Colgalt2 (collagen beta(1-O)galactosyltransferase 2) - Rat Genome Database

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Gene: Colgalt2 (collagen beta(1-O)galactosyltransferase 2) Rattus norvegicus
Analyze
Symbol: Colgalt2
Name: collagen beta(1-O)galactosyltransferase 2
RGD ID: 1304702
Description: Predicted to enable procollagen galactosyltransferase activity. Orthologous to human COLGALT2 (collagen beta(1-O)galactosyltransferase 2); PARTICIPATES IN lysine degradation pathway; O-linked glycan biosynthetic pathway; INTERACTS WITH 2,3,7,8-Tetrachlorodibenzofuran; atrazine; bisphenol A.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: Glt25d2; glycosyltransferase 25 domain containing 2; LOC289081; procollagen galactosyltransferase 2; RGD1304702; similar to chromosome 1 open reading frame 17
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81367,073,551 - 67,178,194 (+)NCBIGRCr8
mRatBN7.21364,523,641 - 64,628,295 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1364,523,658 - 64,627,549 (+)EnsemblmRatBN7.2 Ensembl
Rnor_6.01369,797,558 - 69,902,916 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1369,797,880 - 69,901,170 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01374,769,669 - 74,874,907 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41367,354,323 - 67,459,514 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11367,368,594 - 67,473,670 (+)NCBI
Celera1364,435,489 - 64,540,128 (+)NCBICelera
Cytogenetic Map13q21NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene Ontology Annotations     Click to see Annotation Detail View

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
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. KEGG Annotation Import Pipeline Pipeline to import KEGG annotations from KEGG into RGD
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

Genomics

Comparative Map Data
Colgalt2
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81367,073,551 - 67,178,194 (+)NCBIGRCr8
mRatBN7.21364,523,641 - 64,628,295 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1364,523,658 - 64,627,549 (+)EnsemblmRatBN7.2 Ensembl
Rnor_6.01369,797,558 - 69,902,916 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1369,797,880 - 69,901,170 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01374,769,669 - 74,874,907 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41367,354,323 - 67,459,514 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11367,368,594 - 67,473,670 (+)NCBI
Celera1364,435,489 - 64,540,128 (+)NCBICelera
Cytogenetic Map13q21NCBI
COLGALT2
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381183,929,662 - 184,037,728 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1183,929,854 - 184,037,729 (-)EnsemblGRCh38hg38GRCh38
GRCh371183,898,796 - 184,006,862 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361182,171,589 - 182,273,486 (-)NCBINCBI36Build 36hg18NCBI36
Celera1157,015,884 - 157,117,798 (-)NCBICelera
Cytogenetic Map1q25.3NCBI
HuRef1155,140,707 - 155,242,623 (-)NCBIHuRef
CHM1_11185,327,635 - 185,429,520 (-)NCBICHM1_1
T2T-CHM13v2.01183,289,012 - 183,400,897 (-)NCBIT2T-CHM13v2.0
Colgalt2
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391152,275,485 - 152,386,942 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1152,275,581 - 152,386,446 (+)EnsemblGRCm39 Ensembl
GRCm381152,399,805 - 152,510,695 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1152,399,830 - 152,510,695 (+)EnsemblGRCm38mm10GRCm38
MGSCv371154,246,997 - 154,357,825 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361154,162,139 - 154,272,913 (+)NCBIMGSCv36mm8
Celera1154,823,094 - 154,930,941 (+)NCBICelera
Cytogenetic Map1G2NCBI
cM Map164.77NCBI
Colgalt2
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495540622,674,692 - 22,775,079 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495540622,674,692 - 22,775,079 (-)NCBIChiLan1.0ChiLan1.0
COLGALT2
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2165,681,357 - 65,790,520 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1165,364,526 - 65,465,417 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01159,458,317 - 159,566,856 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11163,615,787 - 163,722,859 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1163,621,898 - 163,727,151 (-)Ensemblpanpan1.1panPan2
COLGALT2
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1717,242,951 - 17,342,562 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl717,245,555 - 17,343,067 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha716,828,930 - 16,944,454 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0716,975,757 - 17,091,912 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl716,943,746 - 17,078,092 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1716,883,772 - 16,999,299 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0716,992,419 - 17,108,055 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0717,123,409 - 17,239,005 (-)NCBIUU_Cfam_GSD_1.0
Colgalt2
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440934488,078,880 - 88,172,792 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049364815,925,629 - 6,019,835 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049364815,925,635 - 6,019,541 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
COLGALT2
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl9125,148,753 - 125,291,057 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.19125,149,806 - 125,291,092 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.29137,479,988 - 137,611,367 (-)NCBISscrofa10.2Sscrofa10.2susScr3
COLGALT2
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12545,318,249 - 45,435,939 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl2545,331,893 - 45,434,429 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366605546,549,857 - 46,653,676 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Colgalt2
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046248149,631,442 - 9,737,254 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046248149,631,386 - 9,736,701 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Colgalt2
1315 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:204
Count of miRNA genes:158
Interacting mature miRNAs:180
Transcripts:ENSRNOT00000030109
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.


