B3galt6 (Beta-1,3-galactosyltransferase 6) - Rat Genome Database

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Gene: B3galt6 (Beta-1,3-galactosyltransferase 6) Rattus norvegicus
Analyze
Symbol: B3galt6
Name: Beta-1,3-galactosyltransferase 6
RGD ID: 1309558
Description: Predicted to enable galactosylxylosylprotein 3-beta-galactosyltransferase activity. Predicted to be involved in glycosaminoglycan biosynthetic process; protein O-linked glycosylation; and proteoglycan biosynthetic process. Predicted to be located in Golgi medial cisterna. Predicted to be active in Golgi membrane. Human ortholog(s) of this gene implicated in Ehlers-Danlos syndrome spondylodysplastic type 2 and spondyloepimetaphyseal dysplasia with joint laxity type 1. Orthologous to human B3GALT6 (beta-1,3-galactosyltransferase 6); PARTICIPATES IN chondroitin sulfate biosynthetic pathway; heparan sulfate biosynthetic pathway; INTERACTS WITH 17alpha-ethynylestradiol; 2,3,7,8-tetrachlorodibenzodioxine; acetamide.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: LOC298690; UDP-Gal:betaGal beta 1,3-galactosyltransferase 6; UDP-Gal:betaGal beta 1,3-galactosyltransferase, polypeptide 6
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
GRCr85171,866,428 - 171,868,564 (-)NCBIGRCr8
mRatBN7.25166,584,202 - 166,586,338 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl5166,584,202 - 166,586,338 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx5169,287,811 - 169,289,948 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.05171,109,235 - 171,111,372 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.05171,071,769 - 171,073,906 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.05173,423,475 - 173,425,611 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl5173,423,475 - 173,425,611 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.05176,899,096 - 176,901,232 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.45172,833,647 - 172,835,783 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.15172,845,264 - 172,846,243 (-)NCBI
Celera5164,784,930 - 164,787,066 (-)NCBICelera
Cytogenetic Map5q36NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component

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. Rat ISS GO annotations from GOA human gene data--August 2006 GOA data from the GO Consortium
3. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
4. OMIM Disease Annotation Pipeline OMIM Disease Annotation Pipeline
5. KEGG Annotation Import Pipeline Pipeline to import KEGG annotations from KEGG into RGD
6. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
7. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:11551958   PMID:19946888  


