B3gnt5 (UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase 5) - Rat Genome Database

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Gene: B3gnt5 (UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase 5) Rattus norvegicus
Analyze
Symbol: B3gnt5
Name: UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase 5
RGD ID: 70955
Description: Predicted to enable beta-galactosyl-N-acetylglucosaminylgalactosylglucosyl-ceramide beta-1,3-acetylglucosaminyltransferase activity. Predicted to be involved in brain development and protein O-linked glycosylation. Predicted to be located in Golgi membrane. Predicted to be active in membrane. Orthologous to human B3GNT5 (UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase 5); PARTICIPATES IN lacto-series glycosphingolipid metabolic pathway; INTERACTS WITH 2,3,7,8-Tetrachlorodibenzofuran; 4,4'-sulfonyldiphenol; ammonium chloride.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: beta-1,3-Gn-T5; beta-1,3-N-acetylglucosaminyltransferase 5; beta-1,3-N-acetylglucosaminyltransferase-5; beta3Gn-T5; BGnT-5; lactosylceramide 1,3-N-acetyl-beta-D-glucosaminyltransferase; lactotriaosylceramide synthase; lc(3)Cer synthase; lc3 synthase; UDP-GlcNAc:beta-Gal beta-1,3-N-acetylglucosaminyltransferase 5
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
mRatBN7.21181,141,102 - 81,153,206 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1181,140,599 - 81,156,166 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1189,878,457 - 89,890,574 (-)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.01182,531,822 - 82,543,939 (-)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.01181,592,958 - 81,605,075 (-)NCBIRnor_WKY
Rnor_6.01184,919,055 - 84,931,160 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1184,919,066 - 84,931,160 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01187,978,737 - 87,990,865 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41183,396,028 - 83,408,584 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11183,456,455 - 83,457,193 (-)NCBI
Celera1179,975,786 - 79,987,947 (-)NCBICelera
Cytogenetic Map11q23NCBI
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
Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component
Golgi membrane  (IEA)
membrane  (IBA)

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. Gene Data Set MGD Curation, June 12, 2002
4. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
5. Electronic Transfer of LocusLink and RefSeq Data NCBI rat LocusLink and RefSeq merged data July 26, 2002
6. KEGG Annotation Import Pipeline Pipeline to import KEGG annotations from KEGG into RGD
7. GOA pipeline RGD automated data pipeline
8. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
9. Molecular cloning and characterization of UDP-GlcNAc:lactosylceramide beta 1,3-N-acetylglucosaminyltransferase (beta 3Gn-T5), an essential enzyme for the expression of HNK-1 and Lewis X epitopes on glycolipids. Togayachi A, etal., J Biol Chem 2001 Jun 22;276(25):22032-40.
Additional References at PubMed
PMID:11384981  


