Human Gene GALNT6 (uc001ryl.1) Description and Page Index
  Description: Homo sapiens UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 6 (GalNAc-T6) (GALNT6), mRNA.
RefSeq Summary (NM_007210): This gene encodes a member of the UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase (GalNAc-T) family of enzymes. GalNAc-Ts initiate mucin-type O-linked glycosylation in the Golgi apparatus by catalyzing the transfer of GalNAc to serine and threonine residues on target proteins. They are characterized by an N-terminal transmembrane domain, a stem region, a lumenal catalytic domain containing a GT1 motif and Gal/GalNAc transferase motif, and a C-terminal ricin/lectin-like domain. GalNAc-Ts have different, but overlapping, substrate specificities and patterns of expression. The encoded protein is capable of glycosylating fibronectin peptide in vitro and is expressed in a fibroblast cell line, indicating that it may be involved in the synthesis of oncofetal fibronectin. [provided by RefSeq, Jul 2008]. Publication Note: This RefSeq record includes a subset of the publications that are available for this gene. Please see the Gene record to access additional publications. ##Evidence-Data-START## Transcript exon combination :: BC035822.1 [ECO:0000332] RNAseq introns :: mixed/partial sample support SAMEA1965299, SAMEA1966682 [ECO:0000350] ##Evidence-Data-END## ##RefSeq-Attributes-START## MANE Ensembl match :: ENST00000356317.8/ ENSP00000348668.2 RefSeq Select criteria :: based on conservation, longest protein ##RefSeq-Attributes-END##
Transcript (Including UTRs)
   Position: hg19 chr12:51,745,833-51,785,200 Size: 39,368 Total Exon Count: 12 Strand: -
Coding Region
   Position: hg19 chr12:51,748,163-51,773,565 Size: 25,403 Coding Exon Count: 10 

Page IndexSequence and LinksUniProtKB CommentsGenetic AssociationsCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr12:51,745,833-51,785,200)mRNA (may differ from genome)Protein (622 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
BioGPSCGAPEnsemblEntrez GeneExonPrimerGeneCards
GeneNetworkH-INVHGNCHPRDLynxMGI
neXtProtOMIMPubMedReactomeStanford SOURCETreefam
UniProtKBWikipedia

-  Comments and Description Text from UniProtKB
  ID: GALT6_HUMAN
DESCRIPTION: RecName: Full=Polypeptide N-acetylgalactosaminyltransferase 6; EC=2.4.1.41; AltName: Full=Polypeptide GalNAc transferase 6; Short=GalNAc-T6; Short=pp-GaNTase 6; AltName: Full=Protein-UDP acetylgalactosaminyltransferase 6; AltName: Full=UDP-GalNAc:polypeptide N-acetylgalactosaminyltransferase 6;
FUNCTION: Catalyzes the initial reaction in O-linked oligosaccharide biosynthesis, the transfer of an N-acetyl-D- galactosamine residue to a serine or threonine residue on the protein receptor. May participate in synthesis of oncofetal fibronectin. Has activity toward Muc1a, Muc2, EA2 and fibronectin peptides.
CATALYTIC ACTIVITY: UDP-N-acetyl-D-galactosamine + polypeptide = UDP + N-acetyl-D-galactosaminyl-polypeptide.
COFACTOR: Manganese (By similarity).
COFACTOR: Calcium (By similarity).
PATHWAY: Protein modification; protein glycosylation.
SUBCELLULAR LOCATION: Golgi apparatus membrane; Single-pass type II membrane protein (By similarity).
TISSUE SPECIFICITY: Expressed in placenta and trachea. Weakly expressed in brain and pancreas. Expressed in fibroblast. Weakly or not expressed in lung, liver, muscle, kidney, spleen, thymus, prostate, testis, ovary, intestine, colon, leukocyte, stomach, thyroid, spinal cord, lymph node, trachea, adrenal gland and bone marrow.
DOMAIN: There are two conserved domains in the glycosyltransferase region: the N-terminal domain (domain A, also called GT1 motif), which is probably involved in manganese coordination and substrate binding and the C-terminal domain (domain B, also called Gal/GalNAc-T motif), which is probably involved in catalytic reaction and UDP-Gal binding (By similarity).
DOMAIN: The ricin B-type lectin domain binds to GalNAc and contributes to the glycopeptide specificity (By similarity).
SIMILARITY: Belongs to the glycosyltransferase 2 family. GalNAc-T subfamily.
SIMILARITY: Contains 1 ricin B-type lectin domain.
SEQUENCE CAUTION: Sequence=BAB15297.1; Type=Erroneous initiation;
WEB RESOURCE: Name=GGDB; Note=GlycoGene database; URL="http://riodb.ibase.aist.go.jp/rcmg/ggdb/";
WEB RESOURCE: Name=Functional Glycomics Gateway - GTase; Note=Polypeptide N-acetylgalactosaminyltransferase 6; URL="http://www.functionalglycomics.org/glycomics/molecule/jsp/glycoEnzyme/viewGlycoEnzyme.jsp?gbpId=gt_hum_488";

