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SLC35A4 Gene

protein-coding   GIFtS: 42
GCID: GC05P139944

Solute Carrier Family 35, Member A4

  See related disease
at  

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
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Aliases
Solute Carrier Family 35, Member A41 2
Probable UDP-Sugar Transporter Protein SLC35A42
Solute Carrier Family 35 (UDP-Galactose Transporter), Member A42
Tumor Rejection Antigen2
Solute Carrier Family 35 Member A43

External Ids:    HGNC: 207531   Entrez Gene: 1138292   Ensembl: ENSG000001760877   UniProtKB: Q96G793   

Export aliases for SLC35A4 gene to outside databases

Previous GC identifers: GC05P140528 GC05P139927 GC05P139972 GC05P139924 GC05P135089


(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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GeneCards Summary for SLC35A4 Gene:
SLC35A4 (solute carrier family 35, member A4) is a protein-coding gene. Diseases associated with SLC35A4 include lung cancer. GO annotations related to this gene include sugar:hydrogen symporter activity. An important paralog of this gene is SLC35A1.


(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 75), Regulatory elements and Epigenetics data according to QIAGEN, and/or SwitchGear Genomics)
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RefSeq DNA sequence:
NC_000005.10  NC_018916.2  NT_029289.12  
Regulatory elements:
   Regulatory transcription factor binding sites in the SLC35A4 gene promoter:
         TBP   p53   NRSF form 1   TFIID   NRSF form 2   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidSLC35A4 promoter sequence
   Search Chromatin IP Primers for SLC35A4

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat SLC35A4


Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: 5q31.3   Ensembl cytogenetic band:  5q31.3   HGNC cytogenetic band: 5q31.3

SLC35A4 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
SLC35A4 gene location

GeneLoc information about chromosome 5         GeneLoc Exon Structure

GeneLoc location for GC05P139944:  view genomic region     (about GC identifiers)

Start:
139,944,041 bp from pter      End:
139,948,688 bp from pter
Size:
4,648 bases      Orientation:
plus strand

(According to 1UniProtKB, HORDE, 2neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, and/or Cloud-Clone Corp.,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Cloud-Clone Corp., Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, and/or Cloud-Clone Corp.)
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UniProtKB/Swiss-Prot: S35A4_HUMAN, Q96G79 (See protein sequence)
Recommended Name: Probable UDP-sugar transporter protein SLC35A4  
Size: 324 amino acids; 34593 Da
Miscellaneous: Classified as NST family 1 subfamily D in a phylogenic study. Family 1 seems to be the most recent
in evolution
Secondary accessions: A8K013

Explore the universe of human proteins at neXtProt for SLC35A4: NX_Q96G79

Explore proteomics data for SLC35A4 at MOPED


See SLC35A4 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

REFSEQ proteins: NP_542401.1  
ENSEMBL proteins: 
 ENSP00000327133   ENSP00000424566  

SLC35A4 Human Recombinant Protein Products:

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(According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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HGNC Gene Families:
SLC: Solute carriers

IUPHAR Guide to PHARMACOLOGY protein family classification: MGC2541
SLC35 family of nucleotide sugar transporters

2 InterPro protein domains:
 IPR007271 Nuc_sug_transpt
 IPR021189 UDP/CMP-sugar_transptr

Graphical View of Domain Structure for InterPro Entry Q96G79

ProtoNet protein and cluster: Q96G79

UniProtKB/Swiss-Prot: S35A4_HUMAN, Q96G79
Similarity: Belongs to the nucleotide-sugar transporter family. SLC35A subfamily


SLC35A4 for domains           About GeneDecksing


(According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, inGenious Targeting Laboratory, genOway,
transcription factor targeting from QIAGEN and/or HOMER, miRNA Gene Targets from miRTarBase, shRNA from OriGene, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, SwitchGear Genomics, Gene Editing from DNA2.0, Clones from OriGene, GenScript, Sino Biological, DNA2.0, and Vector BioLabs, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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     Gene Ontology (GO): 1 molecular function term:    About this table

GO IDQualified GO termEvidencePubMed IDs
GO:0005351sugar:hydrogen symporter activity IEA--
     
SLC35A4 for ontologies           About GeneDecksing


Animal Models:
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miRNA
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miRTarBase miRNAs that target SLC35A4:
hsa-let-7a-5p (MIRT052524), hsa-mir-103a-3p (MIRT027152), hsa-let-7c-5p (MIRT051810), hsa-mir-16-5p (MIRT031866), hsa-mir-125b-5p (MIRT004997), hsa-let-7d-5p (MIRT051713), hsa-mir-93-3p (MIRT038827), hsa-mir-26a-5p (MIRT050186)