Genomics

Comparative Map Data
B3gnt5
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21181,141,102 - 81,153,206 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1181,140,599 - 81,156,166 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1189,878,457 - 89,890,574 (-)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.01182,531,822 - 82,543,939 (-)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.01181,592,958 - 81,605,075 (-)NCBIRnor_WKY
Rnor_6.01184,919,055 - 84,931,160 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1184,919,066 - 84,931,160 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01187,978,737 - 87,990,865 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41183,396,028 - 83,408,584 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11183,456,455 - 83,457,193 (-)NCBI
Celera1179,975,786 - 79,987,947 (-)NCBICelera
Cytogenetic Map11q23NCBI
B3GNT5
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh383183,253,253 - 183,273,385 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p13 Ensembl3183,253,253 - 183,298,504 (+)EnsemblGRCh38hg38GRCh38
GRCh373182,971,041 - 182,991,173 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 363184,453,726 - 184,473,873 (+)NCBINCBI36Build 36hg18NCBI36
Build 343184,453,746 - 184,473,880NCBI
Celera3181,406,353 - 181,426,501 (+)NCBICelera
Cytogenetic Map3q27.1NCBI
HuRef3180,376,825 - 180,396,839 (+)NCBIHuRef
CHM1_13182,934,723 - 182,954,870 (+)NCBICHM1_1
T2T-CHM13v2.03186,060,144 - 186,080,277 (+)NCBIT2T-CHM13v2.0
B3gnt5
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391619,578,943 - 19,591,508 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1619,578,958 - 19,591,503 (+)EnsemblGRCm39 Ensembl
GRCm381619,760,192 - 19,772,760 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1619,760,208 - 19,772,753 (+)EnsemblGRCm38mm10GRCm38
MGSCv371619,760,327 - 19,772,846 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361619,673,797 - 19,685,863 (+)NCBIMGSCv36mm8
Celera1620,328,624 - 20,341,086 (+)NCBICelera
Cytogenetic Map16A3NCBI
B3gnt5
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495542024,046,485 - 24,047,624 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495542024,029,867 - 24,061,801 (-)NCBIChiLan1.0ChiLan1.0
B3GNT5
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan13181,124,288 - 181,148,391 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v03180,283,491 - 180,307,583 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.13188,458,434 - 188,477,816 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl3188,474,226 - 188,475,362 (+)Ensemblpanpan1.1panPan2
B3GNT5
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.13416,208,518 - 16,228,592 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl3416,225,002 - 16,226,147 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha3420,297,025 - 20,317,113 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.03416,116,036 - 16,136,260 (+)NCBIROS_Cfam_1.0
UMICH_Zoey_3.13416,157,034 - 16,177,115 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.03416,140,415 - 16,161,998 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.03416,380,447 - 16,400,540 (+)NCBIUU_Cfam_GSD_1.0
B3gnt5
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024405602112,931,177 - 112,949,506 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_004936566273,714 - 274,847 (-)EnsemblSpeTri2.0
SpeTri2.0NW_004936566271,807 - 289,526 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
B3GNT5
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl13121,206,550 - 121,223,922 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.113121,205,070 - 121,222,997 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.213130,477,285 - 130,494,947 (-)NCBISscrofa10.2Sscrofa10.2susScr3
Pig Cytomap13q23-q41NCBI
B3GNT5
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1156,131,905 - 6,151,882 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl156,134,356 - 6,135,489 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366606314,936,081 - 14,959,281 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
B3gnt5
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462473073,152,728 - 73,153,867 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462473073,122,977 - 73,167,713 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in B3gnt5
21 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:805
Count of miRNA genes:306
Interacting mature miRNAs:393
Transcripts:ENSRNOT00000071848
Prediction methods:Microtar, Miranda, 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
724554Iddm17Insulin dependent diabetes mellitus QTL 170.001blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)111897620886241447Rat
724563Uae10Urinary albumin excretion QTL 106urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)112767241082846715Rat
1300110Stl7Serum triglyceride level QTL 74.64blood triglyceride amount (VT:0002644)plasma triglyceride level (CMO:0000548)112952841882566702Rat
1300135Rf19Renal function QTL 193.38blood creatinine amount (VT:0005328)creatinine clearance (CMO:0000765)114094618882566702Rat
2312566Glom20Glomerulus QTL 203.60.001kidney glomerulus morphology trait (VT:0005325)index of glomerular damage (CMO:0001135)114428575982566702Rat
1581565Pur10Proteinuria QTL 100.0001urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)114480331882846466Rat
1581572Uae35Urinary albumin excretion QTL 350.0001urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)114480331882846466Rat
724561Plsm4Polydactyly-luxate syndrome (PLS) morphotypes QTL 40.0003forelimb integrity trait (VT:0010562)front foot phalanges count (CMO:0001947)115445753486241447Rat
4889521Gluco62Glucose level QTL 622.820.001blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)115513672982993457Rat
7411658Foco27Food consumption QTL 2716.20.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)115635142486241447Rat
631506Bp104Blood pressure QTL 1042.8arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)115980279482566545Rat
70208Niddm22Non-insulin dependent diabetes mellitus QTL 223.61blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)115980279482566553Rat
10058954Gmadr7Adrenal mass QTL 72.490.0049adrenal gland mass (VT:0010420)both adrenal glands wet weight to body weight ratio (CMO:0002411)116034659086241447Rat
1549848Bvd6Brain ventricular dilatation QTL 63.10.0001brain ventricle morphology trait (VT:0000822)hydrocephalus severity score (CMO:0001881)116611332182169223Rat
634339Niddm50Non-insulin dependent diabetes mellitus QTL 503.32blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)116642214886241447Rat
1354593Stl12Serum triglyceride level QTL 123.36blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)116642214886241447Rat
1354656Bvd3Brain ventricular dilatation QTL 33.640.001brain ventricle morphology trait (VT:0000822)hydrocephalus severity score (CMO:0001881)116944607082846715Rat
10450831Scl80Serum cholesterol level QTL 804.70.01blood LDL cholesterol amount (VT:0000181)blood low density lipoprotein cholesterol level (CMO:0000053)117695713183051965Rat

Markers in Region
RH134772  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21181,141,385 - 81,141,593 (+)MAPPERmRatBN7.2
Rnor_6.01184,919,339 - 84,919,546NCBIRnor6.0
Rnor_5.01187,979,021 - 87,979,228UniSTSRnor5.0
RGSC_v3.41183,396,312 - 83,396,519UniSTSRGSC3.4
Celera1179,976,070 - 79,976,277UniSTS
RH 3.4 Map11689.5UniSTS
Cytogenetic Map11q23UniSTS


