Tmem240 (transmembrane protein 240) - Rat Genome Database

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Gene: Tmem240 (transmembrane protein 240) Rattus norvegicus
Analyze
Symbol: Tmem240
Name: transmembrane protein 240
RGD ID: 2318117
Description: Predicted to be located in TMEM240-body. Predicted to be active in synaptic membrane. Human ortholog(s) of this gene implicated in spinocerebellar ataxia type 21. Orthologous to human TMEM240 (transmembrane protein 240); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; fipronil; gentamycin.
Type: protein-coding
RefSeq Status: MODEL
Previously known as: hypothetical protein LOC100362471; LOC100362471
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr85171,625,830 - 171,653,836 (+)NCBIGRCr8
mRatBN7.25166,344,000 - 166,350,210 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl5166,344,386 - 166,350,636 (+)EnsemblmRatBN7.2 Ensembl
Rnor_6.05173,182,815 - 173,189,683 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl5173,183,990 - 173,188,924 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.05176,658,418 - 176,665,293 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.45172,592,952 - 172,598,461 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera5164,544,716 - 164,550,851 (+)NCBICelera
Cytogenetic Map5q36NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Function

References

References - curated
# Reference Title Reference Citation
1. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
2. OMIM Disease Annotation Pipeline OMIM Disease Annotation Pipeline
3. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
4. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:22645316  


Genomics

Comparative Map Data
Tmem240
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr85171,625,830 - 171,653,836 (+)NCBIGRCr8
mRatBN7.25166,344,000 - 166,350,210 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl5166,344,386 - 166,350,636 (+)EnsemblmRatBN7.2 Ensembl
Rnor_6.05173,182,815 - 173,189,683 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl5173,183,990 - 173,188,924 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.05176,658,418 - 176,665,293 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.45172,592,952 - 172,598,461 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera5164,544,716 - 164,550,851 (+)NCBICelera
Cytogenetic Map5q36NCBI
TMEM240
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh3811,534,778 - 1,540,624 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl11,534,778 - 1,540,624 (-)EnsemblGRCh38hg38GRCh38
GRCh3711,470,158 - 1,476,004 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 3611,460,602 - 1,465,597 (-)NCBINCBI36Build 36hg18NCBI36
Celera11,104,704 - 1,110,285 (+)NCBICelera
Cytogenetic Map1p36.33NCBI
HuRef1743,755 - 749,337 (-)NCBIHuRef
CHM1_111,457,436 - 1,462,960 (-)NCBICHM1_1
T2T-CHM13v2.01969,282 - 975,128 (-)NCBIT2T-CHM13v2.0
Tmem240
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm394155,818,336 - 155,825,025 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl4155,819,261 - 155,825,021 (+)EnsemblGRCm39 Ensembl
GRCm384155,734,804 - 155,740,564 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl4155,734,800 - 155,740,564 (+)EnsemblGRCm38mm10GRCm38
MGSCv374155,108,913 - 155,114,673 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv364154,578,678 - 154,583,807 (+)NCBIMGSCv36mm8
Celera4158,006,815 - 158,012,330 (+)NCBICelera
Cytogenetic Map4E2NCBI
cM Map487.18NCBI
Tmem240
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554869,339,479 - 9,344,025 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049554869,339,489 - 9,344,025 (+)NCBIChiLan1.0ChiLan1.0
TMEM240
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v21226,680,234 - 226,686,470 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11225,336,664 - 225,343,493 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01295,102 - 301,161 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.111,456,731 - 1,462,005 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl11,456,731 - 1,462,005 (-)Ensemblpanpan1.1panPan2
TMEM240
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1556,613,561 - 56,619,693 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl556,614,201 - 56,619,693 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha556,689,581 - 56,695,713 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0556,815,734 - 56,821,865 (-)NCBIROS_Cfam_1.0
UMICH_Zoey_3.1556,806,295 - 56,812,427 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0556,698,667 - 56,704,798 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0557,088,912 - 57,095,045 (-)NCBIUU_Cfam_GSD_1.0
Tmem240
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440505827,754,068 - 27,755,639 (-)NCBIHiC_Itri_2
SpeTri2.0NW_0049367371,710,311 - 1,711,882 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
TMEM240
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl663,721,656 - 63,727,526 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1663,721,655 - 63,727,457 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
TMEM240
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.120129,959,081 - 129,965,352 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl20129,959,462 - 129,965,375 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366605434,422,917 - 34,429,116 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Tmem240
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046248188,178,451 - 8,183,043 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046248188,178,425 - 8,183,185 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Tmem240
14 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:83
Count of miRNA genes:73
Interacting mature miRNAs:80
Transcripts:ENSRNOT00000068062
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.


