Tmie (transmembrane inner ear) - Rat Genome Database

Send us a Message



Submit Data |  Help |  Video Tutorials |  News |  Publications |  Download |  REST API |  Citing RGD |  Contact   
Pathways
Gene: Tmie (transmembrane inner ear) Rattus norvegicus
Analyze
Symbol: Tmie
Name: transmembrane inner ear
RGD ID: 1562523
Description: Predicted to be involved in inner ear morphogenesis and sensory perception of sound. Predicted to be located in plasma membrane. Human ortholog(s) of this gene implicated in autosomal recessive nonsyndromic deafness 6 and sensorineural hearing loss. Orthologous to human TMIE (transmembrane inner ear); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 6-propyl-2-thiouracil; acetamide.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: LOC501061; RGD1562523; similar to putative integral membrane protein TMIE; transmembrane inner ear expressed protein
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
GRCr88119,728,123 - 119,743,219 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl8119,728,313 - 119,743,219 (-)EnsemblGRCr8
mRatBN7.28110,849,713 - 110,864,803 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl8110,850,034 - 110,864,803 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx8116,464,077 - 116,478,809 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.08114,663,287 - 114,678,021 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.08112,506,107 - 112,520,841 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.08119,142,116 - 119,157,071 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl8119,142,434 - 119,157,071 (-)Ensemblrn6Rnor6.0
Rnor_5.08118,480,524 - 118,495,446 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.48115,254,502 - 115,269,123 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera8110,132,596 - 110,147,266 (-)NCBICelera
Cytogenetic Map8q32NCBI
JBrowse:




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. Mutations in a novel gene, TMIE, are associated with hearing loss linked to the DFNB6 locus. Naz S, etal., Am J Hum Genet. 2002 Sep;71(3):632-6. Epub 2002 Jul 24.
3. OMIM Disease Annotation Pipeline OMIM Disease Annotation Pipeline
4. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
5. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
6. Comprehensive gene review and curation RGD comprehensive gene curation
Additional References at PubMed
PMID:12140191   PMID:18327602   PMID:20819378  


Genomics

Comparative Map Data
Tmie
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr88119,728,123 - 119,743,219 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl8119,728,313 - 119,743,219 (-)EnsemblGRCr8
mRatBN7.28110,849,713 - 110,864,803 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl8110,850,034 - 110,864,803 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx8116,464,077 - 116,478,809 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.08114,663,287 - 114,678,021 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.08112,506,107 - 112,520,841 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.08119,142,116 - 119,157,071 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl8119,142,434 - 119,157,071 (-)Ensemblrn6Rnor6.0
Rnor_5.08118,480,524 - 118,495,446 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.48115,254,502 - 115,269,123 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera8110,132,596 - 110,147,266 (-)NCBICelera
Cytogenetic Map8q32NCBI
TMIE
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38346,693,778 - 46,710,886 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl346,694,528 - 46,710,886 (+)Ensemblhg38GRCh38
GRCh37346,735,268 - 46,752,376 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36346,717,827 - 46,727,205 (+)NCBIBuild 36Build 36hg18NCBI36
Build 34346,717,826 - 46,727,205NCBI
Celera346,680,576 - 46,691,109 (+)NCBICelera
Cytogenetic Map3p21.31NCBI
HuRef346,785,701 - 46,795,263 (+)NCBIHuRef
CHM1_1346,692,939 - 46,702,529 (+)NCBICHM1_1
T2T-CHM13v2.0346,709,892 - 46,726,971 (+)NCBIT2T-CHM13v2.0
Tmie
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm399110,694,755 - 110,709,141 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl9110,694,779 - 110,709,181 (-)EnsemblGRCm39 EnsemblGRCm39
GRCm389110,865,687 - 110,880,073 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl9110,865,711 - 110,880,113 (-)Ensemblmm10GRCm38
MGSCv379110,768,550 - 110,782,587 (-)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv369110,710,862 - 110,724,899 (-)NCBIMGSCv36mm8
Celera9110,587,099 - 110,606,043 (-)NCBICelera
Cytogenetic Map9F2NCBI
cM Map960.79NCBI
Tmie
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495542025,428,503 - 25,435,701 (-)Ensembl
ChiLan1.0NW_00495542025,428,542 - 25,435,701 (-)NCBIChiLan1.0ChiLan1.0
TMIE
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2246,656,687 - 46,666,796 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1346,661,457 - 46,671,515 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0346,590,527 - 46,608,981 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
TMIE
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12042,052,607 - 42,061,424 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2042,053,817 - 42,061,262 (-)EnsemblcanFam3CanFam3.1
Dog10K_Boxer_Tasha2041,968,797 - 41,977,845 (-)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.02042,535,195 - 42,544,248 (-)NCBIROS_Cfam_1.0ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl2042,535,201 - 42,543,855 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.12041,776,485 - 41,785,526 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.02042,177,543 - 42,186,577 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.02042,458,570 - 42,467,619 (-)NCBIUU_Cfam_GSD_1.0UU_Cfam_GSD_1.0
Tmie
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024405118200,982,111 - 200,991,469 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_004936596531,254 - 541,693 (+)EnsemblSpeTri2.0 Ensembl
SpeTri2.0NW_004936596531,260 - 540,608 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
TMIE
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1329,624,154 - 29,633,013 (+)EnsemblsusScr11Sscrofa11.1
Sscrofa11.11329,623,905 - 29,633,016 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21333,028,518 - 33,030,240 (+)NCBISscrofa10.2Sscrofa10.2susScr3
TMIE
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1228,114,995 - 8,133,827 (+)NCBIChlSab1.1ChlSab1.1chlSab2
Vero_WHO_p1.0NW_023666041159,016,256 - 159,033,772 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Tmie
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462473074,498,281 - 74,505,041 (-)EnsemblHetGla_female_1.0 EnsemblhetGla2HetGla_female_1.0 Ensembl
HetGla 1.0NW_00462473074,498,257 - 74,506,180 (-)NCBIHetGla 1.0HetGla 1.0hetGla2
Tmie
(Rattus rattus - black rat)
Black Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rrattus_CSIRO_v18101,446,997 - 101,455,448 (-)NCBIRrattus_CSIRO_v1

