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SDHAP3 Gene

pseudogene   GIFtS: 23
GCID: GC05M001573

Succinate Dehydrogenase Complex, Subunit A, Flavoprotein...

(Previous names: succinate dehydrogenase complex, subunit A, flavoprotein-like,...)
(Previous symbols: SDHAL, SDHACL)
  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
Succinate Dehydrogenase Complex, Subunit A, Flavoprotein Pseudogene
31 2
SDHACL1 2
SDHAL1 2
SDHA C-Terminal Like1
Similar To Succinate Dehydrogenase Flavoprotein Subunit1
Succinate Dehydrogenase Complex, Subunit A, Flavoprotein-Like1

External Ids:    HGNC: 187811   Entrez Gene: 7286092   Ensembl: ENSG000001859867   

Export aliases for SDHAP3 gene to outside databases

Previous GC identifers: GC05M001628 GC05U901046 GC05M001572 GC05M001553 GC05M001570


(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 SDHAP3 Gene:
SDHAP3 (succinate dehydrogenase complex, subunit A, flavoprotein pseudogene 3) is a pseudogene. Diseases associated with SDHAP3 include endotheliitis.


(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_006576.17  
Regulatory elements:
   Regulatory transcription factor binding sites in the SDHAP3 gene promoter:
         GR   NRSF form 1   GR-beta   ATF-2   CUTL1   NRSF form 2   Gfi-1   YY1   HSF2   GR-alpha   
         Other transcription factors

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Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat SDHAP3


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

Entrez Gene cytogenetic band: 5p15.33   Ensembl cytogenetic band:  5p15.33   HGNC cytogenetic band: 5p15.33

SDHAP3 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
SDHAP3 gene location

GeneLoc information about chromosome 5         GeneLoc Exon Structure

GeneLoc location for GC05M001573:  view genomic region     (about GC identifiers)

Start:
1,568,637 bp from pter      End:
1,594,735 bp from pter
Size:
26,099 bases      Orientation:
minus 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: --


(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, 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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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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Subcellular locations from COMPARTMENTS: 

CompartmentConfidence
mitochondrion3
cytosol2
extracellular1
peroxisome1

(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 SDHAP3
Interactions:

    Search GeneGlobe Interaction Network for SDHAP3

(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
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Browse Tocris compounds for SDHAP3



(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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Unigene Cluster for SDHAP3:

Succinate dehydrogenase complex, subunit A, flavoprotein pseudogene 3
Hs.379186  [show with all ESTs]
Unigene Representative Sequence: AK123503
3 Ensembl transcripts including schematic representations, and UCSC links where relevant:
ENST00000515467 ENST00000436493(uc011cme.2 uc010itg.1) ENST00000413529(uc011cmd.1)

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Additional mRNA sequence: 

AK123503.1 AK297840.1 AL359941.1 BC129998.1 BC150557.1 BC150558.1 CR749689.1 NR_003263.2 

21 DOTS entries:

DT.92464258  DT.97860756  DT.97817039  DT.91864402  DT.92464274  DT.100669790  DT.95100115  DT.100879612 
DT.92464244  DT.95315433  DT.100879621  DT.102843654  DT.120808989  DT.100879608  DT.120808997  DT.100031405 
DT.100840716  DT.120852132  DT.120852151  DT.95299124  DT.95355335 

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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SDHAP3 expression in normal human tissues (normalized intensities)
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS <intensity>2/3
CGAP TAG: --
SDHAP3 Expression
About this image

SDHAP3 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

SDHAP3 Protein Expression

SOURCE GeneReport for Unigene cluster: Hs.379186
    Custom PCR Arrays for SDHAP3
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In Situ
Assay Products:
 

 
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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 SDHAP3 (if available)
TreeFam Gene Tree for SDHAP3 (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 SDHAP3 (see all 670)    About this table    
Genomic DataTranscription Related DataAllele Frequencies
SNP IDValidClinical
significance
Chr 5 posSequence#AA
Chg
TypeMore#Allele
freq
PopTotal
sample
More
----------
rs1434599861,2
--1571625(+) AACTTA/GGAAAT 1 -- ds50010--------
rs1150566121,2
F--1571881(+) TGAGAT/CTGTAC 1 -- ds50011Minor allele frequency- C:0.02NA 120
rs1132715691,2
C--1572046(+) TATTTG/TAAATG 1 -- ds50011Minor allele frequency- T:0.00CSA 1
rs1134980341,2
C--1572047(+) ATTTTC/AAATGG 1 -- ds50011Minor allele frequency- A:0.00CSA 1
rs1113127001,2
C--1572048(+) TTTTAC/AATGGA 1 -- ds50011Minor allele frequency- A:0.00CSA 1
rs2015722041,2
--1572064(+) AAATA-/AAAG  
        
AAAGT
1 -- ds50010--------
rs1138139171,2
C--1572091(+) TTTTAC/TTTAAG 1 -- nc-transcript-variant0--------
rs1123759091,2
C,F--1572216(+) CAATGT/GACTCC 1 -- nc-transcript-variant4Minor allele frequency- G:0.05NA CSA WA 242
rs2019689801,2
C--1572275(+) CATGCA/GTGAGC 1 -- nc-transcript-variant0--------
rs1470012971,2
C--1572289(+) TATACA/GTAATT 1 -- nc-transcript-variant0--------

HapMap Linkage Disequilibrium report for SDHAP3 (1568637 - 1594735 bp)

Structural Variations
     Database of Genomic Variants (DGV) 9 variations for SDHAP3:    About this table    
Variant IDTypeSubtypePubMed ID
esv1266763CNV Insertion17803354
nsv509046CNV Insertion20534489
dgv5918n71CNV Loss21882294
dgv5919n71CNV Loss21882294
nsv10657CNV Loss18304495
nsv881664CNV Loss21882294
dgv5921n71CNV Loss21882294
nsv881206CNV Gain21882294
nsv881648CNV Gain21882294

Site Specific Mutation Identification with PCR Assays
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(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 SDHAP3:    About MalaCards
endotheliitis


SDHAP3 for disorders           About GeneDecksing

Genetic Association Database (GAD): SDHAP3

Export disorders for SDHAP3 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 SDHAP3 gene integrated from 10 sources:
(articles sorted by number of sources associating them with SDHAP3)
    Utopia: connect your pdf to the dynamic
world of online information

  1. A genome-wide association study for blood lipid phenotypes in the Framingham Heart Study. (PubMed id 17903299)4 Kathiresan S....Cupples L.A. (BMC Med. Genet. 2007)
  2. Genome-wide association of echocardiographic dimensions, brachial artery endothelial function and treadmill exercise responses in the Framingham Heart Study. (PubMed id 17903301)4 Vasan R.S....Benjamin E.J. (BMC Med. Genet. 2007)
  3. 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: 728609 HGNC: 18781 Ensembl:ENSG00000185986 euGenes: HUgn728609 ECgene: SDHAP3
H-InvDB: SDHAP3

(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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  --

(Patent information from GeneIP,
Licensable technologies from WIS Yeda, Salk, Tufts,
IP news from LifeMap Sciences, Inc.)
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Patent Information for SDHAP3 gene:
Search GeneIP for patents involving SDHAP3

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
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