Human Gene MGAT5B (uc002jti.3) Description and Page Index
  Description: Homo sapiens mannosyl (alpha-1,6-)-glycoprotein beta-1,6-N-acetyl-glucosaminyltransferase, isozyme B (MGAT5B), transcript variant 2, mRNA.
RefSeq Summary (NM_198955): The MGAT5B gene encodes a beta-1,6-N-acetylglucosaminyltransferase (EC 2.4.1.155) that functions in the synthesis of complex cell surface N-glycans (Kaneko et al., 2003 [PubMed 14623122]).[supplied by OMIM, Nov 2008].
Transcript (Including UTRs)
   Position: hg19 chr17:74,868,729-74,946,471 Size: 77,743 Total Exon Count: 16 Strand: +
Coding Region
   Position: hg19 chr17:74,868,832-74,944,920 Size: 76,089 Coding Exon Count: 16 

Page IndexSequence and LinksGenetic AssociationsMalaCardsCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesmRNA Descriptions
PathwaysOther NamesModel InformationMethods
Data last updated: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr17:74,868,729-74,946,471)mRNA (may differ from genome)Protein (801 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
BioGPSCGAPEnsemblEntrez GeneExonPrimerGeneCards
GeneNetworkH-INVHGNCHPRDLynxMGI
OMIMPubMedStanford SOURCEUniProtKBWikipedia

-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): MGAT5B
CDC HuGE Published Literature: MGAT5B
Positive Disease Associations: Hemoglobin A, Glycosylated , Lipoproteins, LDL
Related Studies:
  1. Hemoglobin A, Glycosylated
    Andrew D Paterson et al. Diabetes 2010, A genome-wide association study identifies a novel major locus for glycemic control in type 1 diabetes, as measured by both A1C and glucose., Diabetes. [PubMed 19875614]
    A major locus for A1C and glucose in individuals with diabetes is near SORCS1. This may influence the design and analysis of genetic studies attempting to identify risk factors for long-term diabetic complications.
  2. Lipoproteins, LDL
    , , . [PubMed 0]

-  MalaCards Disease Associations
  MalaCards Gene Search: MGAT5B
Diseases sorted by gene-association score: walker-warburg syndrome (1)

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene
  • D018817 N-Methyl-3,4-methylenedioxyamphetamine
  • D013749 Tetrachlorodibenzodioxin

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 32.76 RPKM in Brain - Cortex
Total median expression: 150.83 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -26.65103-0.259 Picture PostScript Text
3' UTR -684.611551-0.441 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  Pfam Domains:
PF15024 - Glycosyltransferase family 18

ModBase Predicted Comparative 3D Structure on Q3V5L5-2
FrontTopSide
The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologNo orthologGenome BrowserNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
  Ensembl   
  Protein Sequence   
  Alignment   

