Tmem17 (transmembrane protein 17) - Rat Genome Database

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Gene: Tmem17 (transmembrane protein 17) Rattus norvegicus
Analyze
Symbol: Tmem17
Name: transmembrane protein 17
RGD ID: 1310566
Description: Predicted to be involved in non-motile cilium assembly and smoothened signaling pathway. Predicted to be located in ciliary membrane. Predicted to be part of MKS complex. Predicted to be active in ciliary transition zone. Orthologous to human TMEM17 (transmembrane protein 17); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 2,4-dinitrotoluene; amitrole.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: LOC360985
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
GRCr814100,684,655 - 100,725,471 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl14100,685,093 - 100,725,470 (+)EnsemblGRCr8
mRatBN7.21496,483,648 - 96,524,238 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1496,518,793 - 96,524,233 (+)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx14100,863,078 - 100,869,002 (+)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.014102,105,343 - 102,111,268 (+)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01498,576,957 - 98,582,881 (+)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.014107,268,235 - 107,308,546 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl14107,268,128 - 107,308,542 (+)Ensemblrn6Rnor6.0
Rnor_5.014107,331,758 - 107,371,947 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.414103,162,310 - 103,167,728 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera1495,508,270 - 95,513,688 (+)NCBICelera
RGSC_v3.114103,181,520 - 103,186,939 (+)NCBI
Cytogenetic Map14q22NCBI
JBrowse:




Disease Annotations     Click to see Annotation Detail View

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component
ciliary membrane  (IEA,ISO,ISS)
ciliary transition zone  (IBA,IEA,ISO,ISS)
membrane  (IEA,ISO)
MKS complex  (IEA,ISO,ISS)

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. GOA pipeline RGD automated data pipeline
3. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:12477932   PMID:15489334   PMID:22179047   PMID:26982032  


Genomics

Comparative Map Data
Tmem17
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr814100,684,655 - 100,725,471 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl14100,685,093 - 100,725,470 (+)EnsemblGRCr8
mRatBN7.21496,483,648 - 96,524,238 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1496,518,793 - 96,524,233 (+)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx14100,863,078 - 100,869,002 (+)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.014102,105,343 - 102,111,268 (+)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01498,576,957 - 98,582,881 (+)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.014107,268,235 - 107,308,546 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl14107,268,128 - 107,308,542 (+)Ensemblrn6Rnor6.0
Rnor_5.014107,331,758 - 107,371,947 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.414103,162,310 - 103,167,728 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera1495,508,270 - 95,513,688 (+)NCBICelera
RGSC_v3.114103,181,520 - 103,186,939 (+)NCBI
Cytogenetic Map14q22NCBI
TMEM17
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38262,453,531 - 62,506,195 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl262,500,218 - 62,511,894 (-)Ensemblhg38GRCh38
GRCh37262,727,353 - 62,733,330 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36262,581,252 - 62,586,980 (-)NCBIBuild 36Build 36hg18NCBI36
Build 34262,639,412 - 62,645,127NCBI
Celera262,572,191 - 62,578,440 (-)NCBICelera
Cytogenetic Map2p15NCBI
HuRef262,465,324 - 62,471,573 (-)NCBIHuRef
CHM1_1262,657,923 - 62,664,172 (-)NCBICHM1_1
T2T-CHM13v2.0262,459,855 - 62,512,518 (-)NCBIT2T-CHM13v2.0
Tmem17
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391122,462,283 - 22,469,231 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1122,462,088 - 22,469,234 (+)EnsemblGRCm39 EnsemblGRCm39
GRCm381122,512,283 - 22,519,231 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1122,512,088 - 22,519,234 (+)Ensemblmm10GRCm38
MGSCv371122,412,286 - 22,419,234 (+)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv361122,412,286 - 22,419,234 (+)NCBIMGSCv36mm8
Celera1124,649,073 - 24,656,059 (+)NCBICelera
Cytogenetic Map11A3.2NCBI
cM Map1114.17NCBI
Tmem17
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495542421,627,151 - 21,637,041 (+)Ensembl
ChiLan1.0NW_00495542421,627,889 - 21,634,798 (+)NCBIChiLan1.0ChiLan1.0
TMEM17
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v21263,877,577 - 63,886,644 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan12A63,881,521 - 63,890,578 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v02A62,580,872 - 62,587,936 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.12A63,710,004 - 63,716,422 (-)NCBIPanPan1.1PanPan1.1panPan2
PanPan1.1 Ensembl2A63,710,004 - 63,716,422 (-)EnsemblpanPan2panpan1.1
TMEM17
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11062,355,849 - 62,361,445 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1062,356,277 - 62,361,397 (-)EnsemblcanFam3CanFam3.1
Dog10K_Boxer_Tasha1062,243,628 - 62,249,224 (-)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.01063,363,234 - 63,368,846 (-)NCBIROS_Cfam_1.0ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl1063,363,662 - 63,368,797 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.11063,046,203 - 63,051,806 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.01063,349,705 - 63,355,323 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.01063,646,177 - 63,651,789 (-)NCBIUU_Cfam_GSD_1.0UU_Cfam_GSD_1.0
Tmem17
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440629220,844,325 - 20,850,142 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049364917,719,658 - 7,727,107 (-)EnsemblSpeTri2.0 Ensembl
SpeTri2.0NW_0049364917,721,150 - 7,726,983 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
TMEM17
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl379,415,717 - 79,422,393 (+)EnsemblsusScr11Sscrofa11.1
Sscrofa11.1379,415,767 - 79,422,397 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
TMEM17
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11444,462,402 - 44,468,983 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl1444,462,158 - 44,468,975 (+)EnsemblChlSab1.1 EnsemblchlSab2Vervet-AGM
Vero_WHO_p1.0NW_02366604567,365,751 - 67,371,995 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Tmem17
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462476210,969,765 - 10,976,870 (+)EnsemblHetGla_female_1.0 EnsemblhetGla2HetGla_female_1.0 Ensembl
HetGla 1.0NW_00462476210,970,048 - 10,975,736 (+)NCBIHetGla 1.0HetGla 1.0hetGla2
Tmem17
(Rattus rattus - black rat)
Black Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rrattus_CSIRO_v11194,335,410 - 94,342,140 (-)NCBIRrattus_CSIRO_v1

