Tmem42 (transmembrane protein 42) - Rat Genome Database

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Gene: Tmem42 (transmembrane protein 42) Rattus norvegicus
Analyze
Symbol: Tmem42
Name: transmembrane protein 42
RGD ID: 1307118
Description: Predicted to be located in membrane. Orthologous to human TMEM42 (transmembrane protein 42); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 2,3,7,8-Tetrachlorodibenzofuran; 3-chloropropane-1,2-diol.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: LOC363171; RGD1307118; similar to RIKEN cDNA 0610027O18
RGD Orthologs
Human
Mouse
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Black Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr88131,551,616 - 131,554,749 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl8131,552,257 - 131,555,765 (+)EnsemblGRCr8
mRatBN7.28122,674,793 - 122,677,290 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl8122,674,070 - 122,677,276 (+)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx8128,264,329 - 128,266,828 (+)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.08126,463,270 - 126,465,769 (+)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.08124,291,687 - 124,294,186 (+)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.08132,105,965 - 132,108,462 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl8132,105,443 - 132,108,462 (+)Ensemblrn6Rnor6.0
Rnor_5.08131,260,785 - 131,263,282 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.48127,767,070 - 127,769,567 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera8121,789,143 - 121,791,640 (+)NCBICelera
RGSC_v3.18127,786,495 - 127,789,190 (+)NCBI
Cytogenetic Map8q32NCBI
JBrowse:




Gene Ontology Annotations     Click to see Annotation Detail View

Molecular Function

References

References - curated
# Reference Title Reference Citation
1. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions

Genomics

Comparative Map Data
Tmem42
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr88131,551,616 - 131,554,749 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl8131,552,257 - 131,555,765 (+)EnsemblGRCr8
mRatBN7.28122,674,793 - 122,677,290 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl8122,674,070 - 122,677,276 (+)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx8128,264,329 - 128,266,828 (+)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.08126,463,270 - 126,465,769 (+)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.08124,291,687 - 124,294,186 (+)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.08132,105,965 - 132,108,462 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl8132,105,443 - 132,108,462 (+)Ensemblrn6Rnor6.0
Rnor_5.08131,260,785 - 131,263,282 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.48127,767,070 - 127,769,567 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera8121,789,143 - 121,791,640 (+)NCBICelera
RGSC_v3.18127,786,495 - 127,789,190 (+)NCBI
Cytogenetic Map8q32NCBI
TMEM42
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38344,861,912 - 44,865,664 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl344,861,889 - 44,865,670 (+)Ensemblhg38GRCh38
GRCh37344,903,404 - 44,907,156 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36344,878,412 - 44,882,160 (+)NCBIBuild 36Build 36hg18NCBI36
Build 34344,878,411 - 44,882,156NCBI
Celera344,841,374 - 44,845,122 (+)NCBICelera
Cytogenetic Map3p21.31NCBI
HuRef344,947,268 - 44,951,016 (+)NCBIHuRef
CHM1_1344,853,420 - 44,857,168 (+)NCBICHM1_1
T2T-CHM13v2.0344,877,631 - 44,881,388 (+)NCBIT2T-CHM13v2.0
Tmem42
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm399122,850,072 - 122,852,556 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl9122,850,391 - 122,852,770 (+)EnsemblGRCm39 EnsemblGRCm39
GRCm389123,021,007 - 123,023,491 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl9123,021,326 - 123,023,705 (+)Ensemblmm10GRCm38
MGSCv379122,930,444 - 122,932,609 (+)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv369122,870,024 - 122,872,181 (+)NCBIMGSCv36mm8
Celera9123,474,978 - 123,477,288 (+)NCBICelera
Cytogenetic Map9F4NCBI
cM Map973.52NCBI
TMEM42
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2244,819,278 - 44,824,031 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1344,824,966 - 44,828,803 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0344,763,025 - 44,766,852 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1345,818,006 - 45,830,210 (+)NCBIPanPan1.1PanPan1.1panPan2
PanPan1.1 Ensembl345,818,081 - 45,821,264 (+)EnsemblpanPan2panpan1.1
TMEM42
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12043,446,963 - 43,451,241 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2043,447,894 - 43,451,751 (-)EnsemblcanFam3CanFam3.1
Dog10K_Boxer_Tasha2043,362,557 - 43,366,819 (-)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.02043,932,105 - 43,936,368 (-)NCBIROS_Cfam_1.0ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl2043,933,036 - 43,936,894 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.12043,170,242 - 43,174,505 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.02043,577,754 - 43,582,017 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.02043,854,790 - 43,859,057 (-)NCBIUU_Cfam_GSD_1.0UU_Cfam_GSD_1.0
Tmem42
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024405118198,501,331 - 198,505,150 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_004936695852,218 - 855,036 (-)EnsemblSpeTri2.0 Ensembl
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 - 28,054,891 (+)EnsemblsusScr11Sscrofa11.1
Sscrofa11.11328,045,370 - 28,054,628 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21330,938,202 - 30,956,826 (+)NCBISscrofa10.2Sscrofa10.2susScr3
TMEM42
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1226,334,659 - 6,338,493 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl226,334,700 - 6,338,592 (+)EnsemblChlSab1.1 EnsemblchlSab2Vervet-AGM
Vero_WHO_p1.0NW_023666041160,831,139 - 160,834,926 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Tmem42
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462473075,621,331 - 75,625,402 (-)EnsemblHetGla_female_1.0 EnsemblhetGla2HetGla_female_1.0 Ensembl
HetGla 1.0NW_00462473075,622,212 - 75,625,426 (-)NCBIHetGla 1.0HetGla 1.0hetGla2
Tmem42
(Rattus rattus - black rat)
Black Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rrattus_CSIRO_v18114,161,224 - 114,164,192 (+)NCBIRrattus_CSIRO_v1

miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:247
Count of miRNA genes:163
Interacting mature miRNAs:179
Transcripts:ENSRNOT00000040475
Prediction methods:Microtar, 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.


QTLs in Region (GRCr8)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
738011Anxrr9Anxiety related response QTL 96.1exploratory behavior trait (VT:0010471)number of entries into a discrete space in an experimental apparatus (CMO:0000960)8102413464132782436Rat
2303171Bp331Blood pressure QTL 3315.570.005arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)8105462581132782436Rat
634332Pia18Pristane induced arthritis QTL 184joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)884192326132782436Rat
1300171Bp184Blood pressure QTL 1843.66arterial blood pressure trait (VT:2000000)blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)879394435132782436Rat
61437Cia6Collagen induced arthritis QTL 6joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)891340911131690273Rat

Markers in Region
RH129922  
Rat AssemblyChrPosition (strand)SourceJBrowse
GRCr88131,554,449 - 131,554,625 (+)Marker Load Pipeline
mRatBN7.28122,676,990 - 122,677,166 (+)MAPPERmRatBN7.2
Rnor_6.08132,108,163 - 132,108,338NCBIRnor6.0
Rnor_5.08131,262,983 - 131,263,158UniSTSRnor5.0
RGSC_v3.48127,769,268 - 127,769,443UniSTSRGSC3.4
Celera8121,791,341 - 121,791,516UniSTS
RH 3.4 Map81276.29UniSTS
Cytogenetic Map8q32UniSTS
RH143434  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.28122,675,414 - 122,675,567 (+)MAPPERmRatBN7.2
Rnor_6.08132,106,587 - 132,106,739NCBIRnor6.0
Rnor_5.08131,261,407 - 131,261,559UniSTSRnor5.0
RGSC_v3.48127,767,692 - 127,767,844UniSTSRGSC3.4
Celera8121,789,765 - 121,789,917UniSTS
RH 3.4 Map81277.9UniSTS
Cytogenetic Map8q32UniSTS
RH140734  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.28122,674,820 - 122,674,951 (+)MAPPERmRatBN7.2
Rnor_6.08132,105,993 - 132,106,123NCBIRnor6.0
Rnor_5.08131,260,813 - 131,260,943UniSTSRnor5.0
RGSC_v3.48127,767,098 - 127,767,228UniSTSRGSC3.4
Celera8121,789,171 - 121,789,301UniSTS
RH 3.4 Map81257.0UniSTS
Cytogenetic Map8q32UniSTS