Genomics

Comparative Map Data
B3galt6
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr85171,866,428 - 171,868,564 (-)NCBIGRCr8
mRatBN7.25166,584,202 - 166,586,338 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl5166,584,202 - 166,586,338 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx5169,287,811 - 169,289,948 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.05171,109,235 - 171,111,372 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.05171,071,769 - 171,073,906 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.05173,423,475 - 173,425,611 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl5173,423,475 - 173,425,611 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.05176,899,096 - 176,901,232 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.45172,833,647 - 172,835,783 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.15172,845,264 - 172,846,243 (-)NCBI
Celera5164,784,930 - 164,787,066 (-)NCBICelera
Cytogenetic Map5q36NCBI
B3GALT6
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh3811,232,237 - 1,235,041 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl11,232,237 - 1,235,041 (+)EnsemblGRCh38hg38GRCh38
GRCh3711,167,617 - 1,170,421 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 3611,157,492 - 1,160,284 (+)NCBINCBI36Build 36hg18NCBI36
Build 3411,207,567 - 1,210,341NCBI
Celera11,413,233 - 1,416,025 (-)NCBICelera
Cytogenetic Map1p36.33NCBI
HuRef1424,537 - 441,998 (+)NCBIHuRef
CHM1_111,154,101 - 1,157,447 (+)NCBICHM1_1
T2T-CHM13v2.01660,694 - 663,498 (+)NCBIT2T-CHM13v2.0
B3galt6
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm394156,073,923 - 156,077,135 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl4156,073,923 - 156,077,106 (-)EnsemblGRCm39 Ensembl
GRCm384155,989,466 - 155,992,678 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl4155,989,466 - 155,992,649 (-)EnsemblGRCm38mm10GRCm38
MGSCv374155,363,575 - 155,366,787 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv364154,834,329 - 154,836,449 (-)NCBIMGSCv36mm8
MGSCv364151,449,369 - 151,451,489 (-)NCBIMGSCv36mm8
Celera4158,252,690 - 158,255,872 (-)NCBICelera
Cytogenetic Map4E2NCBI
cM Map487.66NCBI
B3galt6
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554869,554,435 - 9,555,459 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049554869,553,765 - 9,555,675 (-)NCBIChiLan1.0ChiLan1.0
B3GALT6
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v21226,991,483 - 226,993,424 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11225,688,659 - 225,690,138 (-)NCBINHGRI_mPanPan1
PanPan1.111,188,683 - 1,191,648 (+)NCBIpanpan1.1PanPan1.1panPan2
B3GALT6
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1556,421,687 - 56,423,120 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl556,405,372 - 56,422,771 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha556,498,687 - 56,502,557 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0556,624,609 - 56,628,479 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl556,624,609 - 56,625,598 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1556,615,345 - 56,619,215 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0556,507,624 - 56,511,494 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0556,897,625 - 56,901,495 (+)NCBIUU_Cfam_GSD_1.0
B3galt6
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440505827,577,097 - 27,578,700 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049367371,887,855 - 1,888,826 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049367371,887,250 - 1,889,055 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
B3GALT6
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl663,540,141 - 63,541,112 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1663,540,066 - 63,541,962 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2657,996,301 - 57,998,407 (-)NCBISscrofa10.2Sscrofa10.2susScr3
B3GALT6
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.120130,210,828 - 130,212,732 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl20130,211,718 - 130,212,707 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366605434,778,673 - 34,781,453 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
B3galt6
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046248188,360,849 - 8,361,817 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046248188,360,321 - 8,361,975 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in B3galt6
9 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:64
Count of miRNA genes:62
Interacting mature miRNAs:64
Transcripts:ENSRNOT00000027060
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
10053720Scort26Serum corticosterone level QTL 262.060.0147blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)5124965598166875058Rat
631272Lanf1Left ventricular atrial natriuretic factor QTL 112heart left ventricle natriuretic peptide A amount (VT:0010596)heart left ventricle natriuretic peptide A level (CMO:0002165)5151113452166875058Rat
1576314Eutr1Estrogen induced uterine response QTL 1uterus integrity trait (VT:0010575)pyometritis severity score (CMO:0002009)52138965166875058Rat
631562Apr2Acute phase response QTL 23.7blood murinoglobulin 1 amount (VT:0010597)plasma murinoglobulin 1 level (CMO:0001931)5135927956166875058Rat
634349Bp139Blood pressure QTL 1390.001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)5128924607166875058Rat
61444Strs2Sensitivity to stroke QTL 24.7cerebrum integrity trait (VT:0010549)post-insult time to onset of cerebrovascular lesion (CMO:0002343)5135929696166875058Rat
724525Bp147Blood pressure QTL 1474.30.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)5126424772166875058Rat
1549904Neuinf1Neuroinflammation QTL 130nervous system integrity trait (VT:0010566)blood T lymphocyte count (CMO:0000110)5154828214166875058Rat
738018Anxrr4Anxiety related response QTL 45.1exploratory behavior trait (VT:0010471)percentage of entries into a discrete space in an experimental apparatus (CMO:0000961)5130130159166875058Rat
8552908Pigfal4Plasma insulin-like growth factor 1 level QTL 46.6blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)5128506074166875058Rat
7794791Mcs33Mammary carcinoma susceptibility QTL 331.93mammary gland integrity trait (VT:0010552)mammary tumor incidence/prevalence measurement (CMO:0000946)5131345754166875058Rat
1302790Scl20Serum cholesterol level QTL 206.40.0001blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)582394392166664054Rat
1598861Cm64Cardiac mass QTL 642.9heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)5127798274166875058Rat
1641920Colcs1Colorectal carcinoma susceptibility QTL 12.990.0055intestine integrity trait (VT:0010554)benign colorectal tumor surface area measurement (CMO:0001799)5121846814166846814Rat
1598819Bp292Blood pressure QTL 2924.3arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)5127798274166875058Rat
8694169Bw148Body weight QTL 14850.001body mass (VT:0001259)body weight gain (CMO:0000420)5128506074166875058Rat
1331721Bp210Blood pressure QTL 2103.413arterial blood pressure trait (VT:2000000)blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)5143069996166846814Rat