Variants

.
Variants in Tmem17
318 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:52
Count of miRNA genes:49
Interacting mature miRNAs:49
Transcripts:ENSRNOT00000012224
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
634328Hc5Hypercalciuria QTL 52.3urine calcium amount (VT:0002985)urine calcium excretion rate (CMO:0000763)1462398852107398852Rat
2317879Alcrsp27Alcohol response QTL 273.30.63response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)1460854936105854936Rat
9590294Uminl4Urine mineral level QTL 45.660.001urine mineral amount (VT:0015086)urine electrolyte level (CMO:0000593)1459848686104848686Rat
1641900Alcrsp11Alcohol response QTL 11alcohol metabolism trait (VT:0015089)blood ethanol level (CMO:0000535)1474255551109089856Rat
2300197Scl59Serum cholesterol level QTL 59blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)1477914838104348525Rat
9589034Epfw11Epididymal fat weight QTL 1160.001epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)1459848686104848686Rat
631523Pia13Pristane induced arthritis QTL 133.3joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1433424686102238540Rat
1582259Gluco23Glucose level QTL 233.10.0008blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)1474255551109089856Rat

Markers in Region
AA923937  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21496,523,994 - 96,524,193 (+)MAPPERmRatBN7.2
Rnor_6.014107,308,300 - 107,308,498NCBIRnor6.0
Rnor_5.014107,371,704 - 107,371,902UniSTSRnor5.0
RGSC_v3.414103,167,802 - 103,168,000UniSTSRGSC3.4
Celera1495,513,762 - 95,513,960UniSTS
RH 3.4 Map14764.3UniSTS
Cytogenetic Map14q22UniSTS


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 89 59 6 353 189 11 144 81 92 31 17 17