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1298066Bp159Blood pressure QTL 1590.004arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)134608804691088046Rat
10755495Bp387Blood pressure QTL 3873.78arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)133466346187525369Rat
1354655Bp241Blood pressure QTL 2413.9arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1356056920101056920Rat
70220Bp55Blood pressure QTL 555.75arterial blood pressure trait (VT:2000000)blood pressure measurement (CMO:0000003)133737450982374509Rat
71119Thym2Thymus enlargement QTL 23.8thymus mass (VT:0004954)thymus weight to body weight ratio (CMO:0000612)134619797684753113Rat
61391Bp5Blood pressure QTL 55.6arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)132230187567301875Rat
4889861Pur29Proteinuria QTL 2913.80.005urine total protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)133741558480753406Rat
12879441Bp396Blood pressure QTL 396arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)134569998390699983Rat
619615Bp80Blood pressure QTL 800.0354arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)133975454484754544Rat
2303028Bp329Blood pressure QTL 329arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)135849787273485113Rat
1581570Eae17Experimental allergic encephalomyelitis QTL 174.1nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis incidence/prevalence measurement (CMO:0001046)138897350101631289Rat
70170Eae14Experimental allergic encephalomyelitis QTL 140.0024nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis incidence/prevalence measurement (CMO:0001046)132320344868203448Rat
61340Bp25Blood pressure QTL 254.20.004arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)133453521879535218Rat
1581573Uae36Urinary albumin excretion QTL 36urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)13599483377046787Rat
1549897Stresp12Stress response QTL 123.35stress-related behavior trait (VT:0010451)number of approaches toward negative stimulus before onset of defensive burying response (CMO:0001960)133843340883433408Rat
724564Uae11Urinary albumin excretion QTL 115.7urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)135949252277046890Rat
7207885Glom27Glomerulus QTL 273.9kidney glomerulus integrity trait (VT:0010546)kidney crescentic glomeruli count to kidney normal glomeruli count ratio (CMO:0002139)1320605871101339738Rat
738026Lnnr5Liver neoplastic nodule remodeling QTL 53.29liver integrity trait (VT:0010547)liver remodeling tumorous lesion number (CMO:0001461)135987440885581182Rat
1558644Cm45Cardiac mass QTL 453.60.002heart mass (VT:0007028)heart wet weight (CMO:0000069)132369296968692969Rat
70181BpQTLcluster11Blood pressure QTL cluster 116.922arterial blood pressure trait (VT:2000000)absolute change in mean arterial blood pressure (CMO:0000533)133124133193395974Rat
61349Bp31Blood pressure QTL 315.75arterial blood pressure trait (VT:2000000)blood pressure measurement (CMO:0000003)133737450982374509Rat
2303563Bw89Body weight QTL 896body mass (VT:0001259)body weight (CMO:0000012)133228447177284471Rat
1354621Rf47Renal function QTL 473.7kidney renin amount (VT:0010559)kidney renin level (CMO:0002166)1330395351101056920Rat
1581554Pur11Proteinuria QTL 11urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)13599483377046787Rat
12879477Bp401Blood pressure QTL 401arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)133726209282262092Rat
1331750Bp220Blood pressure QTL 2202.98arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)133741558482415584Rat
6893338Cm76Cardiac mass QTL 7600.99heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)132369296968692969Rat
1641901Alcrsp6Alcohol response QTL 6response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)135236217197362171Rat
12879475Bp400Blood pressure QTL 400arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1361825626106807694Rat
1354666Bp244Blood pressure QTL 2444.9arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)131101056920Rat

