Human Gene SLC35B3 (uc010jof.2)
  Description: Homo sapiens solute carrier family 35, member B3 (SLC35B3), transcript variant 3, mRNA.
RefSeq Summary (NM_001142541): This gene is a member of the solute carrier family. The encoded protein is involved in the transport of 3-prime phosphoadenosine 5-prime phosphosulfate (PAPS) from the nucleus or the cytosol to the Golgi lumen. This gene has been reported to be expressed preferentially in the human colon tissues. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Dec 2013].
Transcript (Including UTRs)
   Position: hg19 chr6:8,429,163-8,435,794 Size: 6,632 Total Exon Count: 2 Strand: -
Coding Region
   Position: hg19 chr6:8,430,004-8,430,297 Size: 294 Coding Exon Count: 1 

Page IndexSequence and LinksPrimersCTDGene AllelesRNA-Seq Expression
Microarray ExpressionRNA StructureProtein StructureOther SpeciesGO AnnotationsmRNA Descriptions
Other NamesModel InformationMethods
Data last updated at UCSC: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr6:8,429,163-8,435,794)mRNA (may differ from genome)Protein (97 aa)
Gene SorterGenome BrowserOther Species FASTATable SchemaAlphaFoldBioGPS
EnsemblExonPrimerGeneCardsH-INVHGNCLynx
MGIPubMedTreefamUniProtKB

-  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


-  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: 13.96 RPKM in Cells - Cultured fibroblasts
Total median expression: 357.52 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 -60.61216-0.281 Picture PostScript Text
3' UTR -184.70841-0.220 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
  ModBase Predicted Comparative 3D Structure on B4E2F5
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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 orthologNo orthologNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
      
      
      

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Cellular Component:
GO:0016020 membrane
GO:0016021 integral component of membrane


-  Descriptions from all associated GenBank mRNAs
  BX647208 - Homo sapiens mRNA; cDNA DKFZp686C1153 (from clone DKFZp686C1153).
BX648022 - Homo sapiens mRNA; cDNA DKFZp686E248 (from clone DKFZp686E248).
BC006973 - Homo sapiens solute carrier family 35, member B3, mRNA (cDNA clone MGC:12179 IMAGE:3827889), complete cds.
BX538271 - Homo sapiens mRNA; cDNA DKFZp779C1713 (from clone DKFZp779C1713); complete cds.
BX641086 - Homo sapiens mRNA; cDNA DKFZp686G2469 (from clone DKFZp686G2469).
AF132953 - Homo sapiens CGI-19 protein mRNA, complete cds.
AB231931 - Homo sapiens PAPST2 mRNA for 3'-phosphoadenosine 5'-phosphosulfate transporter, complete cds.
AK313522 - Homo sapiens cDNA, FLJ94080, highly similar to Homo sapiens solute carrier family 35, member B3 (SLC35B3), mRNA.
HQ447287 - Synthetic construct Homo sapiens clone IMAGE:100070598; CCSB005485_01 solute carrier family 35, member B3 (SLC35B3) gene, encodes complete protein.
KJ898799 - Synthetic construct Homo sapiens clone ccsbBroadEn_08193 SLC35B3 gene, encodes complete protein.
CU675477 - Synthetic construct Homo sapiens gateway clone IMAGE:100019243 5' read SLC35B3 mRNA.
AK303940 - Homo sapiens cDNA FLJ55270 complete cds, highly similar to Solute carrier family 35 member B3.
AK304250 - Homo sapiens cDNA FLJ53129 complete cds, highly similar to Solute carrier family 35 member B3.
AK309222 - Homo sapiens cDNA, FLJ99263.

-  Other Names for This Gene
  Alternate Gene Symbols: AK309222, B4E2F5, B4E2F5_HUMAN
UCSC ID: uc010jof.2
RefSeq Accession: NM_001142541
Protein: B4E2F5

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: AK309222.1
exon count: 2CDS single in 3' UTR: no RNA size: 1171
ORF size: 294CDS single in intron: no Alignment % ID: 99.48
txCdsPredict score: 780.00frame shift in genome: no % Coverage: 99.23
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: 934# 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.