Tmtc2 (transmembrane O-mannosyltransferase targeting cadherins 2) - Rat Genome Database

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Gene: Tmtc2 (transmembrane O-mannosyltransferase targeting cadherins 2) Rattus norvegicus
Analyze
Symbol: Tmtc2
Name: transmembrane O-mannosyltransferase targeting cadherins 2
RGD ID: 1309848
Description: Predicted to enable mannosyltransferase activity. Predicted to be involved in calcium ion homeostasis and protein O-linked mannosylation. Predicted to be located in endoplasmic reticulum. Predicted to be active in endoplasmic reticulum membrane. Orthologous to human TMTC2 (transmembrane O-mannosyltransferase targeting cadherins 2); INTERACTS WITH 2-methoxyethanol; 6-propyl-2-thiouracil; amphetamine.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: LOC299762; RGD1309848; similar to RIKEN cDNA D330034A10 gene; transmembrane and tetratricopeptide repeat containing 2; transmembrane and TPR repeat-containing protein 2
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Allele / Splice: Tmtc2Tn(sb-T2/Bart3)2.276Mcwi  
Genetic Models: F344-Tmtc2Tn(sb-T2/Bart3)2.276Mcwi
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2740,392,377 - 40,806,685 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl740,394,220 - 40,807,298 (-)Ensembl
Rnor_6.0747,179,596 - 47,586,777 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl747,181,981 - 47,586,137 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0747,197,110 - 47,603,261 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4743,667,983 - 44,133,854 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1743,688,792 - 44,154,492 (-)NCBI
Celera737,294,447 - 37,702,308 (-)NCBICelera
Cytogenetic Map7q21NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
1,2-dichloroethane  (ISO)
17beta-hydroxy-5alpha-androstan-3-one  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (ISO)
2-methoxyethanol  (EXP)
3,3',4,4'-tetrachlorobiphenyl  (ISO)
3-methylcholanthrene  (ISO)
6-propyl-2-thiouracil  (EXP)
aflatoxin B1  (ISO)
amiodarone  (ISO)
amphetamine  (EXP)
aristolochic acid  (ISO)
arsane  (ISO)
arsenic atom  (ISO)
arsenous acid  (ISO)
atrazine  (ISO)
Benoxacor  (ISO)
benzo[a]pyrene  (ISO)
benzo[b]fluoranthene  (ISO)
benzo[e]pyrene  (ISO)
bisphenol A  (EXP,ISO)
cadmium dichloride  (ISO)
calcitriol  (ISO)
carbon nanotube  (ISO)
chloroprene  (ISO)
choline  (ISO)
cidofovir anhydrous  (ISO)
cisplatin  (ISO)
coumestrol  (ISO)
cyclosporin A  (ISO)
DDT  (EXP)
diarsenic trioxide  (ISO)
dibenz[a,h]anthracene  (ISO)
dibutyl phthalate  (EXP,ISO)
dichloroacetic acid  (ISO)
dioxygen  (ISO)
dorsomorphin  (ISO)
doxorubicin  (ISO)
Enterolactone  (ISO)
entinostat  (ISO)
ethanol  (ISO)
folic acid  (ISO)
formaldehyde  (ISO)
fulvestrant  (ISO)
hydrogen peroxide  (ISO)
ifosfamide  (ISO)
L-methionine  (ISO)
lead(0)  (ISO)
lead(2+)  (ISO)
methapyrilene  (ISO)
methyl methanesulfonate  (ISO)
methylmercury chloride  (ISO)
paracetamol  (EXP,ISO)
perfluorohexanesulfonic acid  (ISO)
perfluorononanoic acid  (ISO)
perfluorooctane-1-sulfonic acid  (ISO)
perfluorooctanoic acid  (ISO)
phenobarbital  (ISO)
pirinixic acid  (ISO)
resveratrol  (ISO)
SB 431542  (ISO)
silicon dioxide  (ISO)
sodium arsenite  (ISO)
sunitinib  (ISO)
tetrachloroethene  (ISO)
tetrachloromethane  (ISO)
thioacetamide  (EXP)
titanium dioxide  (ISO)
trichloroethene  (ISO)
trichostatin A  (ISO)
valproic acid  (ISO)
zoledronic acid  (ISO)

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. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
3. GOA pipeline RGD automated data 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
7. Association of TMTC2 With Human Nonsyndromic Sensorineural Hearing Loss. Runge CL, etal., JAMA Otolaryngol Head Neck Surg. 2016 Jun 16. doi: 10.1001/jamaoto.2016.1444.
Additional References at PubMed
PMID:24764305   PMID:28973932  


