Human Gene NDST1 (uc003lsl.3)
  Description: Homo sapiens N-deacetylase/N-sulfotransferase (heparan glucosaminyl) 1 (NDST1), mRNA.
RefSeq Summary (NM_001543): This gene encodes a member of the heparan sulfate/heparin GlcNAc N-deacetylase/ N-sulfotransferase family. The encoded enzyme is a type II transmembrane protein that resides in the Golgi apparatus. The encoded protein catalyzes the transfer of sulfate from 3'-phosphoadenosine 5'-phosphosulfate to nitrogen of glucosamine in heparan sulfate. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Dec 2014].
Transcript (Including UTRs)
   Position: hg19 chr5:149,900,430-149,919,334 Size: 18,905 Total Exon Count: 6 Strand: +
Coding Region
   Position: hg19 chr5:149,900,817-149,919,023 Size: 18,207 Coding Exon Count: 6 

Page IndexSequence and LinksPrimersGenetic AssociationsMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
mRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr5:149,900,430-149,919,334)mRNA (may differ from genome)Protein (556 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGeneCardsGeneNetwork
H-INVHGNCLynxMalacardsMGIOMIM
PubMedReactomeUniProtKBWikipediaBioGrid CRISPR DB

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): NDST1
CDC HuGE Published Literature: NDST1

-  MalaCards Disease Associations
  MalaCards Gene Search: NDST1
Diseases sorted by gene-association score: mental retardation, autosomal recessive 46* (1330), autosomal recessive non-syndromic intellectual disability* (71), chikungunya (15), treacher collins syndrome 1 (12)
* = Manually curated disease association

-  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: 35.71 RPKM in Cells - Cultured fibroblasts
Total median expression: 728.39 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 -196.20387-0.507 Picture PostScript Text
3' UTR -73.77311-0.237 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:
PF12062 - heparan sulfate-N-deacetylase

ModBase Predicted Comparative 3D Structure on P52848-2
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 orthologGenome BrowserNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
Gene SorterGene Sorter    
 RGD    
 Protein Sequence    
 Alignment    

-  Descriptions from all associated GenBank mRNAs
  LF211059 - JP 2014500723-A/18562: Polycomb-Associated Non-Coding RNAs.
AB209107 - Homo sapiens mRNA for N-deacetylase/N-sulfotransferase (heparan glucosaminyl) 1 variant protein.
AK293746 - Homo sapiens cDNA FLJ59302 complete cds, highly similar to Bifunctional heparan sulfate N-deacetylase/N-sulfotransferase 1 (EC 2.8.2.8).
AK292448 - Homo sapiens cDNA FLJ76493 complete cds, highly similar to Homo sapiens N-deacetylase/N-sulfotransferase (heparan glucosaminyl) 1 (NDST1), mRNA.
U36600 - Homo sapiens heparan N-deacetylase/N-sulfotransferase-1 mRNA, complete cds.
LF343607 - JP 2014500723-A/151110: Polycomb-Associated Non-Coding RNAs.
JD390114 - Sequence 371138 from Patent EP1572962.
JD136449 - Sequence 117473 from Patent EP1572962.
JD195937 - Sequence 176961 from Patent EP1572962.
JD270116 - Sequence 251140 from Patent EP1572962.
U17970 - Human heparan sulfate N-deacetylase/N-sulfotransferase mRNA, complete cds.
BC012888 - Homo sapiens N-deacetylase/N-sulfotransferase (heparan glucosaminyl) 1, mRNA (cDNA clone MGC:9410 IMAGE:3882074), complete cds.
JD073863 - Sequence 54887 from Patent EP1572962.
U18918 - Human heparan sulfate-N-deacetylase/N-sulfotransferase mRNA, clone HSST, complete cds.
DQ596626 - Homo sapiens piRNA piR-34692, complete sequence.
JD496555 - Sequence 477579 from Patent EP1572962.
JD405816 - Sequence 386840 from Patent EP1572962.
JD209946 - Sequence 190970 from Patent EP1572962.
JD132224 - Sequence 113248 from Patent EP1572962.
JD225157 - Sequence 206181 from Patent EP1572962.
JD497188 - Sequence 478212 from Patent EP1572962.
JD188886 - Sequence 169910 from Patent EP1572962.
KJ904484 - Synthetic construct Homo sapiens clone ccsbBroadEn_13878 NDST1 gene, encodes complete protein.
AB590478 - Synthetic construct DNA, clone: pFN21AE2163, Homo sapiens NDST1 gene for N-deacetylase/N-sulfotransferase (heparan glucosaminyl) 1, without stop codon, in Flexi system.
LF343603 - JP 2014500723-A/151106: Polycomb-Associated Non-Coding RNAs.
LF343602 - JP 2014500723-A/151105: Polycomb-Associated Non-Coding RNAs.
MA579184 - JP 2018138019-A/151110: Polycomb-Associated Non-Coding RNAs.
MA579180 - JP 2018138019-A/151106: Polycomb-Associated Non-Coding RNAs.
MA579179 - JP 2018138019-A/151105: Polycomb-Associated Non-Coding RNAs.
MA446636 - JP 2018138019-A/18562: Polycomb-Associated Non-Coding RNAs.

-  Biochemical and Signaling Pathways
  KEGG - Kyoto Encyclopedia of Genes and Genomes
hsa00534 - Glycosaminoglycan biosynthesis - heparan sulfate
hsa01100 - Metabolic pathways

Reactome (by CSHL, EBI, and GO)

Protein P52848 (Reactome details) participates in the following event(s):

R-HSA-2022887 NDST1-4 N-deacetylates GlcNAc residues in heparan
R-HSA-2022860 NDST1-4 can sulfate a glucosamine residue in heparan to form heparan sulfate (HS)
R-HSA-2022928 HS-GAG biosynthesis
R-HSA-1638091 Heparan sulfate/heparin (HS-GAG) metabolism
R-HSA-1630316 Glycosaminoglycan metabolism
R-HSA-71387 Metabolism of carbohydrates
R-HSA-1430728 Metabolism

-  Other Names for This Gene
  Alternate Gene Symbols: BC012888, HSST, HSST1, NM_001543, NP_001534, P52848-2
UCSC ID: uc003lsl.3
RefSeq Accession: NM_001543
Protein: P52848-2, splice isoform of P52848

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: BC012888.1
exon count: 6CDS single in 3' UTR: no RNA size: 2248
ORF size: 1671CDS single in intron: no Alignment % ID: 99.91
txCdsPredict score: 3464.00frame shift in genome: no % Coverage: 97.78
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: 416# 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.