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: ENSRNOT00000027060   ⟹   ENSRNOP00000027060
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl5166,584,202 - 166,586,338 (-)Ensembl
Rnor_6.0 Ensembl5173,423,475 - 173,425,611 (-)Ensembl
RefSeq Acc Id: NM_001106699   ⟹   NP_001100169
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr85171,866,428 - 171,868,564 (-)NCBI
mRatBN7.25166,584,202 - 166,586,338 (-)NCBI
Rnor_6.05173,423,475 - 173,425,611 (-)NCBI
Rnor_5.05176,899,096 - 176,901,232 (-)NCBI
RGSC_v3.45172,833,647 - 172,835,783 (-)RGD
Celera5164,784,930 - 164,787,066 (-)RGD
Sequence:
Protein Sequences
Protein RefSeqs NP_001100169 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDL81348 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000027060.1
RefSeq Acc Id: NP_001100169   ⟸   NM_001106699
- UniProtKB: D3ZQC1 (UniProtKB/TrEMBL),   A6IUU7 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000027060   ⟸   ENSRNOT00000027060

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D3ZQC1-F1-model_v2 AlphaFold D3ZQC1 1-325 view protein structure

Transcriptome

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

Promoters
RGD ID:13694339
Promoter ID:EPDNEW_R4864
Type:single initiation site
Name:B3galt6_1
Description:Beta-1,3-galactosyltransferase 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_6.05173,425,600 - 173,425,660EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1309558 AgrOrtholog
BioCyc Gene G2FUF-38880 BioCyc
BioCyc Pathway PWY-6557 [glycosaminoglycan-protein linkage region biosynthesis] BioCyc
BioCyc Pathway Image PWY-6557 BioCyc
Ensembl Genes ENSRNOG00000019979 Ensembl, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000027060.4 UniProtKB/TrEMBL
Gene3D-CATH 3.90.550.50 UniProtKB/TrEMBL
InterPro Glyco_trans_31 UniProtKB/TrEMBL
KEGG Report rno:298690 UniProtKB/TrEMBL
NCBI Gene 298690 ENTREZGENE
PANTHER BETA-1,3-GALACTOSYLTRANSFERASE 6 UniProtKB/TrEMBL
  Glyco_trans_31 UniProtKB/TrEMBL
Pfam Galactosyl_T UniProtKB/TrEMBL
PhenoGen B3galt6 PhenoGen
RatGTEx ENSRNOG00000019979 RatGTEx
UniProt A6IUU7 ENTREZGENE, UniProtKB/TrEMBL
  D3ZQC1 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-01-11 B3galt6  Beta-1,3-galactosyltransferase 6  B3galt6  UDP-Gal:betaGal beta 1,3-galactosyltransferase 6  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2015-12-09 B3galt6  UDP-Gal:betaGal beta 1,3-galactosyltransferase 6  B3galt6  UDP-Gal:betaGal beta 1,3-galactosyltransferase, polypeptide 6  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-04-30 B3galt6  UDP-Gal:betaGal beta 1,3-galactosyltransferase, polypeptide 6   B3galt6_predicted  UDP-Gal:betaGal beta 1,3-galactosyltransferase, polypeptide 6 (predicted)  'predicted' is removed 2292626 APPROVED
2005-01-12 B3galt6_predicted  UDP-Gal:betaGal beta 1,3-galactosyltransferase, polypeptide 6 (predicted)      Symbol and Name status set to approved 70820 APPROVED