Tgm6 (transglutaminase 6) - Rat Genome Database

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Gene: Tgm6 (transglutaminase 6) Rattus norvegicus
Analyze
Symbol: Tgm6
Name: transglutaminase 6
RGD ID: 1565348
Description: Predicted to enable protein-glutamine gamma-glutamyltransferase activity. Predicted to be active in cytoplasm. Human ortholog(s) of this gene implicated in spinocerebellar ataxia type 35. Orthologous to human TGM6 (transglutaminase 6); INTERACTS WITH bisphenol A; decabromodiphenyl ether; thioacetamide.
Type: protein-coding
RefSeq Status: MODEL
Previously known as: LOC296152; protein-glutamine gamma-glutamyltransferase 6; RGD1565348; similar to transglutaminase 6
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr83137,771,368 - 137,809,000 (+)NCBIGRCr8
mRatBN7.23117,324,268 - 117,355,674 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl3117,321,489 - 117,354,734 (+)EnsemblmRatBN7.2 Ensembl
Rnor_6.03122,644,183 - 122,680,054 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl3122,662,086 - 122,679,128 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.03129,149,397 - 129,180,898 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.43117,722,990 - 117,753,457 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera3116,135,625 - 116,171,345 (+)NCBICelera
Cytogenetic Map3q36NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component
cytoplasm  (IBA,ISO)

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. OMIM Disease Annotation Pipeline OMIM Disease Annotation Pipeline
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
Additional References at PubMed
PMID:23206699   PMID:23331848   PMID:25253745   PMID:29053796  