-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): GALNT6
CDC HuGE Published Literature: GALNT6

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

+  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: 9.51 RPKM in Minor Salivary Gland
Total median expression: 68.40 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 -124.12321-0.387 Picture PostScript Text
3' UTR -824.582330-0.354 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
  InterPro Domains: Graphical view of domain structure
IPR001173 - Glyco_trans_2
IPR000772 - Ricin_B_lectin

Pfam Domains:
PF00535 - Glycosyl transferase family 2
PF00652 - Ricin-type beta-trefoil lectin domain
PF02709 - N-terminal domain of galactosyltransferase

SCOP Domains:
50370 - Ricin B-like lectins
53448 - Nucleotide-diphospho-sugar transferases

ModBase Predicted Comparative 3D Structure on Q8NCL4
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   

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0004653 polypeptide N-acetylgalactosaminyltransferase activity
GO:0016740 transferase activity
GO:0016757 transferase activity, transferring glycosyl groups
GO:0030246 carbohydrate binding
GO:0046872 metal ion binding

Biological Process:
GO:0006486 protein glycosylation
GO:0006493 protein O-linked glycosylation
GO:0016266 O-glycan processing

Cellular Component:
GO:0000139 Golgi membrane
GO:0005794 Golgi apparatus
GO:0016020 membrane
GO:0016021 integral component of membrane
GO:0048471 perinuclear region of cytoplasm