Variants

.
Variants in Tmie
86 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:125
Count of miRNA genes:91
Interacting mature miRNAs:110
Transcripts:ENSRNOT00000028963
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 (GRCr8)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
2303171Bp331Blood pressure QTL 3315.570.005arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)8105462581132782436Rat
1549909Stresp11Stress response QTL 116.830.0019stress-related behavior trait (VT:0010451)number of approaches toward negative stimulus before onset of defensive burying response (CMO:0001960)882352698127352698Rat
631210Bw3Body weight QTL35.9mesenteric fat pad mass (VT:0010427)mesenteric fat pad weight to body weight ratio (CMO:0000654)861019838121662124Rat
9590292Uminl3Urine mineral level QTL 33.620.001urine mineral amount (VT:0015086)urine electrolyte level (CMO:0000593)880768445125768445Rat
8694446Bw170Body weight QTL 17012.070.001retroperitoneal fat pad mass (VT:0010430)retroperitoneal fat pad weight to body weight ratio (CMO:0000635)880768445125768445Rat
631650Stl6Serum triglyceride level QTL 640.0019blood triglyceride amount (VT:0002644)plasma triglyceride level (CMO:0000548)870041301121080908Rat
1581557Eae16Experimental allergic encephalomyelitis QTL 163.8nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis incidence/prevalence measurement (CMO:0001046)868690349119799881Rat
10450865Bw175Body weight QTL 1754.1total fat pad mass (VT:0015008)adipose tissue molecular composition measurement (CMO:0000484)884192326129192326Rat
724539Cm19Cardiac mass QTL 192.6heart mass (VT:0007028)calculated heart weight (CMO:0000073)8103375781129871912Rat
738011Anxrr9Anxiety related response QTL 96.1exploratory behavior trait (VT:0010471)number of entries into a discrete space in an experimental apparatus (CMO:0000960)8102413464132782436Rat
70197BpQTLcluster8Blood pressure QTL cluster 83.482arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)855428333127966348Rat
634332Pia18Pristane induced arthritis QTL 184joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)884192326132782436Rat
2300181Bmd55Bone mineral density QTL 555.70.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)885348065130348065Rat
1300171Bp184Blood pressure QTL 1843.66arterial blood pressure trait (VT:2000000)blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)879394435132782436Rat
2313400Anxrr25Anxiety related response QTL 25aggression-related behavior trait (VT:0015014)tameness/aggressiveness composite score (CMO:0002136)898145073122898010Rat
8694200Abfw4Abdominal fat weight QTL 49.070.001visceral adipose mass (VT:0010063)abdominal fat pad weight to body weight ratio (CMO:0000095)880768445125768445Rat
8694392Bw161Body weight QTL 1618.060.001body lean mass (VT:0010483)lean tissue morphological measurement (CMO:0002184)880768445125768445Rat
61437Cia6Collagen induced arthritis QTL 6joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)891340911131690273Rat


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
10 12 56 140 88 87 59 70 59 6 306 159 11 112 70 81 28 14 14