Genomics

Comparative Map Data
Tmtc2
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2740,392,377 - 40,806,685 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl740,394,220 - 40,807,298 (-)Ensembl
Rnor_6.0747,179,596 - 47,586,777 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl747,181,981 - 47,586,137 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0747,197,110 - 47,603,261 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4743,667,983 - 44,133,854 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1743,688,792 - 44,154,492 (-)NCBI
Celera737,294,447 - 37,702,308 (-)NCBICelera
Cytogenetic Map7q21NCBI
TMTC2
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381282,686,906 - 83,134,866 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p13 Ensembl1282,686,880 - 83,134,870 (+)EnsemblGRCh38hg38GRCh38
GRCh371283,080,685 - 83,528,645 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361281,605,065 - 82,052,196 (+)NCBINCBI36hg18NCBI36
Celera1282,748,495 - 83,195,421 (+)NCBI
Cytogenetic Map12q21.31NCBI
HuRef1280,139,235 - 80,586,094 (+)NCBIHuRef
CHM1_11283,046,833 - 83,493,575 (+)NCBICHM1_1
T2T-CHM13v2.01282,666,441 - 83,114,534 (+)NCBI
Tmtc2
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm3910105,023,524 - 105,410,340 (-)NCBIGRCm39mm39
GRCm39 Ensembl10105,023,524 - 105,410,312 (-)Ensembl
GRCm3810105,187,663 - 105,574,479 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl10105,187,663 - 105,574,451 (-)EnsemblGRCm38mm10GRCm38
MGSCv3710104,624,719 - 105,011,535 (-)NCBIGRCm37mm9NCBIm37
MGSCv3610104,591,773 - 104,978,561 (-)NCBImm8
Celera10107,116,217 - 107,505,137 (-)NCBICelera
Cytogenetic Map10D1NCBI
Tmtc2
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495540520,969,952 - 21,359,783 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495540520,969,836 - 21,357,939 (+)NCBIChiLan1.0ChiLan1.0
TMTC2
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11283,316,647 - 83,761,761 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1283,317,358 - 83,759,281 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01280,209,070 - 80,660,058 (+)NCBIMhudiblu_PPA_v0panPan3
TMTC2
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11524,629,610 - 25,017,936 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1524,629,157 - 25,016,555 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1525,060,632 - 25,448,131 (+)NCBI
ROS_Cfam_1.01525,377,180 - 25,529,388 (+)NCBI
ROS_Cfam_1.0 Ensembl1525,008,752 - 25,526,997 (+)Ensembl
UMICH_Zoey_3.11524,585,728 - 24,973,537 (+)NCBI
Tmtc2
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440494535,255,207 - 35,632,245 (-)NCBI
SpeTri2.0NW_004936507603,222 - 980,229 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
TMTC2
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl598,697,017 - 99,229,550 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1598,695,404 - 99,085,243 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.25103,474,951 - 103,667,323 (-)NCBISscrofa10.2Sscrofa10.2susScr3
TMTC2
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11178,130,490 - 78,569,546 (+)NCBIChlSab1.1chlSab2
ChlSab1.1 Ensembl1178,296,438 - 78,569,740 (+)EnsemblChlSab1.1chlSab2
Vero_WHO_p1.0NW_023666037166,791,023 - 167,244,956 (-)NCBIVero_WHO_p1.0
Tmtc2
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046248371,998,083 - 2,398,451 (+)EnsemblHetGla_female_1.0hetGla2
HetGla 1.0NW_0046248371,998,443 - 2,398,290 (+)NCBIHetGla_female_1.0hetGla2

