Tmem170a (transmembrane protein 170A) - Rat Genome Database

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Gene: Tmem170a (transmembrane protein 170A) Rattus norvegicus
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Symbol: Tmem170a
Name: transmembrane protein 170A
RGD ID: 1559505
Description: Predicted to be involved in endoplasmic reticulum tubular network organization; nuclear envelope organization; and nuclear pore complex assembly. Predicted to be located in endoplasmic reticulum membrane and nuclear envelope. Orthologous to human TMEM170A (transmembrane protein 170A); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 2,3,7,8-Tetrachlorodibenzofuran; acetamide.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: hypothetical protein LOC498953; LOC498953; RGD1559505; similar to RIKEN cDNA 9030409E16; uncharacterized protein LOC498953
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81956,743,221 - 56,756,085 (-)NCBIGRCr8GRCr8GRCr8
mRatBN7.21939,833,947 - 39,846,807 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1939,833,980 - 39,846,783 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx1946,694,062 - 46,705,013 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01947,347,393 - 47,358,344 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01949,592,373 - 49,603,691 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.01944,090,418 - 44,101,365 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1944,088,612 - 44,101,365 (-)Ensemblrn6Rnor6.0
Rnor_5.01954,897,334 - 54,901,842 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.41941,804,662 - 41,809,223 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera1939,195,099 - 39,206,045 (-)NCBICelera
Cytogenetic Map19q12NCBI
JBrowse:




Disease Annotations     Click to see Annotation Detail View

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

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. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:26906412  


Genomics

Comparative Map Data
Tmem170a
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81956,743,221 - 56,756,085 (-)NCBIGRCr8GRCr8GRCr8
mRatBN7.21939,833,947 - 39,846,807 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1939,833,980 - 39,846,783 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx1946,694,062 - 46,705,013 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01947,347,393 - 47,358,344 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01949,592,373 - 49,603,691 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.01944,090,418 - 44,101,365 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1944,088,612 - 44,101,365 (-)Ensemblrn6Rnor6.0
Rnor_5.01954,897,334 - 54,901,842 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.41941,804,662 - 41,809,223 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera1939,195,099 - 39,206,045 (-)NCBICelera
Cytogenetic Map19q12NCBI
TMEM170A
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381675,443,054 - 75,464,737 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1675,443,054 - 75,465,497 (-)Ensemblhg38GRCh38
GRCh371675,476,952 - 75,498,635 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361674,038,418 - 74,056,085 (-)NCBIBuild 36Build 36hg18NCBI36
Celera1659,775,225 - 59,792,897 (-)NCBICelera
Cytogenetic Map16q23.1NCBI
HuRef1661,232,391 - 61,249,969 (-)NCBIHuRef
CHM1_11676,893,252 - 76,910,917 (-)NCBICHM1_1
T2T-CHM13v2.01681,488,941 - 81,510,632 (-)NCBIT2T-CHM13v2.0
Tmem170
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm398112,589,670 - 112,603,378 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl8112,589,670 - 112,603,382 (-)EnsemblGRCm39 EnsemblGRCm39
GRCm388111,863,038 - 111,876,746 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl8111,863,038 - 111,876,750 (-)Ensemblmm10GRCm38
MGSCv378114,388,798 - 114,400,575 (-)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv368114,751,571 - 114,763,348 (-)NCBIMGSCv36mm8
Celera8116,093,449 - 116,105,227 (-)NCBICelera
Cytogenetic Map8E1NCBI
cM Map858.08NCBI
Tmem170a
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554842,057,934 - 2,078,157 (+)Ensembl
ChiLan1.0NW_0049554842,057,934 - 2,078,157 (+)NCBIChiLan1.0ChiLan1.0
TMEM170A
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v21885,161,560 - 85,211,043 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11691,083,918 - 91,133,716 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01656,012,951 - 56,062,442 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11675,361,367 - 75,382,857 (-)NCBIPanPan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1675,361,367 - 75,382,857 (-)EnsemblpanPan2panpan1.1
TMEM170A
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1575,287,997 - 75,307,064 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl575,288,139 - 75,303,755 (+)EnsemblcanFam3CanFam3.1
Dog10K_Boxer_Tasha575,265,104 - 75,284,192 (+)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.0575,601,763 - 75,620,852 (+)NCBIROS_Cfam_1.0ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl575,601,926 - 75,620,840 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1575,537,598 - 75,556,680 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0575,372,773 - 75,391,857 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0575,863,907 - 75,883,002 (+)NCBIUU_Cfam_GSD_1.0UU_Cfam_GSD_1.0
Tmem170a
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440934935,404,564 - 35,419,021 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_00493647524,169,224 - 24,184,505 (-)EnsemblSpeTri2.0 Ensembl
SpeTri2.0NW_00493647524,168,798 - 24,184,519 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
TMEM170A
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl612,195,137 - 12,215,744 (+)EnsemblsusScr11Sscrofa11.1
Sscrofa11.1612,195,123 - 12,215,753 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2612,036,386 - 12,055,073 (+)NCBISscrofa10.2Sscrofa10.2susScr3
TMEM170A
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1560,932,401 - 60,948,951 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl560,928,179 - 60,949,019 (-)EnsemblChlSab1.1 EnsemblchlSab2Vervet-AGM
Vero_WHO_p1.0NW_02366604715,110,909 - 15,127,642 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Tmem170a
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462474611,458,662 - 11,476,640 (+)EnsemblHetGla_female_1.0 EnsemblhetGla2HetGla_female_1.0 Ensembl
HetGla 1.0NW_00462474611,458,868 - 11,479,425 (+)NCBIHetGla 1.0HetGla 1.0hetGla2