Sequence


Ensembl Acc Id: ENSRNOT00000012224   ⟹   ENSRNOP00000012224
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl14100,685,093 - 100,725,470 (+)Ensembl
mRatBN7.2 Ensembl1496,518,793 - 96,524,233 (+)Ensembl
Rnor_6.0 Ensembl14107,268,128 - 107,308,542 (+)Ensembl
RefSeq Acc Id: NM_001010961   ⟹   NP_001010961
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr814100,719,672 - 100,725,466 (+)NCBI
mRatBN7.21496,518,439 - 96,524,233 (+)NCBI
Rnor_6.014107,302,808 - 107,308,226 (+)NCBI
Rnor_5.014107,331,758 - 107,371,947 (+)NCBI
RGSC_v3.414103,162,310 - 103,167,728 (+)RGD
Celera1495,508,270 - 95,513,688 (+)RGD
Sequence:
RefSeq Acc Id: XM_017599320   ⟹   XP_017454809
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr814100,684,655 - 100,725,471 (+)NCBI
mRatBN7.21496,483,723 - 96,524,238 (+)NCBI
Rnor_6.014107,268,235 - 107,308,546 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017599321   ⟹   XP_017454810
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr814100,684,655 - 100,725,471 (+)NCBI
mRatBN7.21496,483,723 - 96,524,238 (+)NCBI
Rnor_6.014107,268,235 - 107,308,546 (+)NCBI
Sequence:
RefSeq Acc Id: XM_039092230   ⟹   XP_038948158
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr814100,684,655 - 100,725,471 (+)NCBI
mRatBN7.21496,483,648 - 96,524,238 (+)NCBI
RefSeq Acc Id: XM_063273406   ⟹   XP_063129476
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr814100,712,476 - 100,725,471 (+)NCBI
RefSeq Acc Id: NP_001010961   ⟸   NM_001010961
- UniProtKB: Q5HZE5 (UniProtKB/Swiss-Prot),   A6JQ51 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_017454809   ⟸   XM_017599320
- Peptide Label: isoform X1
- UniProtKB: Q5HZE5 (UniProtKB/Swiss-Prot),   A6JQ51 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_017454810   ⟸   XM_017599321
- Peptide Label: isoform X1
- UniProtKB: Q5HZE5 (UniProtKB/Swiss-Prot),   A6JQ51 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000012224   ⟸   ENSRNOT00000012224
RefSeq Acc Id: XP_038948158   ⟸   XM_039092230
- Peptide Label: isoform X2
RefSeq Acc Id: XP_063129476   ⟸   XM_063273406
- Peptide Label: isoform X1
- UniProtKB: Q5HZE5 (UniProtKB/Swiss-Prot),   A6JQ51 (UniProtKB/TrEMBL)

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q5HZE5-F1-model_v2 AlphaFold Q5HZE5 1-198 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:1310566 AgrOrtholog
BioCyc Gene G2FUF-14817 BioCyc
Ensembl Genes ENSRNOG00000009220 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000012224 ENTREZGENE
  ENSRNOT00000012224.6 UniProtKB/Swiss-Prot
IMAGE_CLONE IMAGE:7320241 IMAGE-MGC_LOAD
InterPro Uncharacterised_TM-17 UniProtKB/Swiss-Prot
KEGG Report rno:360985 UniProtKB/Swiss-Prot
MGC_CLONE MGC:105637 IMAGE-MGC_LOAD
NCBI Gene 360985 ENTREZGENE
PANTHER PTHR13531 UniProtKB/Swiss-Prot
  TRANSMEMBRANE PROTEIN 17 UniProtKB/Swiss-Prot
Pfam Transmemb_17 UniProtKB/Swiss-Prot
PhenoGen Tmem17 PhenoGen
RatGTEx ENSRNOG00000009220 RatGTEx
UniProt A6JQ49_RAT UniProtKB/TrEMBL
  A6JQ51 ENTREZGENE, UniProtKB/TrEMBL
  Q5HZE5 ENTREZGENE, UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2005-12-06 Tmem17  transmembrane protein 17  Tmem17_predicted  transmembrane protein 17 (predicted)  Symbol and Name updated 1559027 APPROVED
2005-01-12 Tmem17_predicted  transmembrane protein 17 (predicted)      Symbol and Name status set to approved 70820 APPROVED