Position Markers
D7Got37  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2740,498,993 - 40,499,147 (+)MAPPERmRatBN7.2
Rnor_6.0747,285,795 - 47,285,948NCBIRnor6.0
Rnor_5.0747,301,048 - 47,301,201UniSTSRnor5.0
RGSC_v3.4743,772,693 - 43,772,847RGDRGSC3.4
RGSC_v3.4743,772,694 - 43,772,847UniSTSRGSC3.4
RGSC_v3.1743,792,965 - 43,793,118RGD
Celera737,397,958 - 37,398,111UniSTS
RH 3.4 Map7359.9UniSTS
RH 3.4 Map7359.9RGD
RH 2.0 Map7321.2RGD
Cytogenetic Map7q21UniSTS
D7Got36  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2740,444,264 - 40,444,450 (+)MAPPERmRatBN7.2
Rnor_6.0747,231,373 - 47,231,558NCBIRnor6.0
Rnor_5.0747,246,668 - 47,246,853UniSTSRnor5.0
RGSC_v3.4743,720,176 - 43,720,362RGDRGSC3.4
RGSC_v3.4743,720,177 - 43,720,362UniSTSRGSC3.4
RGSC_v3.1743,740,448 - 43,740,633RGD
Celera737,343,805 - 37,343,990UniSTS
RH 3.4 Map7364.3RGD
RH 3.4 Map7364.3UniSTS
Cytogenetic Map7q21UniSTS
AU047328  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2740,751,092 - 40,751,340 (+)MAPPERmRatBN7.2
Rnor_6.0747,531,856 - 47,532,101NCBIRnor6.0
Rnor_5.0747,548,158 - 47,548,403UniSTSRnor5.0
RGSC_v3.4744,076,063 - 44,076,308UniSTSRGSC3.4
Celera737,646,306 - 37,646,540UniSTS
Cytogenetic Map7q21UniSTS
RH133880  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2740,392,554 - 40,392,752 (+)MAPPERmRatBN7.2
Rnor_6.0747,179,774 - 47,179,971NCBIRnor6.0
Rnor_5.0747,195,445 - 47,195,642UniSTSRnor5.0
RGSC_v3.4743,666,318 - 43,666,515UniSTSRGSC3.4
Celera737,292,782 - 37,292,979UniSTS
RH 3.4 Map7368.2UniSTS
Cytogenetic Map7q21UniSTS
BE112859  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2740,764,983 - 40,765,145 (+)MAPPERmRatBN7.2
Rnor_6.0747,544,477 - 47,544,638NCBIRnor6.0
Rnor_5.0747,561,601 - 47,561,762UniSTSRnor5.0
RGSC_v3.4744,092,194 - 44,092,355UniSTSRGSC3.4
Celera737,660,656 - 37,660,817UniSTS
RH 3.4 Map7351.6UniSTS
Cytogenetic Map7q21UniSTS
RH140341  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2740,452,128 - 40,452,250 (+)MAPPERmRatBN7.2
Rnor_6.0747,239,237 - 47,239,358NCBIRnor6.0
Rnor_5.0747,254,532 - 47,254,653UniSTSRnor5.0
RGSC_v3.4743,728,041 - 43,728,162UniSTSRGSC3.4
Celera737,351,667 - 37,351,787UniSTS
RH 3.4 Map7364.4UniSTS
Cytogenetic Map7q21UniSTS
AA800171  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2740,400,253 - 40,400,428 (+)MAPPERmRatBN7.2
Rnor_6.0747,187,473 - 47,187,647NCBIRnor6.0
Rnor_5.0747,203,144 - 47,203,318UniSTSRnor5.0
RGSC_v3.4743,674,017 - 43,674,191UniSTSRGSC3.4
Celera737,300,481 - 37,300,655UniSTS
RH 3.4 Map7358.8UniSTS
Cytogenetic Map7q21UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
61410Bw19Body weight QTL 196.20.001body mass (VT:0001259)body weight (CMO:0000012)7144782185Rat
631503Bp102Blood pressure QTL 1021.9arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)7144822433Rat
634336Anxrr17Anxiety related response QTL 173.66locomotor behavior trait (VT:0001392)number of entries into a discrete space in an experimental apparatus (CMO:0000960)7924703115097879Rat
10755438Coatc9Coat color QTL 90coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)7352928048529280Rat
9590102Sffal5Serum free fatty acids level QTL 58.620.001blood free fatty acid amount (VT:0001553)plasma free fatty acids level (CMO:0000546)7532901950329019Rat
10755440Coatc10Coat color QTL 100coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)7749649952496499Rat
10059592Kidm45Kidney mass QTL 453.950.025kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)7757398552573985Rat
2298547Neuinf5Neuroinflammation QTL 53.7nervous system integrity trait (VT:0010566)spinal cord Cd74 protein level (CMO:0002131)7946224658265113Rat
1643004Pain2Pain QTL 21mechanical nociception trait (VT:0002734)self mutilation severity score (CMO:0002145)7946224698011544Rat
1578652Bmd15Bone mineral density QTL 155.2femur mineral mass (VT:0010011)trabecular volumetric bone mineral density (CMO:0001729)7986646760460686Rat
738033Anxrr6Anxiety related response QTL 64.1exploratory behavior trait (VT:0010471)percentage of entries into a discrete space in an experimental apparatus (CMO:0000961)71557388960573889Rat
2317059Aia15Adjuvant induced arthritis QTL 152.46joint integrity trait (VT:0010548)right rear ankle joint diameter (CMO:0002150)71700459862004598Rat
10755451Coatc11Coat color QTL 110coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)71794435762944357Rat
1354637Scl30Serum cholesterol level QTL 303.7blood cholesterol amount (VT:0000180)blood total cholesterol level (CMO:0000051)71965431749753746Rat
1354644Spl4Serum phospholipid level QTL 44.9blood phospholipid amount (VT:0006084)blood phospholipid level (CMO:0001169)71965431749753746Rat
1354639Spl5Serum phospholipid level QTL 53.9blood LDL phospholipid amount (VT:0010505)blood low density lipoprotein phospholipid level (CMO:0001568)71965431752888450Rat
1300132Bp182Blood pressure QTL 1823.49arterial blood pressure trait (VT:2000000)blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)71965431784928080Rat
7411569Bw137Body weight QTL 1370.001body mass (VT:0001259)body weight gain (CMO:0000420)72192119566921195Rat
1641885Alcrsp9Alcohol response QTL 9alcohol metabolism trait (VT:0015089)blood ethanol level (CMO:0000535)72409960669099606Rat
1549840Bss5Bone structure and strength QTL 59.8femur strength trait (VT:0010010)femur midshaft polar moment of inertia (CMO:0001669)72475184169751841Rat
70190Mcs6Mammary carcinoma susceptibility QTL 62.29mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)72673740163902784Rat
1300138Hrtrt9Heart rate QTL 94.72heart pumping trait (VT:2000009)heart rate (CMO:0000002)72940968353612950Rat
10402855Bp379Blood pressure QTL 3790.21arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)72940968374409683Rat
1300127Srn1Serum renin concentration QTL 13.87blood renin amount (VT:0003349)plasma renin activity level (CMO:0000116)72940968384928080Rat
10755453Coatc12Coat color QTL 120coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)73111283276112832Rat
7411605Foco14Food consumption QTL 1424.10.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)73429328279293282Rat
631534Lnnr1Liver neoplastic nodule remodeling QTL 13.850.001liver integrity trait (VT:0010547)liver remodeling tumorous lesion number to liver total tumorous lesion number ratio (CMO:0001705)73429328279293282Rat
631513Scl7Serum cholesterol level QTL 74.1blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)73796056982960569Rat