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1576314Eutr1Estrogen induced uterine response QTL 1uterus integrity trait (VT:0010575)pyometritis severity score (CMO:0002009)52138965166875058Rat
1302790Scl20Serum cholesterol level QTL 206.40.0001blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)582394392166664054Rat
1641920Colcs1Colorectal carcinoma susceptibility QTL 12.990.0055intestine integrity trait (VT:0010554)benign colorectal tumor surface area measurement (CMO:0001799)5121846814166846814Rat
10053720Scort26Serum corticosterone level QTL 262.060.0147blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)5124965598166875058Rat
724525Bp147Blood pressure QTL 1474.30.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)5126424772166875058Rat
1598819Bp292Blood pressure QTL 2924.3arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)5127798274166875058Rat
1598861Cm64Cardiac mass QTL 642.9heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)5127798274166875058Rat
8552908Pigfal4Plasma insulin-like growth factor 1 level QTL 46.6blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)5128506074166875058Rat
8694169Bw148Body weight QTL 14850.001body mass (VT:0001259)body weight gain (CMO:0000420)5128506074166875058Rat
634349Bp139Blood pressure QTL 1390.001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)5128924607166875058Rat
738018Anxrr4Anxiety related response QTL 45.1exploratory behavior trait (VT:0010471)percentage of entries into a discrete space in an experimental apparatus (CMO:0000961)5130130159166875058Rat
7794791Mcs33Mammary carcinoma susceptibility QTL 331.93mammary gland integrity trait (VT:0010552)mammary tumor incidence/prevalence measurement (CMO:0000946)5131345754166875058Rat
631562Apr2Acute phase response QTL 23.7blood murinoglobulin 1 amount (VT:0010597)plasma murinoglobulin 1 level (CMO:0001931)5135927956166875058Rat
61444Strs2Sensitivity to stroke QTL 24.7cerebrum integrity trait (VT:0010549)post-insult time to onset of cerebrovascular lesion (CMO:0002343)5135929696166875058Rat
1331721Bp210Blood pressure QTL 2103.413arterial blood pressure trait (VT:2000000)blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)5143069996166846814Rat
631272Lanf1Left ventricular atrial natriuretic factor QTL 112heart left ventricle natriuretic peptide A amount (VT:0010596)heart left ventricle natriuretic peptide A level (CMO:0002165)5151113452166875058Rat
1549904Neuinf1Neuroinflammation QTL 130nervous system integrity trait (VT:0010566)blood T lymphocyte count (CMO:0000110)5154828214166875058Rat

Markers in Region
RH127981  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.25166,350,464 - 166,350,677 (+)MAPPERmRatBN7.2
Rnor_6.05173,189,753 - 173,189,965NCBIRnor6.0
Rnor_5.05176,665,363 - 176,665,575UniSTSRnor5.0
RGSC_v3.45172,598,716 - 172,598,928UniSTSRGSC3.4
Celera5164,550,921 - 164,551,133UniSTS
RH 3.4 Map51174.7UniSTS
Cytogenetic Map5q36UniSTS
RH134507  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.25166,343,138 - 166,343,333 (+)MAPPERmRatBN7.2
Rnor_6.05173,182,427 - 173,182,621NCBIRnor6.0
Rnor_5.05176,658,037 - 176,658,231UniSTSRnor5.0
RGSC_v3.45172,590,909 - 172,591,103UniSTSRGSC3.4
Celera5164,543,624 - 164,543,818UniSTS
RH 3.4 Map51174.7UniSTS
Cytogenetic Map5q36UniSTS


