TMC1 (transmembrane channel like 1) - Rat Genome Database

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Gene: TMC1 (transmembrane channel like 1) Canis lupus familiaris
Analyze
Symbol: TMC1
Name: transmembrane channel like 1
RGD ID: 12070351
Description: ENCODES a protein that exhibits mechanosensitive monoatomic ion channel activity (ortholog); INVOLVED IN auditory receptor cell development (ortholog); calcium ion transmembrane transport (ortholog); detection of mechanical stimulus involved in sensory perception of sound (ortholog); ASSOCIATED WITH autosomal dominant nonsyndromic deafness 36 (ortholog); autosomal recessive nonsyndromic deafness (ortholog); autosomal recessive nonsyndromic deafness 7 (ortholog); FOUND IN external side of plasma membrane (inferred); membrane (inferred); plasma membrane (inferred)
Type: protein-coding
RefSeq Status: MODEL
Previously known as: transmembrane channel-like protein 1
RGD Orthologs
Human
Mouse
Rat
Chinchilla
Bonobo
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: CanFam3.1 - Dog CanFam3.1 Assembly
Position:
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1185,041,039 - 85,159,607 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl185,041,574 - 85,187,369 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha185,506,885 - 85,601,896 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0185,491,047 - 85,586,140 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl185,491,544 - 85,637,265 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1185,259,912 - 85,354,773 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0184,963,710 - 85,058,783 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0185,722,917 - 85,817,907 (-)NCBIUU_Cfam_GSD_1.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


References
Additional References at PubMed
PMID:16978186   PMID:30032202  


Genomics

Comparative Map Data
TMC1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1185,041,039 - 85,159,607 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl185,041,574 - 85,187,369 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha185,506,885 - 85,601,896 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0185,491,047 - 85,586,140 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl185,491,544 - 85,637,265 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1185,259,912 - 85,354,773 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0184,963,710 - 85,058,783 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0185,722,917 - 85,817,907 (-)NCBIUU_Cfam_GSD_1.0
TMC1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38972,521,608 - 72,838,297 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl972,521,608 - 72,838,297 (+)EnsemblGRCh38hg38GRCh38
GRCh37975,136,524 - 75,453,213 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36974,326,537 - 74,641,087 (+)NCBINCBI36Build 36hg18NCBI36
Build 34972,366,270 - 72,680,821NCBI
Celera945,709,595 - 46,024,123 (+)NCBICelera
Cytogenetic Map9q21.13NCBI
HuRef944,959,937 - 45,274,606 (+)NCBIHuRef
CHM1_1975,283,347 - 75,597,903 (+)NCBICHM1_1
T2T-CHM13v2.0984,672,507 - 84,989,215 (+)NCBIT2T-CHM13v2.0
Tmc1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391920,760,820 - 20,931,566 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1920,760,822 - 20,931,566 (-)EnsemblGRCm39 Ensembl
GRCm381920,783,456 - 21,037,126 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1920,783,458 - 20,954,202 (-)EnsemblGRCm38mm10GRCm38
MGSCv371920,857,948 - 21,028,692 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361920,851,751 - 21,021,299 (-)NCBIMGSCv36mm8
Celera1921,504,691 - 21,681,769 (-)NCBICelera
Cytogenetic Map19BNCBI
cM Map1913.98NCBI
Tmc1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81227,701,781 - 227,872,534 (-)NCBIGRCr8
mRatBN7.21218,275,249 - 218,446,013 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1218,276,417 - 218,445,955 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1226,704,373 - 226,886,796 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01233,640,940 - 233,823,358 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01226,458,957 - 226,641,395 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01238,336,919 - 238,525,792 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1238,336,919 - 238,441,500 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01245,706,178 - 245,816,628 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
Rnor_5.01245,633,195 - 245,678,137 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41223,911,499 - 224,108,034 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11224,075,517 - 224,193,990 (-)NCBI
Celera1215,544,754 - 215,710,467 (-)NCBICelera
Cytogenetic Map1q51NCBI
Tmc1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_004955434398,829 - 529,810 (-)EnsemblChiLan1.0
ChiLan1.0NW_004955434398,734 - 500,378 (-)NCBIChiLan1.0ChiLan1.0
TMC1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v21171,709,074 - 72,028,283 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1971,715,008 - 72,034,211 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0951,974,326 - 52,200,228 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1971,310,247 - 71,620,858 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl971,400,783 - 71,620,858 (+)Ensemblpanpan1.1panPan2
Tmc1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024404947132,346,646 - 132,503,539 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049365038,719,540 - 8,825,795 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049365038,669,465 - 8,826,340 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
TMC1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1225,929,109 - 226,109,469 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11225,714,601 - 226,111,045 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21252,241,161 - 252,655,554 (+)NCBISscrofa10.2Sscrofa10.2susScr3
TMC1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11283,672,786 - 83,883,985 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl1283,735,988 - 83,877,251 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366603872,127,719 - 72,312,549 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Tmc1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462473694,840 - 203,597 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462473693,146 - 563,264 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in TMC1
1792 total Variants