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 3 1 12 43 6 9
Low 26 13 6 7 6 2 2 24 13 25 11 2
Below cutoff 15 42 35 35 6 8 7 10 7 6

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000071848   ⟹   ENSRNOP00000067153
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1181,141,114 - 81,156,166 (-)Ensembl
Rnor_6.0 Ensembl1184,919,066 - 84,931,160 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000093901   ⟹   ENSRNOP00000085318
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1181,140,599 - 81,153,399 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000103393   ⟹   ENSRNOP00000079466
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1181,140,599 - 81,153,361 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000106647   ⟹   ENSRNOP00000086439
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1181,140,599 - 81,149,930 (-)Ensembl
RefSeq Acc Id: NM_053932   ⟹   NP_446384
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21181,141,102 - 81,153,206 (-)NCBI
Rnor_6.01184,919,055 - 84,931,160 (-)NCBI
Rnor_5.01187,978,737 - 87,990,865 (-)NCBI
RGSC_v3.41183,396,028 - 83,408,584 (-)RGD
Celera1179,975,786 - 79,987,947 (-)RGD
Sequence:
Protein Sequences
Protein RefSeqs NP_446384 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein BAB40941 (Get FASTA)   NCBI Sequence Viewer  
  EDL77982 (Get FASTA)   NCBI Sequence Viewer  
  Q99NB2 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_446384   ⟸   NM_053932
- UniProtKB: Q99NB2 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSRNOP00000067153   ⟸   ENSRNOT00000071848
RefSeq Acc Id: ENSRNOP00000085318   ⟸   ENSRNOT00000093901
RefSeq Acc Id: ENSRNOP00000079466   ⟸   ENSRNOT00000103393
RefSeq Acc Id: ENSRNOP00000086439   ⟸   ENSRNOT00000106647

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q99NB2-F1-model_v2 AlphaFold Q99NB2 1-377 view protein structure

Transcriptome

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

Promoters
RGD ID:13698286
Promoter ID:EPDNEW_R8811
Type:initiation region
Name:B3gnt5_1
Description:UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase 5
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_6.01184,931,244 - 84,931,304EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:70955 AgrOrtholog
BioCyc Gene G2FUF-20699 BioCyc
BioCyc Pathway PWY-7839 [lacto-series glycosphingolipids biosynthesis] BioCyc
  PWY-7841 [neolacto-series glycosphingolipids biosynthesis] BioCyc
Ensembl Genes ENSRNOG00000046258 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Protein ENSRNOP00000067153.1 UniProtKB/Swiss-Prot
  ENSRNOP00000079466.1 UniProtKB/Swiss-Prot
  ENSRNOP00000085318 ENTREZGENE
  ENSRNOP00000085318.1 UniProtKB/Swiss-Prot
  ENSRNOP00000086439.1 UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000071848.3 UniProtKB/Swiss-Prot
  ENSRNOT00000093901 ENTREZGENE
  ENSRNOT00000093901.1 UniProtKB/Swiss-Prot
  ENSRNOT00000103393.1 UniProtKB/Swiss-Prot
  ENSRNOT00000106647.1 UniProtKB/Swiss-Prot
Gene3D-CATH 3.90.550.50 UniProtKB/Swiss-Prot
InterPro Glyco_trans_31 UniProtKB/Swiss-Prot
KEGG Report rno:116740 UniProtKB/Swiss-Prot
NCBI Gene 116740 ENTREZGENE
PANTHER LACTOSYLCERAMIDE 1,3-N-ACETYL-BETA-D-GLUCOSAMINYLTRANSFERASE UniProtKB/Swiss-Prot
  PTHR11214 UniProtKB/Swiss-Prot
Pfam Galactosyl_T UniProtKB/Swiss-Prot
PhenoGen B3gnt5 PhenoGen
UniProt B3GN5_RAT UniProtKB/Swiss-Prot, ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2002-07-09 B3gnt5  UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase 5      Symbol and Name updated to reflect Human and Mouse nomenclature 70877 APPROVED

RGD Curation Notes
Note Type Note Reference
gene_expression expressed in fetal/neonatal rat cerebral cortex with a peak around embryonic day 19 decreasing through postnatal day 14, and in fetal cerebellum in a biphasic manner with peaks on days E19 and P8 70806
gene_expression not expressed in the adult cerebral cortex, but comparatively high expression in adult cerebellum 70806
gene_regulation n HL-60 cells, expression is up-regulated by retinoic acid and down-regulated by 12-O-tetradecanoylphorbol-13-acetate 70806