Variants

.
Variants in Tmem170a
3 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:756
Count of miRNA genes:298
Interacting mature miRNAs:378
Transcripts:ENSRNOT00000074824
Prediction methods:Microtar, Miranda, 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
61447Tcas1Tongue tumor susceptibility QTL 16.08tongue integrity trait (VT:0010553)squamous cell carcinoma of the tongue maximum tumor diameter (CMO:0001875)191922068964220689Rat
631840Niddm38Non-insulin dependent diabetes mellitus QTL 383.86blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)191032907674246245Rat
724546Kidm3Kidney mass QTL 33.1kidney mass (VT:0002707)calculated kidney weight (CMO:0000160)194622677874246245Rat
7411549Bw130Body weight QTL 13050.001body mass (VT:0001259)body weight gain (CMO:0000420)193236531174246245Rat
1331737Uae29Urinary albumin excretion QTL 295.5urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)193628974246245Rat
724518Uae19Urinary albumin excretion QTL 195.5urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)192409397369093973Rat
61423Cia14Collagen induced arthritis QTL 143joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)191083361874246245Rat
2303628Vencon9Ventilatory control QTL 90.005respiration trait (VT:0001943)minute ventilation (CMO:0000132)192318858668188586Rat
2313395Anxrr26Anxiety related response QTL 26aggression-related behavior trait (VT:0015014)tameness/aggressiveness composite score (CMO:0002136)194438513474246245Rat
1578764Stresp19Stress response QTL 193.60.001blood renin amount (VT:0003349)plasma renin activity level (CMO:0000116)193253961574246245Rat
1331788Rf45Renal function QTL 452.818kidney blood vessel physiology trait (VT:0100012)absolute change in renal blood flow rate (CMO:0001168)193177788874246245Rat
1554318Bmd5Bone mineral density QTL 512.10.0001lumbar vertebra mineral mass (VT:0010511)volumetric bone mineral density (CMO:0001553)192318858668188586Rat
2317848Alcrsp21Alcohol response QTL 211.8999999761581420.05response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)192010930665109306Rat
7247442Uae39Urinary albumin excretion QTL 39urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)19219431774246245Rat
1549835Tcas7Tongue tumor susceptibility QTL 70.001tongue integrity trait (VT:0010553)squamous cell carcinoma of the head and neck tumor number (CMO:0001876)194172254674246245Rat
724566Uae12Urinary albumin excretion QTL 125urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)19219431774246245Rat


