Tmem254 (transmembrane protein 254) - Rat Genome Database

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Gene: Tmem254 (transmembrane protein 254) Rattus norvegicus
Analyze
Symbol: Tmem254
Name: transmembrane protein 254
RGD ID: 1305689
Description: Predicted to be located in membrane. Orthologous to human TMEM254 (transmembrane protein 254); INTERACTS WITH 17beta-estradiol; 2,3,7,8-tetrachlorodibenzodioxine; 3,3',4,4',5-pentachlorobiphenyl.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: Fam213a; family with sequence similarity 213, member A; homolog of C10orf57; homolog of C10orf57 (human); LOC290529; MGC105674; RGD1305689; similar to DNA segment, Chr 14, ERATO Doi 449, expressed; transmembrane protein C10orf57 homolog
RGD Orthologs
Human
Mouse
Chinchilla
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
GRCr8161,510,705 - 1,514,591 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl161,510,709 - 1,514,343 (-)EnsemblGRCr8
mRatBN7.2161,503,931 - 1,507,819 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl161,503,933 - 1,507,895 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx161,510,261 - 1,514,148 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0162,656,098 - 2,659,985 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0161,516,858 - 1,520,746 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0163,817,402 - 3,821,270 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl163,817,402 - 3,821,270 (+)Ensemblrn6Rnor6.0
Rnor_5.0163,783,384 - 3,787,313 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.4161,542,246 - 1,546,190 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera161,479,734 - 1,483,581 (-)NCBICelera
RGSC_v3.1161,542,246 - 1,546,190 (-)NCBI
Cytogenetic Map16p16NCBI
JBrowse:




Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component
membrane  (IEA)

Molecular Function

References

References - curated
# Reference Title Reference Citation
1. GOA pipeline RGD automated data pipeline
2. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:12477932   PMID:15489334  


Genomics

Comparative Map Data
Tmem254
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8161,510,705 - 1,514,591 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl161,510,709 - 1,514,343 (-)EnsemblGRCr8
mRatBN7.2161,503,931 - 1,507,819 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl161,503,933 - 1,507,895 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx161,510,261 - 1,514,148 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0162,656,098 - 2,659,985 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0161,516,858 - 1,520,746 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0163,817,402 - 3,821,270 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl163,817,402 - 3,821,270 (+)Ensemblrn6Rnor6.0
Rnor_5.0163,783,384 - 3,787,313 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.4161,542,246 - 1,546,190 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera161,479,734 - 1,483,581 (-)NCBICelera
RGSC_v3.1161,542,246 - 1,546,190 (-)NCBI
Cytogenetic Map16p16NCBI
TMEM254
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381080,078,665 - 80,092,551 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1080,078,646 - 80,092,557 (+)Ensemblhg38GRCh38
GRCh371081,838,421 - 81,852,307 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361081,828,406 - 81,842,286 (+)NCBIBuild 36Build 36hg18NCBI36
Build 341081,828,405 - 81,842,287NCBI
Celera1075,829,384 - 75,843,265 (+)NCBICelera
Cytogenetic Map10q22.3NCBI
HuRef1075,681,811 - 75,695,863 (+)NCBIHuRef
CHM1_11082,121,425 - 82,135,331 (+)NCBICHM1_1
T2T-CHM13v2.01080,947,824 - 80,961,714 (+)NCBIT2T-CHM13v2.0
Tmem254
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391425,923,722 - 25,928,096 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1425,923,724 - 25,928,096 (-)EnsemblGRCm39 EnsemblGRCm39
GRCm381425,923,298 - 25,927,672 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1425,923,300 - 25,927,672 (-)Ensemblmm10GRCm38
GRCm38.p6 Ensembl1426,063,919 - 26,067,355 (-)Ensemblmm10GRCm38
GRCm38.p6 Ensembl1426,203,369 - 26,207,041 (-)Ensemblmm10GRCm38
MGSCv371426,742,784 - 26,747,158 (-)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv361424,757,354 - 24,760,394 (-)NCBIMGSCv36mm8
MGSCv361421,014,716 - 21,017,756 (-)NCBIMGSCv36mm8
Cytogenetic Map14A3NCBI
cM Map1415.49NCBI
Tmem254
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495543713,061,162 - 13,067,024 (+)Ensembl
ChiLan1.0NW_00495543713,061,162 - 13,067,024 (+)NCBIChiLan1.0ChiLan1.0
TMEM254
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2891,807,963 - 91,822,512 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11091,813,288 - 91,827,536 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01076,179,649 - 76,193,828 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11078,837,374 - 78,851,309 (-)NCBIPanPan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1078,837,380 - 78,851,301 (-)EnsemblpanPan2panpan1.1
TMEM254
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1429,315,393 - 29,323,721 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl429,317,162 - 29,324,194 (-)EnsemblcanFam3CanFam3.1
Dog10K_Boxer_Tasha429,439,876 - 29,448,174 (-)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.0429,617,448 - 29,625,815 (-)NCBIROS_Cfam_1.0ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl429,619,219 - 29,625,800 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1429,487,034 - 29,495,315 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0429,689,741 - 29,698,103 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0430,043,663 - 30,052,080 (-)NCBIUU_Cfam_GSD_1.0UU_Cfam_GSD_1.0
Tmem254
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440721351,686,620 - 51,696,402 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_004936521179,357 - 189,824 (+)EnsemblSpeTri2.0 Ensembl
SpeTri2.0NW_004936521178,856 - 189,132 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
TMEM254
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1481,931,301 - 81,940,401 (-)EnsemblsusScr11Sscrofa11.1
Sscrofa11.11481,931,294 - 81,940,443 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21488,542,475 - 88,551,615 (-)NCBISscrofa10.2Sscrofa10.2susScr3
TMEM254
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1951,710,027 - 51,724,078 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl951,708,127 - 51,724,156 (-)EnsemblChlSab1.1 EnsemblchlSab2Vervet-AGM
Vero_WHO_p1.0NW_02366604812,054,600 - 12,068,904 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Tmem254
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462475412,544,580 - 12,550,168 (-)EnsemblHetGla_female_1.0 EnsemblhetGla2HetGla_female_1.0 Ensembl
HetGla 1.0NW_00462475412,543,266 - 12,549,910 (-)NCBIHetGla 1.0HetGla 1.0hetGla2
Tmem254
(Rattus rattus - black rat)
Black Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rrattus_CSIRO_v1132,052,594 - 2,056,298 (-)NCBIRrattus_CSIRO_v1

