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SDC4P Gene

pseudogene   GIFtS: 24
GCID: GC22M030877

Syndecan 4 Pseudogene

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(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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This gene clusters with an RNA gene
Subcategory (RNA class): lncRNA

Quality score for the ORGUL clustered with this gene is 5

Aliases
Syndecan 4 Pseudogene1 2

External Ids:    HGNC: 189031   Entrez Gene: 3768442   Ensembl: ENSG000002141617   
ORGUL members:    fRNAdb10:FR216741 FR216741      
NCBI13:AF520746    
RNAdb15:LIT2098    

Export aliases for SDC4P gene to outside databases

Previous GC identifers: GC22U990241 GC22M029202 GC22M029203 GC22M029204 GC22M013839


(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 SDC4P Gene:
SDC4P (syndecan 4 pseudogene) is a pseudogene, and is affiliated with the lncRNA class.

fRNAdb sequence ontology for SDC4P:
mature_transcript - A transcript which has undergone the necessary modifications, if any, for its function. In eukaryotes this includes, for example, processing of introns, cleavage, base modification, and modifications to the 5' and/or the 3' ends, other than addition of bases. In bacteria functional mRNAs are usually not modified.

View fRNAdb secondary structures for SDC4P

(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 at NCBI GenBank:
NC_000022.10  NC_018933.2  NT_011520.13  
Regulatory elements:
   Regulatory transcription factor binding sites in the SDC4P gene promoter:
         NF-1   AML1a   NRSF form 1   MyoD   NRSF form 2   GATA-1   C/EBPalpha   HEN1   
         Other transcription factors

Browse SwitchGear Promoter luciferase reporter plasmids
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Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat SDC4P


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

Entrez Gene cytogenetic band: 22q12.2   Ensembl cytogenetic band:  22q12.2   HGNC cytogenetic band: 22q12.2

SDC4P Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
SDC4P gene location

GeneLoc information about chromosome 22         GeneLoc Exon Structure

GeneLoc location for GC22M030877:  view genomic region     (about GC identifiers)

Start:
30,877,277 bp from pter      End:
30,877,898 bp from pter
Size:
622 bases      Orientation:
minus strand
ORGUL member locations:
Legend (see complete legend)

ORGUL Member Locations for SDC4P

(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, Cloud-Clone Corp., and/or eBioscience,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, Cloud-Clone Corp., and/or eBioscience, Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, Cloud-Clone Corp, and/or others.)
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UniProtKB: --


(According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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(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, Vector BioLabs and/or Addgene, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Flow cytometry from eBioscience, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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Animal Models:
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(According to UniProtKB, COMPARTMENTS Subcellular localization database, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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(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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Interactions:

    Search GeneGlobe Interaction Network for SDC4P

(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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(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,
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, and/or Addgene, Primers from OriGene, and/or QIAGEN, Flow cytometry from eBioscience )
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1 fRNAdb Secondary structure:


Unigene Cluster for SDC4P:

Syndecan 4 pseudogene
Hs.534651
Unigene Representative Sequence: AF520746
1 Ensembl transcript including schematic representation, and UCSC links where relevant:
ENST00000453285(uc003aic.1)
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Additional mRNA sequence: 

AF520746.1 NR_001580.1 

1 DOTS entry:

DT.100700750 

2 AceView cDNA sequences:

NR_001580 AF520746 

GeneLoc Exon Structure


(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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SDC4P expression in normal human tissues (normalized intensities)
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS <intensity>2/3
CGAP TAG: TCCAACACTG
SDC4P Expression
About this image

SDC4P Protein expression data from MOPED1, PaxDb2 and MaxQB3 --

SOURCE GeneReport for Unigene cluster: Hs.534651
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In Situ
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(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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ENSEMBL Gene Tree for SDC4P (if available)
TreeFam Gene Tree for SDC4P (if available)

(Paralogs according to 1HomoloGene,
2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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(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 SDC4P (see all 65)    About this table                                 

Genomic DataTranscription Related DataAllele Frequencies
SNP IDValidClinical
significance
Chr 22 posSequence#AA
Chg
TypeMore#Allele
freq
PopTotal
sample
More
----------
rs113272831,2
C--30876805(+) CAACA-/ATAACA 1 -- ds50010--------
rs7379421,2
C,F,O,A,H--30876835(+) CAGGCA/GGAACA 1 -- ds500121Minor allele frequency- G:0.12NS EA NA WA 2334
rs1882725111,2
--30876891(+) TGGGCA/GTGGTG 1 -- ds50010--------
rs96089351,2
C,F,A--30876892(+) GGGCGT/CGGTGG 1 -- ds500110Minor allele frequency- C:0.23NA WA CSA EA 371
rs1163812751,2
F--30876903(+) CTCACG/ACCTGT 1 -- ds50011Minor allele frequency- A:0.04WA 118
rs1463808951,2
--30876915(+) ATCACA/GTTGCT 1 -- ds50010--------
rs1113290871,2
C,F--30877063(+) TGAGGT/CAGGAG 1 -- ds50012Minor allele frequency- C:0.33WA CSA 3
rs1906196961,2
--30877081(+) TGAATC/TGGGGA 1 -- ds50010--------
rs1823356381,2
--30877252(+) CTCTGA/CAAAAT 1 -- ds50010--------
rs1877376871,2
--30877299(+) GCTCAG/TAGAAG 1 -- nc-transcript-variant0--------

HapMap Linkage Disequilibrium report for SDC4P (30877277 - 30877898 bp)

Structural Variations
     Database of Genomic Variants (DGV) 1 variation for SDC4P:    About this table    
Variant IDTypeSubtypePubMed ID
nsv829171CNV Loss20364138

Site Specific Mutation Identification with PCR Assays
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DNA2.0 Custom Variant and Variant Library Synthesis for SDC4P

(in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
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Find genes that share disorders with SDC4P           About GenesLikeMe

Genetic Association Database (GAD): SDC4P

Export disorders for SDC4P 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 SDC4P gene integrated from 10 sources:
(articles sorted by number of sources associating them with SDC4P)
    Utopia: connect your pdf to the dynamic
world of online information

  1. Identification of a syndecan 4 pseudogene. (PubMed id 12652906)1, 3, 9 Spring S.C. and Terman B.I. (DNA Seq. 2002)
  2. Genetic variants associated with breast size also influence breast cancer risk. (PubMed id 22747683)1 Eriksson N....Tung J.Y. (BMC Med. Genet. 2012)
  3. (PubMed id 15608161)10 

(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: 376844 HGNC: 18903 AceView: SDC4P Ensembl:ENSG00000214161 euGenes: HUgn376844
ECgene: SDC4P H-InvDB: SDC4P

(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 SDC4P 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 SDC4P gene:
Search GeneIP for patents involving SDC4P

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, eBioscience, and/or others, Gene Editing from DNA2.0. Clones from OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Addgene, Cell lines from GenScript, and ESI BIO, Flow cytometery from eBioscience, 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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