Markers in Region
D13Rat99  
Rat AssemblyChrPosition (strand)SourceJBrowse
GRCr81367,121,362 - 67,121,570 (+)Marker Load Pipeline
mRatBN7.21364,571,449 - 64,571,657 (+)MAPPERmRatBN7.2
Rnor_6.01369,845,399 - 69,845,606NCBIRnor6.0
Rnor_5.01374,817,483 - 74,817,690UniSTSRnor5.0
RGSC_v3.41367,402,725 - 67,403,056RGDRGSC3.4
RGSC_v3.41367,402,808 - 67,403,015UniSTSRGSC3.4
RGSC_v3.11367,416,888 - 67,417,095RGD
Celera1364,483,345 - 64,483,552UniSTS
RH 3.4 Map13303.7UniSTS
RH 3.4 Map13303.7RGD
RH 2.0 Map13399.9RGD
SHRSP x BN Map1323.7598RGD
Cytogenetic Map13q21UniSTS


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
nervous system
renal system
reproductive system
respiratory system
9 11 49 113 91 90 59 25 59 6 218 97 93 45 60 31

Sequence


Ensembl Acc Id: ENSRNOT00000030109   ⟹   ENSRNOP00000034843
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1364,523,658 - 64,627,549 (+)Ensembl
Rnor_6.0 Ensembl1369,797,880 - 69,901,170 (+)Ensembl
RefSeq Acc Id: NM_001427297   ⟹   NP_001414226
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81367,073,551 - 67,178,194 (+)NCBI
Protein Sequences
Protein RefSeqs NP_001414226 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDM09562 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000034843.7
Ensembl Acc Id: ENSRNOP00000034843   ⟸   ENSRNOT00000030109
RefSeq Acc Id: NP_001414226   ⟸   NM_001427297
- Peptide Label: precursor
- UniProtKB: A6ICT5 (UniProtKB/TrEMBL),   D3Z9Z7 (UniProtKB/TrEMBL)

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D3Z9Z7-F1-model_v2 AlphaFold D3Z9Z7 1-624 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:1304702 AgrOrtholog
BioCyc Gene G2FUF-17907 BioCyc
BioCyc Pathway PWY-7894 [procollagen hydroxylation and glycosylation] BioCyc
BioCyc Pathway Image PWY-7894 BioCyc
Ensembl Genes ENSRNOG00000028207 Ensembl, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000030109.7 UniProtKB/TrEMBL
InterPro Collagen_mod_GT25 UniProtKB/TrEMBL
  Glyco_trans_25 UniProtKB/TrEMBL
  Nucleotide-diphossugar_trans UniProtKB/TrEMBL
NCBI Gene 289081 ENTREZGENE
PANTHER PROCOLLAGEN GALACTOSYLTRANSFERASE 2 UniProtKB/TrEMBL
  PROCOLLAGEN-LYSINE,2-OXOGLUTARATE 5-DIOXYGENASE/GLYCOSYLTRANSFERASE 25 FAMILY MEMBER UniProtKB/TrEMBL
Pfam Glyco_tranf_2_4 UniProtKB/TrEMBL
  Glyco_transf_25 UniProtKB/TrEMBL
PhenoGen Colgalt2 PhenoGen
RatGTEx ENSRNOG00000028207 RatGTEx
Superfamily-SCOP SSF53448 UniProtKB/TrEMBL
UniProt A6ICT5 ENTREZGENE, UniProtKB/TrEMBL
  D3Z9Z7 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2013-03-20 Colgalt2  collagen beta(1-O)galactosyltransferase 2  Glt25d2  glycosyltransferase 25 domain containing 2  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-04-30 Glt25d2  glycosyltransferase 25 domain containing 2   Glt25d2_predicted  glycosyltransferase 25 domain containing 2 (predicted)  'predicted' is removed 2292626 APPROVED
2006-03-30 Glt25d2_predicted  glycosyltransferase 25 domain containing 2 (predicted)  RGD1304702_predicted  similar to chromosome 1 open reading frame 17 (predicted)  Symbol and Name updated 1299863 APPROVED
2005-01-20 RGD1304702_predicted  similar to chromosome 1 open reading frame 17 (predicted)  LOC289081_predicted    Symbol and Name status set to approved 1331353 APPROVED
2005-01-12 LOC289081_predicted  similar to chromosome 1 open reading frame 17 (predicted)      Symbol and Name status set to provisional 70820 PROVISIONAL