Genomics

Comparative Map Data
Tgm6
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr83137,771,368 - 137,809,000 (+)NCBIGRCr8
mRatBN7.23117,324,268 - 117,355,674 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl3117,321,489 - 117,354,734 (+)EnsemblmRatBN7.2 Ensembl
Rnor_6.03122,644,183 - 122,680,054 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl3122,662,086 - 122,679,128 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.03129,149,397 - 129,180,898 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.43117,722,990 - 117,753,457 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera3116,135,625 - 116,171,345 (+)NCBICelera
Cytogenetic Map3q36NCBI
TGM6
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38202,380,901 - 2,432,753 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl202,380,901 - 2,432,753 (+)EnsemblGRCh38hg38GRCh38
GRCh37202,361,547 - 2,413,399 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36202,309,554 - 2,361,399 (+)NCBINCBI36Build 36hg18NCBI36
Build 34202,309,553 - 2,361,399NCBI
Celera202,426,476 - 2,478,323 (+)NCBICelera
Cytogenetic Map20p13NCBI
HuRef202,311,504 - 2,363,345 (+)NCBIHuRef
CHM1_1202,361,930 - 2,413,804 (+)NCBICHM1_1
T2T-CHM13v2.0202,411,268 - 2,463,114 (+)NCBIT2T-CHM13v2.0
Tgm6
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm392129,954,336 - 129,996,153 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl2129,954,336 - 129,996,152 (+)EnsemblGRCm39 Ensembl
GRCm382130,112,416 - 130,154,233 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl2130,112,416 - 130,154,232 (+)EnsemblGRCm38mm10GRCm38
MGSCv372129,949,021 - 129,979,961 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv362129,814,726 - 129,845,666 (+)NCBIMGSCv36mm8
Celera2131,348,816 - 131,376,853 (+)NCBICelera
Cytogenetic Map2F1NCBI
cM Map263.19NCBI
Tgm6
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495541513,470,701 - 13,499,422 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495541513,470,268 - 13,499,500 (+)NCBIChiLan1.0ChiLan1.0
TGM6
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2213,383,409 - 3,426,166 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1203,373,270 - 3,422,991 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0202,509,000 - 2,543,650 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1202,259,725 - 2,306,743 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl202,259,725 - 2,306,743 (+)Ensemblpanpan1.1panPan2
TGM6
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12418,698,016 - 18,721,975 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2418,700,099 - 18,721,930 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2418,524,775 - 18,542,390 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.02419,153,260 - 19,170,959 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl2419,157,075 - 19,179,449 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.12418,709,140 - 18,726,810 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.02418,821,595 - 18,837,655 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.02419,148,694 - 19,166,354 (-)NCBIUU_Cfam_GSD_1.0
Tgm6
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024408640167,760,795 - 167,788,903 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_00493648516,192,808 - 16,220,290 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_00493648516,192,808 - 16,220,267 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
TGM6
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1733,107,568 - 33,156,324 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11733,106,974 - 33,142,548 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21737,524,555 - 37,530,428 (-)NCBISscrofa10.2Sscrofa10.2susScr3
TGM6
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1254,100,262 - 54,152,019 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl254,101,063 - 54,139,923 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_023666087516,858 - 569,719 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Tgm6
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046247413,646,131 - 3,672,382 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046247413,654,288 - 3,672,382 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Tgm6
256 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:45
Count of miRNA genes:42
Interacting mature miRNAs:45
Transcripts:ENSRNOT00000009097
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 (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1358885Bp251Blood pressure QTL 2513.8arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)314489145121056321Rat
1358888Bp264Blood pressure QTL 2644.43arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)314489145121056321Rat
737818Hcar12Hepatocarcinoma resistance QTL 122.6liver integrity trait (VT:0010547)volume of individual liver tumorous lesion (CMO:0001078)329463235118376539Rat
70216Cm14Cardiac mass QTL 142.1heart mass (VT:0007028)heart wet weight (CMO:0000069)331172320163586636Rat
1358362Srcrt2Stress Responsive Cort QTL 22.78blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)338192233133483320Rat
2301970Bw81Body weight QTL 815.19body mass (VT:0001259)body weight (CMO:0000012)341874578155617519Rat
2301971Cm71Cardiac mass QTL 714.63heart left ventricle mass (VT:0007031)heart left ventricle weight (CMO:0000776)341874578155617519Rat
1581503Cm58Cardiac mass QTL 582.70.05heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)343827364121056321Rat
1559282Emca5Estrogen-induced mammary cancer QTL 53.9mammary gland integrity trait (VT:0010552)percentage of study population developing mammary tumors during a period of time (CMO:0000948)343827364169034231Rat
2292591Esta4Estrogen-induced thymic atrophy QTL 4thymus mass (VT:0004954)thymus wet weight (CMO:0000855)347233211147415807Rat
631665Bw8Body weight QTL 85.5body mass (VT:0001259)body weight (CMO:0000012)350437042119183768Rat
1581568Rf53Renal function QTL 53urine total protein amount (VT:0000032)urine protein excretion rate to body weight ratio (CMO:0001099)356395968161299569Rat
8662816Vetf4Vascular elastic tissue fragility QTL 44renal artery integrity trait (VT:0010642)number of ruptures of the internal elastic lamina of the renal arteries (CMO:0002563)359242096157323038Rat
1300111Rf12Renal function QTL 123.78renal blood flow trait (VT:2000006)absolute change in renal blood flow rate (CMO:0001168)361017749121056321Rat
12879848Bw181Body weght QTL 1810.015body mass (VT:0001259)body weight (CMO:0000012)370348525121056321Rat
2301414Kidm37Kidney mass QTL 370.001kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)370653097121056321Rat
1600376Arunc5Aerobic running capacity QTL 50.21exercise endurance trait (VT:0002332)maximum distance run on treadmill (CMO:0001406)373376539118376539Rat
1581546Pur13Proteinuria QTL 132.930.0335urine total protein amount (VT:0000032)urine protein excretion rate (CMO:0000759)378196190146592722Rat
631649Bp123Blood pressure QTL 1233.2arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)389772419134772419Rat
8694437Bw167Body weight QTL 16722.460.001retroperitoneal fat pad mass (VT:0010430)retroperitoneal fat pad weight to body weight ratio (CMO:0000635)391797474136797474Rat
631841Niddm39Non-insulin dependent diabetes mellitus QTL 393.36blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)394856903159898684Rat
724532Cm17Cardiac mass QTL 172heart mass (VT:0007028)calculated heart weight (CMO:0000073)395735366140735366Rat
1354611Despr2Despair related QTL 23.030.0028locomotor behavior trait (VT:0001392)amount of time spent in voluntary immobility (CMO:0001043)397084464142084464Rat
2293087Iddm27Insulin dependent diabetes mellitus QTL 272.68blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)397551417147415807Rat
2312659Slep7Serum leptin concentration QTL 70.001blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)398535255168026850Rat
2312670Bw94Body weight QTL 940.01inguinal fat pad mass (VT:0010424)inguinal fat pad weight to body weight ratio (CMO:0001253)398535255168026850Rat
2312673Scl63Serum cholesterol level QTL 630.001blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)398535255168026850Rat
2302373Gluco39Glucose level QTL 395.01blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)398535386161695835Rat
619618Rf3Renal disease susceptibility QTL 36.50.001urine albumin amount (VT:0002871)urine albumin excretion rate to body weight ratio (CMO:0001270)3107693393152693393Rat
1331758Bp207Blood pressure QTL 2072.848arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)3112287552135181505Rat
1578754Stresp16Stress response QTL 1640.001blood renin amount (VT:0003349)plasma renin activity level (CMO:0000116)3112681431157681431Rat
1358204Insglur1Insulin/glucose ratio QTL 13.8blood glucose amount (VT:0000188)serum insulin level (CMO:0000358)3115638168135181505Rat
1358204Insglur1Insulin/glucose ratio QTL 13.8blood glucose amount (VT:0000188)serum glucose level (CMO:0000543)3115638168135181505Rat