Block miRNA regulation of human, mouse, rat SLC35A4 using miScript Target Protectors
Selected qRT-PCR Assays for microRNAs that regulate SLC35A4 (see all 23):
hsa-miR-3938 hsa-miR-125a-5p hsa-miR-137 hsa-miR-330-5p hsa-miR-15a hsa-miR-124 hsa-miR-424 hsa-miR-125b
SwitchGear 3'UTR luciferase reporter plasmidSLC35A4 3' UTR sequence
Inhib. RNA
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Predesigned siRNA for gene silencing in human, mouse, rat SLC35A4

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Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat SLC35A4

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In Situ Assay
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Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for SLC35A4


(According to UniProtKB, COMPARTMENTS Subcellular localization database, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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Subcellular locations from UniProtKB/Swiss-Prot
S35A4_HUMAN, Q96G79: Membrane; Multi-pass membrane protein (Potential). Golgi apparatus (By similarity)
Subcellular locations from COMPARTMENTS: 

CompartmentConfidence
plasma membrane3
golgi apparatus2

Gene Ontology (GO): 3 cellular component terms:    About this table

GO IDQualified GO termEvidencePubMed IDs
GO:0000139Golgi membrane IEA--
GO:0016020membrane ----
GO:0016021integral component of membrane IEA--

SLC35A4 for ontologies           About GeneDecksing


(SuperPaths according to PathCards, Pathways according to R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Sino Biological, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to QIAGEN, and/or STRING, Interactions according to 1UniProtKB, 2MINT, 3I2D, and/or 4STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene).
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    Custom Pathway & Disease-focused RT2 Profiler PCR Arrays for SLC35A4
Interactions:

    Search GeneGlobe Interaction Network for SLC35A4

Gene Ontology (GO): 1 biological process term:    About this table

GO IDQualified GO termEvidencePubMed IDs
GO:0008643carbohydrate transport ----

SLC35A4 for ontologies           About GeneDecksing



(Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience, ApexBio, HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB)
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Browse Small Molecules at EMD Millipore
   Browse drugs & compounds from Enzo Life Sciences
  Browse compounds at ApexBio 

Browse Tocris compounds for SLC35A4 (S35A4)



(Secondary structures according to fRNAdb,
GenBank/EMBL/DDBJ Accessions according to
Unigene (Build 236 Homo sapiens; Apr 25 2013) or GenBank,
RefSeq according to Entrez Gene,
DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
Conferences by KenesGroup, exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN, SwitchGear Genomics,
Tagged/untagged cDNA clones from OriGene, GenScript, DNA2.0, Vector BioLabs, Primers from OriGene, and/or QIAGEN )
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REFSEQ mRNAs for SLC35A4 gene: 
NM_080670.2  

Unigene Cluster for SLC35A4:

Solute carrier family 35, member A4
Hs.406840  [show with all ESTs]
Unigene Representative Sequence: AF445025
4 Ensembl transcripts including schematic representations, and UCSC links where relevant:
ENST00000323146(uc003lgg.1) ENST00000508770 ENST00000514199(uc003lgh.1)
ENST00000514137
miRNA
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Block miRNA regulation of human, mouse, rat SLC35A4 using miScript Target Protectors
Selected qRT-PCR Assays for microRNAs that regulate SLC35A4 (see all 23):
hsa-miR-3938 hsa-miR-125a-5p hsa-miR-137 hsa-miR-330-5p hsa-miR-15a hsa-miR-124 hsa-miR-424 hsa-miR-125b
SwitchGear 3'UTR luciferase reporter plasmidSLC35A4 3' UTR sequence
Inhib. RNA
Products:
     
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Predesigned siRNA for gene silencing in human, mouse, rat SLC35A4
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GenScript: all cDNA clones in your preferred vector: SLC35A4 (NM_080670)
DNA2.0 Custom Codon Optimized Gene Synthesis Service for SLC35A4
Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat SLC35A4
Primer
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OriGene qPCR primer pairs and template standards for SLC35A4
OriGene qSTAR qPCR primer pairs in human, mouse for SLC35A4
Pre-validated RT2 qPCR Primer Assay in human, mouse, rat SLC35A4
  QuantiTect SYBR Green Assays in human, mouse, rat SLC35A4
  QuantiFast Probe-based Assays in human, mouse, rat SLC35A4

Additional mRNA sequence: 

AF445025.1 AJ420598.1 AK122601.1 AK289378.1 AK307282.1 AL833972.1 BC009906.2 

16 DOTS entries:

DT.101984984  DT.100810892  DT.95204941  DT.75156810  DT.92458990  DT.100810894  DT.100810882  DT.120809307 
DT.97855095  DT.95374368  DT.100030141  DT.92458992  DT.120809256  DT.91799426  DT.92458996  DT.99957431 