Variants

.
Variants in Tmem254
29 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:67
Count of miRNA genes:63
Interacting mature miRNAs:63
Transcripts:ENSRNOT00000015011
Prediction methods:Miranda, Rnahybrid
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
1600378Arunc4Aerobic running capacity QTL 40.03exercise endurance trait (VT:0002332)longest distance run on treadmill (CMO:0001406)1638712345387123Rat
1549842Bp248Blood pressure QTL 2480.01arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1638712345387123Rat
2307172Activ4Activity QTL 43.710.00023locomotor behavior trait (VT:0001392)number of entries into a discrete space in an experimental apparatus (CMO:0000960)16133425095Rat
1354584Despr6Despair related QTL 63.10.0067locomotor behavior trait (VT:0001392)amount of time spent in voluntary immobility (CMO:0001043)16139568015Rat
2303566Bw90Body weight QTL 902body mass (VT:0001259)body weight (CMO:0000012)16139568015Rat
631524Bp75Blood pressure QTL 750.05arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)161177108157035Rat
2312663Slep9Serum leptin concentration QTL 90.001blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)1683908666195506Rat
2312660Bw95Body weight QTL 950.05inguinal fat pad mass (VT:0010424)inguinal fat pad weight to body weight ratio (CMO:0001253)1683908666195506Rat
12903955Kidm69Kidney mass QTL 690.001kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)168392304234212Rat
2312666Insul16Insulin level QTL 160.01blood insulin amount (VT:0001560)serum insulin level (CMO:0000358)1683908666195506Rat
634355Rends4Renal damage susceptibility QTL 40.05kidney blood vessel morphology trait (VT:0000530)organ lesion measurement (CMO:0000677)16126734272Rat
61405Niddm6Non-insulin dependent diabetes mellitus QTL 63.660.001blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)16126734272Rat
2293343Glom16Glomerulus QTL 167.4kidney glomerulus integrity trait (VT:0010546)kidney sclerotic glomeruli count to total glomeruli count ratio (CMO:0001269)1683908652786090Rat
2312669Stl23Serum triglyceride level QTL 230.01blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)1683908666195506Rat
631830Alc7Alcohol consumption QTL 72.9consumption behavior trait (VT:0002069)ethanol drink intake rate (CMO:0001407)16126734272Rat


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 67 165 91 90 59 92 59 6 356 192 11 144 81 92 31 17 17