Expression

RNA-SEQ Expression

alimentary part of gastrointestinal system
appendage
circulatory system
ectoderm
endocrine system
endoderm
exocrine system
hemolymphoid system
hepatobiliary system
integumental system
mesenchyme
mesoderm
musculoskeletal system
nervous system
renal system
reproductive system
respiratory system
sensory system
visual system
16 12 67 160 91 90 59 92 59 6 356 192 11 139 81 92 31 17 17

Sequence


Ensembl Acc Id: ENSRNOT00000040475   ⟹   ENSRNOP00000043044
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl8131,552,257 - 131,555,765 (+)Ensembl
mRatBN7.2 Ensembl8122,674,070 - 122,677,276 (+)Ensembl
Rnor_6.0 Ensembl8132,105,443 - 132,108,462 (+)Ensembl
RefSeq Acc Id: NM_001191886   ⟹   NP_001178815
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr88131,552,252 - 131,554,749 (+)NCBI
mRatBN7.28122,674,793 - 122,677,290 (+)NCBI
Rnor_6.08132,105,965 - 132,108,462 (+)NCBI
Rnor_5.08131,260,785 - 131,263,282 (+)NCBI
Celera8121,789,143 - 121,791,640 (+)NCBI
Sequence:
RefSeq Acc Id: XM_063265859   ⟹   XP_063121929
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr88131,551,616 - 131,553,478 (+)NCBI
RefSeq Acc Id: NP_001178815   ⟸   NM_001191886
- UniProtKB: A6I498 (UniProtKB/TrEMBL),   A6I497 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000043044   ⟸   ENSRNOT00000040475
RefSeq Acc Id: XP_063121929   ⟸   XM_063265859
- Peptide Label: isoform X1

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D3Z8L0-F1-model_v2 AlphaFold D3Z8L0 1-157 view protein structure

Transcriptome

eQTL   View at Phenogen
WGCNA   View at Phenogen
Tissue/Strain Expression   View at Phenogen

Promoters
RGD ID:13696402
Promoter ID:EPDNEW_R6927
Type:multiple initiation site
Name:Tmem42_1
Description:transmembrane protein 42
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.08132,106,265 - 132,106,325EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1307118 AgrOrtholog
BioCyc Gene G2FUF-28624 BioCyc
Ensembl Genes ENSRNOG00000032027 Ensembl, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000040475.7 UniProtKB/TrEMBL
InterPro TMEM42 UniProtKB/TrEMBL
KEGG Report rno:363171 UniProtKB/TrEMBL
NCBI Gene 363171 ENTREZGENE
PANTHER PTHR31965 UniProtKB/TrEMBL
  TRANSMEMBRANE PROTEIN 42 UniProtKB/TrEMBL
PhenoGen Tmem42 PhenoGen
RatGTEx ENSRNOG00000032027 RatGTEx
Superfamily-SCOP Multidrug resistance efflux transporter EmrE UniProtKB/TrEMBL
UniProt A6I497 ENTREZGENE, UniProtKB/TrEMBL
  A6I498 ENTREZGENE, UniProtKB/TrEMBL
  D3Z8L0_RAT UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-04-30 Tmem42  transmembrane protein 42   Tmem42_predicted  transmembrane protein 42 (predicted)  'predicted' is removed 2292626 APPROVED
2006-03-30 Tmem42_predicted  transmembrane protein 42 (predicted)  RGD1307118_predicted  similar to RIKEN cDNA 0610027O18 (predicted)  Symbol and Name updated 1299863 APPROVED
2005-01-20 RGD1307118_predicted  similar to RIKEN cDNA 0610027O18 (predicted)  LOC363171_predicted    Symbol and Name status set to approved 1331353 APPROVED
2005-01-12 LOC363171_predicted  similar to RIKEN cDNA 0610027O18 (predicted)      Symbol and Name status set to provisional 70820 PROVISIONAL