-  Descriptions from all associated GenBank mRNAs
  AK057861 - Homo sapiens cDNA FLJ25132 fis, clone CBR06774.
AB235153 - Homo sapiens KIAA2008 mRNA for hypothetical protein.
BC041577 - Homo sapiens mannosyl (alpha-1,6-)-glycoprotein beta-1,6-N-acetyl-glucosaminyltransferase, isozyme B, mRNA (cDNA clone IMAGE:4636485).
BC062354 - Homo sapiens mannosyl (alpha-1,6-)-glycoprotein beta-1,6-N-acetyl-glucosaminyltransferase, isozyme B, mRNA (cDNA clone IMAGE:4643626), complete cds.
AB109185 - Homo sapiens GnT-IX mRNA for N-Acetylglucosaminyltransferase IX, complete cds.
AB384348 - Synthetic construct DNA, clone: pF1KSDA2008, Homo sapiens MGAT5B gene for alpha-1,6-mannosylglycoprotein 6-beta-N-acetylglucosaminyltransferase B, complete cds, without stop codon, in Flexi system.
AB114297 - Homo sapiens hGnTVb mRNA for UDP-N-acetylglucosamine: alpha1,6-D-mannoside beta1,6-N-acetylglucosaminyltransferase b, complete cds.
BC144361 - Homo sapiens cDNA clone IMAGE:9052882, containing frame-shift errors.
BC156823 - Synthetic construct Homo sapiens clone IMAGE:100062526, MGC:190543 mannosyl (alpha-1,6-)-glycoprotein beta-1,6-N-acetyl-glucosaminyltransferase, isozyme B (MGAT5B) mRNA, encodes complete protein.
JD128217 - Sequence 109241 from Patent EP1572962.
JD139262 - Sequence 120286 from Patent EP1572962.
JD213717 - Sequence 194741 from Patent EP1572962.
JD408409 - Sequence 389433 from Patent EP1572962.
JD358436 - Sequence 339460 from Patent EP1572962.
JD219428 - Sequence 200452 from Patent EP1572962.
JD513106 - Sequence 494130 from Patent EP1572962.
JD119460 - Sequence 100484 from Patent EP1572962.
JD483514 - Sequence 464538 from Patent EP1572962.
JD454692 - Sequence 435716 from Patent EP1572962.
BC036948 - Homo sapiens mannosyl (alpha-1,6-)-glycoprotein beta-1,6-N-acetyl-glucosaminyltransferase, isozyme B, mRNA (cDNA clone IMAGE:5503346), with apparent retained intron.
BC063862 - Homo sapiens mannosyl (alpha-1,6-)-glycoprotein beta-1,6-N-acetyl-glucosaminyltransferase, isozyme B, mRNA (cDNA clone IMAGE:6181037), complete cds.
KJ903839 - Synthetic construct Homo sapiens clone ccsbBroadEn_13233 MGAT5B gene, encodes complete protein.
AK123189 - Homo sapiens cDNA FLJ41195 fis, clone BRACE2045596, weakly similar to CTD-BINDING SR-LIKE PROTEIN RA4.
JD541797 - Sequence 522821 from Patent EP1572962.
JD086240 - Sequence 67264 from Patent EP1572962.
JD422353 - Sequence 403377 from Patent EP1572962.
JD462856 - Sequence 443880 from Patent EP1572962.
JD260330 - Sequence 241354 from Patent EP1572962.
JD443320 - Sequence 424344 from Patent EP1572962.
JD256327 - Sequence 237351 from Patent EP1572962.
JD459295 - Sequence 440319 from Patent EP1572962.
JD040210 - Sequence 21234 from Patent EP1572962.
JD475830 - Sequence 456854 from Patent EP1572962.
JD106760 - Sequence 87784 from Patent EP1572962.
JD136678 - Sequence 117702 from Patent EP1572962.
JD294322 - Sequence 275346 from Patent EP1572962.
JD256283 - Sequence 237307 from Patent EP1572962.
JD566264 - Sequence 547288 from Patent EP1572962.
JD177900 - Sequence 158924 from Patent EP1572962.
JD306596 - Sequence 287620 from Patent EP1572962.
JD056050 - Sequence 37074 from Patent EP1572962.
JD376285 - Sequence 357309 from Patent EP1572962.
JD554259 - Sequence 535283 from Patent EP1572962.
JD374218 - Sequence 355242 from Patent EP1572962.
JD564918 - Sequence 545942 from Patent EP1572962.
JD190855 - Sequence 171879 from Patent EP1572962.
JD405930 - Sequence 386954 from Patent EP1572962.
JD375779 - Sequence 356803 from Patent EP1572962.
JD458154 - Sequence 439178 from Patent EP1572962.
JD226648 - Sequence 207672 from Patent EP1572962.
JD102430 - Sequence 83454 from Patent EP1572962.
JD129748 - Sequence 110772 from Patent EP1572962.
JD163704 - Sequence 144728 from Patent EP1572962.
JD449510 - Sequence 430534 from Patent EP1572962.
JD295046 - Sequence 276070 from Patent EP1572962.
JD180599 - Sequence 161623 from Patent EP1572962.
JD092846 - Sequence 73870 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  KEGG - Kyoto Encyclopedia of Genes and Genomes
hsa00510 - N-Glycan biosynthesis
hsa01100 - Metabolic pathways

-  Other Names for This Gene
  Alternate Gene Symbols: KIAA2008, NM_198955, NP_945193, Q3V5L5-2
UCSC ID: uc002jti.3
RefSeq Accession: NM_198955
Protein: Q3V5L5-2, splice isoform of Q3V5L5 CCDS: CCDS45788.1, CCDS11751.1, CCDS59299.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_198955.1
exon count: 16CDS single in 3' UTR: no RNA size: 4068
ORF size: 2406CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 4912.00frame shift in genome: no % Coverage: 99.80
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: no # AT/AC introns 0
selenocysteine: no end bleed into intron: 204# strange splices: 0
Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.