Sequence


Ensembl Acc Id: ENSRNOT00000015011   ⟹   ENSRNOP00000015011
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl161,503,933 - 1,507,895 (-)Ensembl
Rnor_6.0 Ensembl163,817,402 - 3,821,270 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000088566   ⟹   ENSRNOP00000069971
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl161,510,709 - 1,514,343 (-)Ensembl
mRatBN7.2 Ensembl161,503,937 - 1,507,410 (-)Ensembl
Rnor_6.0 Ensembl163,817,757 - 3,820,684 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000108510   ⟹   ENSRNOP00000093036
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl161,503,933 - 1,506,284 (-)Ensembl
RefSeq Acc Id: NM_001008297   ⟹   NP_001008298
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8161,510,705 - 1,514,591 (-)NCBI
mRatBN7.2161,503,931 - 1,507,819 (-)NCBI
Rnor_6.0163,817,402 - 3,821,270 (+)NCBI
Rnor_5.0163,783,384 - 3,787,313 (+)NCBI
RGSC_v3.4161,542,246 - 1,546,190 (-)RGD
Celera161,479,734 - 1,483,581 (-)RGD
Sequence:
RefSeq Acc Id: XM_006252573   ⟹   XP_006252635
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8161,510,705 - 1,514,325 (-)NCBI
mRatBN7.2161,503,931 - 1,507,501 (-)NCBI
Rnor_6.0163,817,709 - 3,821,270 (+)NCBI
Rnor_5.0163,783,384 - 3,787,313 (+)NCBI
Sequence:
RefSeq Acc Id: XM_039094246   ⟹   XP_038950174
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8161,510,705 - 1,514,152 (-)NCBI
mRatBN7.2161,503,931 - 1,507,383 (-)NCBI
RefSeq Acc Id: NP_001008298   ⟸   NM_001008297
- UniProtKB: Q5U220 (UniProtKB/Swiss-Prot),   A6KMI5 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006252635   ⟸   XM_006252573
- Peptide Label: isoform X1
- UniProtKB: A0A0G2JWQ4 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000015011   ⟸   ENSRNOT00000015011
Ensembl Acc Id: ENSRNOP00000069971   ⟸   ENSRNOT00000088566
RefSeq Acc Id: XP_038950174   ⟸   XM_039094246
- Peptide Label: isoform X2
Ensembl Acc Id: ENSRNOP00000093036   ⟸   ENSRNOT00000108510

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q5U220-F1-model_v2 AlphaFold Q5U220 1-123 view protein structure

Transcriptome

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

Promoters
RGD ID:13699902
Promoter ID:EPDNEW_R10426
Type:initiation region
Name:Tmem254_1
Description:transmembrane protein 254
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Alternative Promoters:null; see alsoEPDNEW_R10427  
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0163,817,323 - 3,817,383EPDNEW
RGD ID:13699924
Promoter ID:EPDNEW_R10427
Type:single initiation site
Name:Tmem254_2
Description:transmembrane protein 254
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Alternative Promoters:null; see alsoEPDNEW_R10426  
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0163,817,779 - 3,817,839EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1305689 AgrOrtholog
BioCyc Gene G2FUF-12263 BioCyc
Ensembl Genes ENSRNOG00000011276 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000015011.6 UniProtKB/Swiss-Prot
  ENSRNOT00000088566 ENTREZGENE
IMAGE_CLONE IMAGE:7304524 IMAGE-MGC_LOAD
InterPro TMEM254 UniProtKB/Swiss-Prot
KEGG Report rno:290529 UniProtKB/Swiss-Prot
MGC_CLONE MGC:105674 IMAGE-MGC_LOAD
NCBI Gene 290529 ENTREZGENE
PANTHER PTHR34104 UniProtKB/Swiss-Prot
  TRANSMEMBRANE PROTEIN 254 UniProtKB/Swiss-Prot
Pfam DUF4499 UniProtKB/Swiss-Prot
PhenoGen Tmem254 PhenoGen
RatGTEx ENSRNOG00000011276 RatGTEx
UniProt A0A0G2JWQ4 ENTREZGENE, UniProtKB/TrEMBL
  A6KMI5 ENTREZGENE, UniProtKB/TrEMBL
  Q5U220 ENTREZGENE, UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2012-11-19 Tmem254  transmembrane protein 254  RGD1305689  homolog of C10orf57 (human)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2012-10-10 RGD1305689  homolog of C10orf57 (human)  Fam213a  family with sequence similarity 213, member A  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2011-12-06 Fam213a  family with sequence similarity 213, member A  RGD1305689  similar to DNA segment, Chr 14, ERATO Doi 449, expressed  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2005-12-06 RGD1305689  similar to DNA segment, Chr 14, ERATO Doi 449, expressed  RGD1305689_predicted  similar to DNA segment, Chr 14, ERATO Doi 449, expressed (predicted)  Symbol and Name updated 1559027 APPROVED
2005-01-20 RGD1305689_predicted  similar to DNA segment, Chr 14, ERATO Doi 449, expressed (predicted)  LOC290529_predicted    Symbol and Name status set to approved 1331353 APPROVED
2005-01-12 LOC290529_predicted  similar to DNA segment, Chr 14, ERATO Doi 449, expressed (predicted)      Symbol and Name status set to provisional 70820 PROVISIONAL