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 exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system reproductive system respiratory system appendage
High
Medium
Low 9 1 1 2 1 1
Below cutoff 17 2 9 2 2 4 18 12 7 2

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000009097   ⟹   ENSRNOP00000009097
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl3117,321,489 - 117,354,734 (+)Ensembl
Rnor_6.0 Ensembl3122,662,086 - 122,679,128 (+)Ensembl
RefSeq Acc Id: XM_063284796   ⟹   XP_063140866
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr83137,771,368 - 137,809,000 (+)NCBI
Protein Sequences
Protein RefSeqs XP_063140866 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AJD87526 (Get FASTA)   NCBI Sequence Viewer  
  EDL80173 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000009097.5
Reference Protein Sequences
RefSeq Acc Id: ENSRNOP00000009097   ⟸   ENSRNOT00000009097
RefSeq Acc Id: XP_063140866   ⟸   XM_063284796
Protein Domains
Transglutaminase C-terminal   Transglutaminase-like

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-F1M4T7-F1-model_v2 AlphaFold F1M4T7 1-705 view protein structure

Transcriptome

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

Promoters
RGD ID:13692432
Promoter ID:EPDNEW_R2951
Type:single initiation site
Name:Tgm6_1
Description:transglutaminase 6
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_6.03122,662,076 - 122,662,136EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1565348 AgrOrtholog
BioCyc Gene G2FUF-47878 BioCyc
Ensembl Genes ENSRNOG00000006830 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000009097.5 UniProtKB/TrEMBL
Gene3D-CATH 2.60.40.10 UniProtKB/TrEMBL
  3.90.260.10 UniProtKB/TrEMBL
InterPro Gln_gamma-glutamylTfrase_euk UniProtKB/TrEMBL
  Ig-like_fold UniProtKB/TrEMBL
  Ig_E-set UniProtKB/TrEMBL
  Papain_like_cys_pep_sf UniProtKB/TrEMBL
  Transglutaminase-like UniProtKB/TrEMBL
  Transglutaminase-like_sf UniProtKB/TrEMBL
  Transglutaminase_C UniProtKB/TrEMBL
  Transglutaminase_C_sf UniProtKB/TrEMBL
  Transglutaminase_CS UniProtKB/TrEMBL
  Transglutaminase_N UniProtKB/TrEMBL
NCBI Gene 296152 ENTREZGENE
PANTHER PROTEIN-GLUTAMINE GAMMA-GLUTAMYLTRANSFERASE UniProtKB/TrEMBL
  PROTEIN-GLUTAMINE GAMMA-GLUTAMYLTRANSFERASE 6 UniProtKB/TrEMBL
Pfam Transglut_C UniProtKB/TrEMBL
  Transglut_core UniProtKB/TrEMBL
  Transglut_N UniProtKB/TrEMBL
PhenoGen Tgm6 PhenoGen
PIRSF TGM_EBP42 UniProtKB/TrEMBL
PROSITE TRANSGLUTAMINASES UniProtKB/TrEMBL
RatGTEx ENSRNOG00000006830 RatGTEx
SMART TGc UniProtKB/TrEMBL
Superfamily-SCOP Ig_E-set UniProtKB/TrEMBL
  SSF54001 UniProtKB/TrEMBL
  Transglut_C UniProtKB/TrEMBL
UniProt A0A0B5AG44_RAT UniProtKB/TrEMBL
  F1M4T7_RAT UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-04-30 Tgm6  transglutaminase 6   Tgm6_predicted  transglutaminase 6 (predicted)  'predicted' is removed 2292626 APPROVED
2006-03-30 Tgm6_predicted  transglutaminase 6 (predicted)  RGD1565348_predicted  similar to transglutaminase 6 (predicted)  Symbol and Name updated 1299863 APPROVED
2006-03-07 RGD1565348_predicted  similar to transglutaminase 6 (predicted)  LOC296152  similar to transglutaminase 6  Symbol and Name status set to approved 1299863 APPROVED
2006-02-09 LOC296152  similar to transglutaminase 6      Symbol and Name status set to provisional 70820 PROVISIONAL