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

endocrine system hemolymphoid system integumental system musculoskeletal system nervous system reproductive system respiratory system adipose tissue
High
Medium
Low 2
Below cutoff 6 1 1 2 7 6 2 2

Sequence


Reference Sequences
RefSeq Acc Id: ENSCAFT00000002833   ⟹   ENSCAFP00000002627
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
CanFam3.1 Ensembl185,041,574 - 85,187,369 (-)Ensembl
RefSeq Acc Id: ENSCAFT00845000079   ⟹   ENSCAFP00845000060
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
ROS_Cfam_1.0 Ensembl185,491,544 - 85,637,265 (-)Ensembl
RefSeq Acc Id: XM_038452286   ⟹   XP_038308214
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
Dog10K_Boxer_Tasha185,506,885 - 85,601,896 (-)NCBI
RefSeq Acc Id: XM_038452320   ⟹   XP_038308248
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
Dog10K_Boxer_Tasha185,506,885 - 85,601,896 (-)NCBI
RefSeq Acc Id: XM_038465029   ⟹   XP_038320957
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
UMICH_Zoey_3.1185,259,912 - 85,354,773 (-)NCBI
RefSeq Acc Id: XM_038525616   ⟹   XP_038381544
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
UU_Cfam_GSD_1.0185,722,917 - 85,817,907 (-)NCBI
RefSeq Acc Id: XM_038525617   ⟹   XP_038381545
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
UU_Cfam_GSD_1.0185,722,917 - 85,817,907 (-)NCBI
RefSeq Acc Id: XM_038589819   ⟹   XP_038445747
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
UNSW_CanFamBas_1.0184,963,710 - 85,058,783 (-)NCBI
RefSeq Acc Id: XM_038589820   ⟹   XP_038445748
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
UNSW_CanFamBas_1.0184,963,710 - 85,058,783 (-)NCBI
RefSeq Acc Id: XM_038653746   ⟹   XP_038509674
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
ROS_Cfam_1.0185,491,047 - 85,586,140 (-)NCBI
RefSeq Acc Id: XM_038653747   ⟹   XP_038509675
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
ROS_Cfam_1.0185,491,047 - 85,586,140 (-)NCBI
Reference Protein Sequences
RefSeq Acc Id: ENSCAFP00000002627   ⟸   ENSCAFT00000002833
RefSeq Acc Id: XP_038320957   ⟸   XM_038465029
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038445748   ⟸   XM_038589820
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038445747   ⟸   XM_038589819
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038509675   ⟸   XM_038653747
- Peptide Label: isoform X2
- UniProtKB: A0A8C0R7X2 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038509674   ⟸   XM_038653746
- Peptide Label: isoform X1
- UniProtKB: A0A8C0R7X2 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038308248   ⟸   XM_038452320
- Peptide Label: isoform X2
- UniProtKB: A0A8C0R7X2 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038308214   ⟸   XM_038452286
- Peptide Label: isoform X1
- UniProtKB: A0A8C0R7X2 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038381545   ⟸   XM_038525617
- Peptide Label: isoform X2
- UniProtKB: A0A8C0R7X2 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038381544   ⟸   XM_038525616
- Peptide Label: isoform X1
- UniProtKB: A0A8C0R7X2 (UniProtKB/TrEMBL)
RefSeq Acc Id: ENSCAFP00845000060   ⟸   ENSCAFT00845000079
Protein Domains
TMC


Additional Information

Database Acc Id Source(s)
Ensembl Genes ENSCAFG00000001801 Ensembl, UniProtKB/TrEMBL
  ENSCAFG00030022950 UniProtKB/TrEMBL
  ENSCAFG00040000264 UniProtKB/TrEMBL
  ENSCAFG00845000046 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSCAFT00000002833.5 UniProtKB/TrEMBL
  ENSCAFT00030042203.1 UniProtKB/TrEMBL
  ENSCAFT00040000445.1 UniProtKB/TrEMBL
  ENSCAFT00845000079 ENTREZGENE
  ENSCAFT00845000079.1 UniProtKB/TrEMBL
InterPro TMC UniProtKB/TrEMBL
  TMC_dom UniProtKB/TrEMBL
NCBI Gene TMC1 ENTREZGENE
PANTHER PTHR23302 UniProtKB/TrEMBL
  TRANSMEMBRANE CHANNEL-LIKE PROTEIN 1 UniProtKB/TrEMBL
Pfam TMC UniProtKB/TrEMBL
UniProt A0A8C0PBZ6_CANLF UniProtKB/TrEMBL
  A0A8C0PK96_CANLF UniProtKB/TrEMBL
  A0A8C0R7X2 ENTREZGENE
  A0A8I3MGY3_CANLF UniProtKB/TrEMBL
VGNC ID VGNC:47420 ENTREZGENE