Selected AceView cDNA sequences (see all 586):

BF354987 AI620366 BM920259 BE718375 BI909156 NM_080670 BE718436 BU733061 
BE718451 AA258159 BE718407 BE718409 BI760535 CF125322 BE535472 BM468941 
BQ672949 CF126050 BM722155 CB133711 BQ351584 BQ227085 BE718418 BQ351588 

GeneLoc Exon Structure

3 Alternative Splicing Database (ASD) splice patterns (SP) for SLC35A4    About this scheme

ExUns: 1a · 1b ^ 2a · 2b ^ 3 ^ 4a · 4b · 4c
SP1:              -                                 
SP2:              -                                 
SP3:                                                


ECgene alternative splicing isoforms for SLC35A4

(RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MaxQB, plus additional links to SOURCE, and/or BioGPS, and/or UniProtKB,
PCR Arrays from QIAGEN, Primers from OriGene, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
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SLC35A4 expression in normal human tissues (normalized intensities)
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS <intensity>2/3
CGAP TAG: CTTCCCACTC
SLC35A4 Expression
About this image

SLC35A4 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

SLC35A4 Protein Expression

SOURCE GeneReport for Unigene cluster: Hs.406840
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In Situ
Assay Products:
 

 
Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for SLC35A4

(Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD , 5MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or 6Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
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This gene was present in the common ancestor of animals.

Orthologs for SLC35A4 gene from Selected species (see all 13)    About this table
Organism Taxonomic
classification
Gene Description Human
Similarity
Orthology
Type
Details
mouse
(Mus musculus)
Mammalia Slc35a41 , 5 solute carrier family 35, member A41, 5 85.96(n)1
88.85(a)1
  18 (19.46 cM)5
678431  NM_001083317.11  NP_001076786.11 
 366795795 
chicken
(Gallus gallus)
Aves SLC35A41 solute carrier family 35, member A4 64.29(n)
60.71(a)
  416136  XM_004944741.1  XP_004944798.1 
lizard
(Anolis carolinensis)
Reptilia SLC35A46
solute carrier family 35, member A4
61(a)
1 ↔ 1
4(77876878-77877810)
African clawed frog
(Xenopus laevis)
Amphibia 480344402   -- 74.59(n)    48034440 
zebrafish
(Danio rerio)
Actinopterygii BI709828.12   -- 73.33(n)    BI709828.1 
fruit fly
(Drosophila melanogaster)
Insecta CG140406
--
19(a)
1 → many
2L(5052843-5054575)


ENSEMBL Gene Tree for SLC35A4 (if available)
TreeFam Gene Tree for SLC35A4 (if available)

(Paralogs according to 1HomoloGene,
2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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Paralogs for SLC35A4 gene
SLC35A12  SLC35A22  SLC35A32  SLC35A52  

SLC35A4 for paralogs           About GeneDecksing


1 Pseudogenes.org Pseudogene for SLC35A4
PGOHUM00000263129


(SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, 4UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD), the Human Cytochrome P450 Allele Nomenclature Database, and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers, Cancer Mutation PCR Arrays and Assays, and Copy Number PCR Arrays from QIAGEN)
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Selected SNPs for SLC35A4 (see all 94)    About this table    
Genomic DataTranscription Related DataAllele Frequencies
SNP IDValidClinical
significance
Chr 5 posSequence#AA
Chg
TypeMore#Allele
freq
PopTotal
sample
More
----------
rs175241231,2
C,F,H--139946265(+) CATCTA/GTGCGG 1 -- ut51 ese37Minor allele frequency- G:0.01NA NS 832
rs115513121,2
C,F--139946269(+) TATGCG/AGCTCA 1 -- ut51 ese31Minor allele frequency- A:0.04NA 120
rs1421672061,2
--139946371(+) AGGCAA/GGATGA 1 -- ut510--------
rs1448159221,2
C--139946392(+) CTTCAA/GGTGGA 1 -- ut510--------
rs115513131,2
C,H--139946545(+) CCATGG/TGACTC 1 -- ut512Minor allele frequency- T:0.01NS NA 182
rs1485892001,2
--139946584(+) CAGCCC/TCTTAC 1 -- ut510--------
rs1429918691,2
C--139946764(+) GTGTAA/GAGGAT 2 K E mis10--------
rs2018833741,2
--139946839(+) CTGCCA/GTGTAC 2 M V mis10--------
rs2012849101,2
C--139946846(+) GTACGG/TTGCCC 2 G V mis10--------
rs617453361,2
C,F--139946888(+) CGGCCG/AAGTGC 2 /Q /R mis14Minor allele frequency- A:0.04NS WA NA EU 6063