-  Descriptions from all associated GenBank mRNAs
  AB265820 - Homo sapiens GALNT6 mRNA for UDP-N-acetyl-alpha-D-galactosamine: polypeptide N-acetylgalactosaminyltransferase 6, complete cds.
AK074658 - Homo sapiens cDNA FLJ90177 fis, clone MAMMA1000591, highly similar to UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 6.
BC035822 - Homo sapiens UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 6 (GalNAc-T6), mRNA (cDNA clone MGC:46032 IMAGE:5552059), complete cds.
AK296852 - Homo sapiens cDNA FLJ55709 complete cds, highly similar to Polypeptide N-acetylgalactosaminyltransferase 6 (EC 2.4.1.41).
BC114505 - Homo sapiens UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 6 (GalNAc-T6), mRNA (cDNA clone MGC:119400 IMAGE:40006926), complete cds.
BC114949 - Homo sapiens cDNA clone IMAGE:40006928, containing frame-shift errors.
DQ891224 - Synthetic construct clone IMAGE:100003854; FLH170296.01X; RZPDo839D1198D UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 6 (GalNAc-T6) (GALNT6) gene, encodes complete protein.
DQ894407 - Synthetic construct Homo sapiens clone IMAGE:100008867; FLH170292.01L; RZPDo839D1197D UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 6 (GalNAc-T6) (GALNT6) gene, encodes complete protein.
Y08565 - Homo sapiens mRNA for UDP-GalNAc:polypeptide N-acetylgalactosaminyltransferase (GalNAc-T6 gene).
KJ898382 - Synthetic construct Homo sapiens clone ccsbBroadEn_07776 GALNT6 gene, encodes complete protein.
KJ898383 - Synthetic construct Homo sapiens clone ccsbBroadEn_07777 GALNT6 gene, encodes complete protein.
CU690216 - Synthetic construct Homo sapiens gateway clone IMAGE:100019956 5' read GALNT6 mRNA.
JD144589 - Sequence 125613 from Patent EP1572962.
JD283318 - Sequence 264342 from Patent EP1572962.
JD112299 - Sequence 93323 from Patent EP1572962.
JD144588 - Sequence 125612 from Patent EP1572962.
JD089486 - Sequence 70510 from Patent EP1572962.
JD112298 - Sequence 93322 from Patent EP1572962.
JD188045 - Sequence 169069 from Patent EP1572962.
JD056828 - Sequence 37852 from Patent EP1572962.
AK025961 - Homo sapiens cDNA: FLJ22308 fis, clone HRC05050.
AK225124 - Homo sapiens mRNA for Polypeptide N-acetylgalactosaminyltransferase 6 variant, clone: CBL05075.
JD292467 - Sequence 273491 from Patent EP1572962.
JD451811 - Sequence 432835 from Patent EP1572962.
JD067665 - Sequence 48689 from Patent EP1572962.
JD438071 - Sequence 419095 from Patent EP1572962.
JD063944 - Sequence 44968 from Patent EP1572962.
JD043027 - Sequence 24051 from Patent EP1572962.
JD365218 - Sequence 346242 from Patent EP1572962.
JD096001 - Sequence 77025 from Patent EP1572962.
JD177410 - Sequence 158434 from Patent EP1572962.
JD063046 - Sequence 44070 from Patent EP1572962.
JD377698 - Sequence 358722 from Patent EP1572962.
JD224085 - Sequence 205109 from Patent EP1572962.
JD557145 - Sequence 538169 from Patent EP1572962.
JD564027 - Sequence 545051 from Patent EP1572962.
JD235822 - Sequence 216846 from Patent EP1572962.
JD319402 - Sequence 300426 from Patent EP1572962.
JD062943 - Sequence 43967 from Patent EP1572962.
JD487092 - Sequence 468116 from Patent EP1572962.
JD446316 - Sequence 427340 from Patent EP1572962.
JD168307 - Sequence 149331 from Patent EP1572962.
JD358143 - Sequence 339167 from Patent EP1572962.
JD224805 - Sequence 205829 from Patent EP1572962.
JD117062 - Sequence 98086 from Patent EP1572962.
JD021229 - Sequence 2253 from Patent EP1572962.
AK092496 - Homo sapiens cDNA FLJ35177 fis, clone PLACE6013885, highly similar to Polypeptide N-acetylgalactosaminyltransferase 6 (EC 2.4.1.41).
JD482640 - Sequence 463664 from Patent EP1572962.
JD366415 - Sequence 347439 from Patent EP1572962.
JD534798 - Sequence 515822 from Patent EP1572962.
JD546632 - Sequence 527656 from Patent EP1572962.
JD232347 - Sequence 213371 from Patent EP1572962.
JD184248 - Sequence 165272 from Patent EP1572962.
JD268519 - Sequence 249543 from Patent EP1572962.
JD292183 - Sequence 273207 from Patent EP1572962.
JD431392 - Sequence 412416 from Patent EP1572962.
JD180094 - Sequence 161118 from Patent EP1572962.
JD437049 - Sequence 418073 from Patent EP1572962.
JD554809 - Sequence 535833 from Patent EP1572962.
JD394734 - Sequence 375758 from Patent EP1572962.
JC506825 - Sequence 193 from Patent EP2733220.
JC737937 - Sequence 193 from Patent WO2014075939.
JD036187 - Sequence 17211 from Patent EP1572962.
JD136301 - Sequence 117325 from Patent EP1572962.
JD213566 - Sequence 194590 from Patent EP1572962.
JD194930 - Sequence 175954 from Patent EP1572962.
JD537429 - Sequence 518453 from Patent EP1572962.
JD544761 - Sequence 525785 from Patent EP1572962.
JD067140 - Sequence 48164 from Patent EP1572962.
JD176645 - Sequence 157669 from Patent EP1572962.
JD395033 - Sequence 376057 from Patent EP1572962.
JD286849 - Sequence 267873 from Patent EP1572962.
JD286848 - Sequence 267872 from Patent EP1572962.
JD532297 - Sequence 513321 from Patent EP1572962.
JD558803 - Sequence 539827 from Patent EP1572962.
JD430979 - Sequence 412003 from Patent EP1572962.
JD201443 - Sequence 182467 from Patent EP1572962.
JD388461 - Sequence 369485 from Patent EP1572962.
JD440906 - Sequence 421930 from Patent EP1572962.
JD498184 - Sequence 479208 from Patent EP1572962.
JD148237 - Sequence 129261 from Patent EP1572962.
JD463752 - Sequence 444776 from Patent EP1572962.
JD478503 - Sequence 459527 from Patent EP1572962.
JD543183 - Sequence 524207 from Patent EP1572962.
JD249723 - Sequence 230747 from Patent EP1572962.
JD376086 - Sequence 357110 from Patent EP1572962.
JD480245 - Sequence 461269 from Patent EP1572962.
JD046332 - Sequence 27356 from Patent EP1572962.
JD302444 - Sequence 283468 from Patent EP1572962.
JD434029 - Sequence 415053 from Patent EP1572962.
JD345380 - Sequence 326404 from Patent EP1572962.
JD489377 - Sequence 470401 from Patent EP1572962.
JD426313 - Sequence 407337 from Patent EP1572962.
JD190509 - Sequence 171533 from Patent EP1572962.
JD268144 - Sequence 249168 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  KEGG - Kyoto Encyclopedia of Genes and Genomes
hsa00512 - O-Glycan biosynthesis
hsa01100 - Metabolic pathways

Reactome (by CSHL, EBI, and GO)

Protein Q8NCL4 (Reactome details) participates in the following event(s):

R-HSA-913675 GALNTs transfer GalNAc from UDP-GalNAc to mucins to form Tn antigens
R-HSA-913709 O-linked glycosylation of mucins
R-HSA-5173105 O-linked glycosylation
R-HSA-597592 Post-translational protein modification
R-HSA-392499 Metabolism of proteins

-  Other Names for This Gene
  Alternate Gene Symbols: GALT6_HUMAN, NM_007210, NP_009141, Q8IYH4, Q8NCL4, Q9H6G2, Q9UIV5
UCSC ID: uc001ryl.1
RefSeq Accession: NM_007210
Protein: Q8NCL4 (aka GALT6_HUMAN or GLT6_HUMAN)
CCDS: CCDS8813.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_007210.3
exon count: 12CDS single in 3' UTR: no RNA size: 4520
ORF size: 1869CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 3769.00frame shift in genome: no % Coverage: 100.00
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: 0# 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.