Genetic Models
This gene Tmtc2 is modified in the following models/strains
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:87
Count of miRNA genes:66
Interacting mature miRNAs:73
Transcripts:ENSRNOT00000006086
Prediction methods:Microtar, 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.


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

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium 5 4 4 59 14 22 11
Low 3 42 43 28 19 28 8 9 15 21 19 8
Below cutoff 1 9 9 9 2

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_001171177 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017594739 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039078703 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039078704 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039078706 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039078707 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AAHX01048913 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AAHX01048914 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AAHX01048915 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AAHX01048916 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AAHX01048917 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AAHX01048918 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AAHX01048919 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AAHX01048920 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AAHX01048921 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AAHX01048922 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AAHX01048923 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AAHX01048924 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AAHX01048925 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AAHX01048926 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AAHX01048927 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AAHX01048928 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AAHX01048929 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AAHX01048930 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AAHX01048931 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AAHX01048932 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AAHX01048933 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AAHX01048934 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AAHX01048935 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AAHX01048936 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH473960 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JACYVU010000185 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000006086   ⟹   ENSRNOP00000006086
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl740,394,220 - 40,807,298 (-)Ensembl
Rnor_6.0 Ensembl747,181,981 - 47,586,137 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000093853   ⟹   ENSRNOP00000086192
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl740,453,179 - 40,807,298 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000113359   ⟹   ENSRNOP00000094183
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl740,454,451 - 40,807,298 (-)Ensembl
RefSeq Acc Id: NM_001171177   ⟹   NP_001164648
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2740,394,220 - 40,806,651 (-)NCBI
Rnor_6.0747,181,439 - 47,586,137 (-)NCBI
Rnor_5.0747,197,110 - 47,603,261 (-)NCBI
Celera737,294,447 - 37,702,308 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039078703   ⟹   XP_038934631
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2740,449,802 - 40,806,685 (-)NCBI
RefSeq Acc Id: XM_039078704   ⟹   XP_038934632
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2740,394,808 - 40,806,685 (-)NCBI
RefSeq Acc Id: XM_039078706   ⟹   XP_038934634
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2740,453,850 - 40,806,685 (-)NCBI
RefSeq Acc Id: XM_039078707   ⟹   XP_038934635
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2740,392,377 - 40,806,672 (-)NCBI
Reference Sequences
RefSeq Acc Id: NP_001164648   ⟸   NM_001171177
- Peptide Label: precursor
- Sequence:
RefSeq Acc Id: ENSRNOP00000006086   ⟸   ENSRNOT00000006086
RefSeq Acc Id: XP_038934635   ⟸   XM_039078707
- Peptide Label: isoform X3
RefSeq Acc Id: XP_038934632   ⟸   XM_039078704
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038934631   ⟸   XM_039078703
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038934634   ⟸   XM_039078706
- Peptide Label: isoform X2
RefSeq Acc Id: ENSRNOP00000094183   ⟸   ENSRNOT00000113359
RefSeq Acc Id: ENSRNOP00000086192   ⟸   ENSRNOT00000093853