Sequence


Ensembl Acc Id: ENSRNOT00000028963   ⟹   ENSRNOP00000029990
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl8119,728,313 - 119,743,219 (-)Ensembl
mRatBN7.2 Ensembl8110,850,034 - 110,864,803 (-)Ensembl
Rnor_6.0 Ensembl8119,142,434 - 119,157,071 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000153716   ⟹   ENSRNOP00000100638
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl8119,728,444 - 119,737,692 (-)Ensembl
RefSeq Acc Id: NM_001109299   ⟹   NP_001102769
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr88119,728,444 - 119,743,219 (-)NCBI
mRatBN7.28110,850,034 - 110,864,803 (-)NCBI
Rnor_6.08119,142,434 - 119,157,071 (-)NCBI
Rnor_5.08118,480,524 - 118,495,446 (-)NCBI
RGSC_v3.48115,254,502 - 115,269,123 (-)RGD
Celera8110,132,596 - 110,147,266 (-)RGD
Sequence:
RefSeq Acc Id: XM_006243995   ⟹   XP_006244057
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr88119,728,123 - 119,734,770 (-)NCBI
mRatBN7.28110,849,713 - 110,857,527 (-)NCBI
Rnor_6.08119,142,116 - 119,149,937 (-)NCBI
Rnor_5.08118,480,524 - 118,495,446 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006243996   ⟹   XP_006244058
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr88119,728,123 - 119,736,639 (-)NCBI
mRatBN7.28110,849,713 - 110,858,084 (-)NCBI
Rnor_6.08119,142,117 - 119,150,662 (-)NCBI
Rnor_5.08118,480,524 - 118,495,446 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039081994   ⟹   XP_038937922
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr88119,728,123 - 119,734,784 (-)NCBI
mRatBN7.28110,849,713 - 110,857,531 (-)NCBI
RefSeq Acc Id: XM_063266009   ⟹   XP_063122079
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr88119,728,123 - 119,736,639 (-)NCBI
RefSeq Acc Id: XM_063266010   ⟹   XP_063122080
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr88119,728,123 - 119,736,639 (-)NCBI
RefSeq Acc Id: NP_001102769   ⟸   NM_001109299
- UniProtKB: D4AE26 (UniProtKB/TrEMBL),   A6I3H9 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006244058   ⟸   XM_006243996
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: XP_006244057   ⟸   XM_006243995
- Peptide Label: isoform X1
- Sequence:
Ensembl Acc Id: ENSRNOP00000029990   ⟸   ENSRNOT00000028963
RefSeq Acc Id: XP_038937922   ⟸   XM_039081994
- Peptide Label: isoform X1
RefSeq Acc Id: XP_063122080   ⟸   XM_063266010
- Peptide Label: isoform X3
RefSeq Acc Id: XP_063122079   ⟸   XM_063266009
- Peptide Label: isoform X2
- UniProtKB: A6I3H9 (UniProtKB/TrEMBL),   D4AE26 (UniProtKB/TrEMBL)
Ensembl Acc Id: ENSRNOP00000100638   ⟸   ENSRNOT00000153716

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D4AE26-F1-model_v2 AlphaFold D4AE26 1-153 view protein structure

Transcriptome

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

Promoters
RGD ID:13696339
Promoter ID:EPDNEW_R6864
Type:multiple initiation site
Name:Tmie_1
Description:transmembrane inner ear
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_6.08119,157,015 - 119,157,075EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1562523 AgrOrtholog
BioCyc Gene G2FUF-29048 BioCyc
Ensembl Genes ENSRNOG00000027799 Ensembl, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000028963.4 UniProtKB/TrEMBL
  ENSRNOT00000153716.1 UniProtKB/TrEMBL
InterPro TMIE UniProtKB/TrEMBL
KEGG Report rno:501061 UniProtKB/TrEMBL
NCBI Gene 501061 ENTREZGENE
PANTHER PTHR28635 UniProtKB/TrEMBL
  TRANSMEMBRANE INNER EAR EXPRESSED PROTEIN UniProtKB/TrEMBL
Pfam TMIE UniProtKB/TrEMBL
PhenoGen Tmie PhenoGen
PROSITE PROKAR_LIPOPROTEIN UniProtKB/TrEMBL
RatGTEx ENSRNOG00000027799 RatGTEx
UniProt A0ABK0KZC1_RAT UniProtKB/TrEMBL
  A6I3H9 ENTREZGENE, UniProtKB/TrEMBL
  D4AE26 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-03-04 Tmie  transmembrane inner ear  Tmie_predicted  similar to putative integral membrane protein TMIE (predicted)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2007-02-05 Tmie_predicted    RGD1562523_predicted  similar to putative integral membrane protein TMIE (predicted)  Symbol updated to reflect Human and Mouse nomenclature 1299863 PROVISIONAL
2007-02-05 Tmie_predicted    RGD1562523_predicted  similar to putative integral membrane protein TMIE (predicted)  Symbol updated to reflect Human and Mouse nomenclature 1299863 PROVISIONAL
2006-03-07 RGD1562523_predicted  similar to putative integral membrane protein TMIE (predicted)  LOC501061  similar to putative integral membrane protein TMIE  Symbol and Name status set to approved 1299863 APPROVED
2006-02-09 LOC501061  similar to putative integral membrane protein TMIE      Symbol and Name status set to provisional 70820 PROVISIONAL