HapMap Linkage Disequilibrium report for SLC35A4 (139944041 - 139948688 bp)

Structural Variations
     Database of Genomic Variants (DGV) 1 variation for SLC35A4:    About this table    
Variant IDTypeSubtypePubMed ID
nsv462462CNV Loss19166990

Site Specific Mutation Identification with PCR Assays
SeqTarget long-range PCR primers for resequencing SLC35A4
DNA2.0 Custom Variant and Variant Library Synthesis for SLC35A4

(in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Conferences by KenesGroup, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
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1 disease for SLC35A4:    About MalaCards
lung cancer


SLC35A4 for disorders           About GeneDecksing


Export disorders for SLC35A4 gene to outside databases

(in PubMed. Associations of this gene to articles via 1Entrez Gene, 2UniProtKB/Swiss-Prot, 3HGNC, 4GAD, 5PharmGKB, 6HMDB, 7DrugBank, 8UniProtKB/TrEMBL, 9 Novoseek, and/or 10fRNAdb)
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PubMed articles for SLC35A4 gene integrated from 10 sources:
(articles sorted by number of sources associating them with SLC35A4)
    Utopia: connect your pdf to the dynamic
world of online information

  1. Pathway Analysis of ChIP-Seq-Based NRF1 Target Genes Suggests a Logical Hypothesis of their Involvement in the Pathogenesis of Neurodegenerative Diseases. (PubMed id 24250222)1 Satoh J....Yamamoto Y. (Gene Regul Syst Bio 2013)
  2. hORFeome v3.1: a resource of human open reading frames representing over 10,000 human genes. (PubMed id 17207965)1 Lamesch P.... Vidal M. (Genomics 2007)
  3. The full-ORF clone resource of the German cDNA consortium. (PubMed id 17974005)2 Bechtel S.... Schupp I. (BMC Genomics 2007)
  4. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)2 Gerhard D.S.... Malek J. (Genome Res. 2004)
  5. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)2 Ota T.... Sugano S. (Nat. Genet. 2004)
  6. Gene and peptide analyses of newly defined lung cancer antigens recognized by HLA-A2402-restricted tumor-specific cytotoxic T lymphocytes. (PubMed id 12782588)1 Yamada A.... Itoh K. (Cancer Res. 2003)
  7. The nucleotide-sugar transporter family: a phylogenetic approach. (PubMed id 12770764)2 Martinez-Duncker I.... Oriol R. (Biochimie 2003)
  8. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. (PubMed id 12477932)1 Strausberg R.L....Marra M.A. (Proc. Natl. Acad. Sci. U.S.A. 2002)

(in PubMed, OMIM, and NCBI Bookshelf)
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 ANDOR
Aliases
Free Text  

  Query String
PubMed
OMIM
NCBI Bookshelf
  (Note: In FireFox, select the above section and copy using Ctrl-C)

(According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
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Entrez Gene: 113829 HGNC: 20753 AceView: SLC35A4 Ensembl:ENSG00000176087 euGenes: HUgn113829
ECgene: SLC35A4 H-InvDB: SLC35A4

(According to HUGE)
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  --

(According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL, and/or others, e.g. Wikipedia and GeneReviews, via UniProtKB/Swiss-Prot)
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NameDescription
PharmGKB entry for SLC35A4 Pharmacogenomics, SNPs, Pathways

(Patent information from GeneIP,
Licensable technologies from WIS Yeda, Salk, Tufts,
IP news from LifeMap Sciences, Inc.)
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Patent Information for SLC35A4 gene:
Search GeneIP for patents involving SLC35A4

GeneCards and IP:
Japan Patent Office Licenses GeneCards     European Patent Office Licenses GeneCards     Improving the IP Search



(Antibodies, recombinant proteins, and assays from EMD Millipore, R&D Systems, OriGene, QIAGEN, GenScript, Cell Signaling Technology, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Cloud-Clone Corp., Thermo Fisher Scientific, LSBio, Gene Editing from DNA2.0. Clones from OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Cell lines from GenScript, and ESI BIO, PCR Arrays from QIAGEN, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, Enzo Life Sciences, and/or ApexBio, In Situ Hybridization Assays from
Advanced Cell Diagnostics, Animal models from inGenious Targeting Laboratory, genOway)
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GeneCards Homepage - Last full update: 7 May 2014 - Incrementals: 9 May 2014 , 2 Jun 2014 , 26 Jun 2014 , 30 Jun 2014

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