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-F1M369-F1-model_v2 AlphaFold F1M369 1-836 view protein structure

Transcriptome

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


Strain Variation

Strain Sequence Variants (MRatBN7.2)
ACI/EurMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
ACI/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN-Lx/CubMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/SsN (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BUF/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH2/CubMcwi (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH3/CubMcwi (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
DA/OlaHsd (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/DuCrl (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/NCrl (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/Stm (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FHH/EurMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FXLE16/Stm (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FXLE18/Stm (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
GK/FarMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB10/IpcvMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB2/IpcvMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB20/IpcvMcwi (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB31/IpcvMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB4/IpcvMcwi (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LE/Stm (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEW/Crl (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF10A/StmMcwi (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF11/Stm (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1A/Stm (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1C/Stm (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF2B/Stm (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF3/Stm (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF4/Stm (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LH/MavRrrcAek (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LL/MavRrrcAek (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LN/MavRrrcAek (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/NRrrcMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MR/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MWF/Hsd (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
PVG/Seac (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHR/OlalpcvMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHRSP/A3NCrl (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SR/JrHsd (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SS/JrHsdMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WAG/RijCrl (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/NCrl (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WN/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1309848 AgrOrtholog
BioCyc Gene G2FUF-34194 BioCyc
BioCyc Pathway PWY-7922 [protein O-mannosylation II (mammals, core M1 and core M2)] BioCyc
  PWY-7979 [protein O-mannosylation III (mammals, core M3)] BioCyc
Ensembl Genes ENSRNOG00000004585 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000006086 ENTREZGENE
  ENSRNOP00000006086.7 UniProtKB/TrEMBL
  ENSRNOP00000086192 ENTREZGENE
  ENSRNOP00000086192.1 UniProtKB/TrEMBL
  ENSRNOP00000094183.1 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000006086 ENTREZGENE
  ENSRNOT00000006086.7 UniProtKB/TrEMBL
  ENSRNOT00000093853 ENTREZGENE
  ENSRNOT00000093853.1 UniProtKB/TrEMBL
  ENSRNOT00000113359.1 UniProtKB/TrEMBL
Gene3D-CATH 1.25.40.10 UniProtKB/TrEMBL
InterPro DUF1736 UniProtKB/TrEMBL
  TPR-like_helical UniProtKB/TrEMBL
  TPR_1 UniProtKB/TrEMBL
  TPR_repeat UniProtKB/TrEMBL
NCBI Gene 299762 ENTREZGENE
Pfam DUF1736 UniProtKB/TrEMBL
  TPR_1 UniProtKB/TrEMBL
  TPR_8 UniProtKB/TrEMBL
PhenoGen Tmtc2 PhenoGen
PROSITE TPR UniProtKB/TrEMBL
SMART TPR UniProtKB/TrEMBL
Superfamily-SCOP SSF48452 UniProtKB/TrEMBL
UniProt A0A8I6A5J6_RAT UniProtKB/TrEMBL
  A0A8I6ALM4_RAT UniProtKB/TrEMBL
  F1M369_RAT UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-04-30 Tmtc2  transmembrane and tetratricopeptide repeat containing 2   Tmtc2_predicted  transmembrane and tetratricopeptide repeat containing 2 (predicted)  'predicted' is removed 2292626 APPROVED
2006-03-30 Tmtc2_predicted  transmembrane and tetratricopeptide repeat containing 2 (predicted)  RGD1309848_predicted  similar to RIKEN cDNA D330034A10 gene (predicted)  Symbol and Name updated 1299863 APPROVED
2005-01-20 RGD1309848_predicted  similar to RIKEN cDNA D330034A10 gene (predicted)  LOC299762_predicted    Symbol and Name status set to approved 1331353 APPROVED
2005-01-12 LOC299762_predicted  similar to RIKEN cDNA D330034A10 gene (predicted)      Symbol and Name status set to provisional 70820 PROVISIONAL