Island
SO ACC ID:SO:0000170
Source:MPROMDB
Tissues & Cell Lines:3T3L1_Day0,   3T3L1_Day2,   3T3L1_Day3,   BoneMarrow_0Hour,   BoneMarrow_2Hour,   BoneMarrow_4Hour
Transcripts:NM_001164823,   NM_025339
Position:
Mouse AssemblyChrPosition (strand)Source
MGSCv369122,929,951 - 122,930,602 (+)MPROMDB
RGD ID:8671322
Promoter ID:EPDNEW_M13691
Type:multiple initiation site
Name:Tmem42_1
Description:Mus musculus transmembrane protein 42 , transcript variant 1,mRNA.
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm389123,021,350 - 123,021,410EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene MGI:1277176 AgrOrtholog
Ensembl Genes ENSMUSG00000066233 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Ensembl Protein ENSMUSP00000081784 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSMUSP00000149571 ENTREZGENE, UniProtKB/TrEMBL
  ENSMUSP00000149811 UniProtKB/TrEMBL
Ensembl Transcript ENSMUST00000084733 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSMUST00000213514 ENTREZGENE, UniProtKB/TrEMBL
  ENSMUST00000214785 UniProtKB/TrEMBL
InterPro TMEM42 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report mmu:66079 UniProtKB/Swiss-Prot
MGD MGI:1277176 ENTREZGENE
NCBI Gene 66079 ENTREZGENE
PANTHER PTHR31965 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Tmem42 PhenoGen
UniGene Mm.482265 ENTREZGENE
UniProt A0A1L1SRQ7 ENTREZGENE, UniProtKB/TrEMBL
  A0A1L1SS99_MOUSE UniProtKB/TrEMBL
  Q9CR22 ENTREZGENE, UniProtKB/Swiss-Prot