Expression


RNA-SEQ Expression
High: > 1000 TPM value   Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM   Below Cutoff: < 0.5 TPM

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium 58
Low 1 38 21 5 18 5 4 4 16 33 37 11 4
Below cutoff 2 5 26 26 1 26 4 7 2 4 4

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000068062   ⟹   ENSRNOP00000063372
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl5166,344,386 - 166,350,636 (+)Ensembl
Rnor_6.0 Ensembl5173,183,990 - 173,188,924 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000110105   ⟹   ENSRNOP00000081055
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl5166,345,210 - 166,349,806 (+)Ensembl
RefSeq Acc Id: XM_002729582   ⟹   XP_002729628
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr85171,625,830 - 171,653,836 (+)NCBI
mRatBN7.25166,344,000 - 166,349,813 (+)NCBI
Rnor_6.05173,183,686 - 173,189,101 (+)NCBI
Rnor_5.05176,658,418 - 176,665,293 (+)NCBI
RGSC_v3.45172,592,952 - 172,598,461 (+)RGD
Sequence:
RefSeq Acc Id: XM_008764408   ⟹   XP_008762630
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr85171,625,830 - 171,653,836 (+)NCBI
mRatBN7.25166,344,000 - 166,350,210 (+)NCBI
Rnor_6.05173,183,681 - 173,189,683 (+)NCBI
Sequence:
RefSeq Acc Id: XM_063288670   ⟹   XP_063144740
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr85171,625,830 - 171,631,442 (+)NCBI
Protein Sequences
Protein RefSeqs XP_002729628 (Get FASTA)   NCBI Sequence Viewer  
  XP_008762630 (Get FASTA)   NCBI Sequence Viewer  
  XP_063144740 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000063372.1
  ENSRNOP00000081055.1
Reference Protein Sequences
RefSeq Acc Id: XP_002729628   ⟸   XM_002729582
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_008762630   ⟸   XM_008764408
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: ENSRNOP00000063372   ⟸   ENSRNOT00000068062
RefSeq Acc Id: ENSRNOP00000081055   ⟸   ENSRNOT00000110105
RefSeq Acc Id: XP_063144740   ⟸   XM_063288670
- Peptide Label: isoform X3

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D3ZYD8-F1-model_v2 AlphaFold D3ZYD8 1-173 view protein structure

Transcriptome

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


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:2318117 AgrOrtholog
BioCyc Gene G2FUF-38904 BioCyc
Ensembl Genes ENSRNOG00000042211 Ensembl
  ENSRNOG00000066137 Ensembl, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000068062.2 UniProtKB/TrEMBL
  ENSRNOT00000110105.1 UniProtKB/TrEMBL
InterPro TMEM240 UniProtKB/TrEMBL
KEGG Report rno:100362471 UniProtKB/TrEMBL
NCBI Gene 100362471 ENTREZGENE
PANTHER PTHR28666 UniProtKB/TrEMBL
  TRANSMEMBRANE PROTEIN 240 UniProtKB/TrEMBL
Pfam TMEM240 UniProtKB/TrEMBL
PhenoGen Tmem240 PhenoGen
RatGTEx ENSRNOG00000042211 RatGTEx
  ENSRNOG00000066137 RatGTEx
UniProt A0A8I5ZS31_RAT UniProtKB/TrEMBL
  D3ZYD8_RAT UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2022-06-02 Tmem240  transmembrane protein 240  Tmem240  transmembrane protein 240  Data merged from RGD:149736377 737654 PROVISIONAL
2021-08-09 Tmem240  transmembrane protein 240      Symbol and Name status set to provisional 45752 PROVISIONAL
2012-08-29 Tmem240  transmembrane protein 240  LOC100362471  hypothetical protein LOC100362471  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2010-05-05 LOC100362471  hypothetical protein LOC100362471      Symbol and Name status set to provisional 70820 PROVISIONAL