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 67 162 91 90 59 92 59 6 356 192 11 141 81 92 31 17 17

Sequence


Ensembl Acc Id: ENSRNOT00000074824   ⟹   ENSRNOP00000064093
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1939,833,980 - 39,846,783 (-)Ensembl
Rnor_6.0 Ensembl1944,088,612 - 44,095,250 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000082182   ⟹   ENSRNOP00000075609
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1944,090,418 - 44,101,365 (-)Ensembl
RefSeq Acc Id: NM_001134608   ⟹   NP_001128080
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81956,745,069 - 56,756,018 (-)NCBI
mRatBN7.21939,835,795 - 39,846,744 (-)NCBI
Rnor_6.01944,090,418 - 44,101,365 (-)NCBI
Rnor_5.01954,897,334 - 54,901,842 (-)NCBI
RGSC_v3.41941,804,662 - 41,809,223 (-)RGD
Celera1939,195,099 - 39,206,045 (-)RGD
Sequence:
RefSeq Acc Id: XM_039097934   ⟹   XP_038953862
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81956,743,221 - 56,756,085 (-)NCBI
mRatBN7.21939,833,947 - 39,846,807 (-)NCBI
Protein Sequences
Protein RefSeqs NP_001128080 (Get FASTA)   NCBI Sequence Viewer  
  XP_038953862 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDL92590 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000064093.3
RefSeq Acc Id: NP_001128080   ⟸   NM_001134608
- UniProtKB: M0R417 (UniProtKB/TrEMBL),   A6IZB2 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000075609   ⟸   ENSRNOT00000082182
Ensembl Acc Id: ENSRNOP00000064093   ⟸   ENSRNOT00000074824
RefSeq Acc Id: XP_038953862   ⟸   XM_039097934
- Peptide Label: isoform X1

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-A0A0G2KB13-F1-model_v2 AlphaFold A0A0G2KB13 1-142 view protein structure

Transcriptome

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

Promoters
RGD ID:13701154
Promoter ID:EPDNEW_R11678
Type:single initiation site
Name:Tmem170a_1
Description:transmembrane protein 170A
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_6.01944,101,406 - 44,101,466EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1559505 AgrOrtholog
BioCyc Gene G2FUF-5640 BioCyc
Ensembl Genes ENSRNOG00000049019 Ensembl, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000074824.3 UniProtKB/TrEMBL
InterPro Transmembrane_pr_170 UniProtKB/TrEMBL
KEGG Report rno:498953 UniProtKB/TrEMBL
NCBI Gene 498953 ENTREZGENE
PANTHER PTHR22779 UniProtKB/TrEMBL
  TRANSMEMBRANE PROTEIN 170A UniProtKB/TrEMBL
Pfam Tmemb_170 UniProtKB/TrEMBL
PhenoGen Tmem170a PhenoGen
RatGTEx ENSRNOG00000049019 RatGTEx
UniProt A6IZB2 ENTREZGENE, UniProtKB/TrEMBL
  M0R417 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2012-10-11 Tmem170a  transmembrane protein 170A  RGD1559505  similar to RIKEN cDNA 9030409E16  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-04-30 RGD1559505  similar to RIKEN cDNA 9030409E16   RGD1559505_predicted  similar to RIKEN cDNA 9030409E16 (predicted)  'predicted' is removed 2292626 APPROVED
2006-03-07 RGD1559505_predicted  similar to RIKEN cDNA 9030409E16 (predicted)  LOC498953  similar to RIKEN cDNA 9030409E16  Symbol and Name status set to approved 1299863 APPROVED
2006-02-09 LOC498953  similar to RIKEN cDNA 9030409E16      Symbol and Name status set to provisional 70820 PROVISIONAL