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Category   Symbol Source: HGNC EntrezGene Ensembl GeneCards RNA genes CroW21
GIFtS

ABCA11P Gene

pseudogene   GIFtS: 31
GCID: GC04M000420

ATP-Binding Cassette, Sub-Family A (ABC1), Member 11, Pseudogene


(Previous symbol: ABCA11)
  Search for ABCA11P
at  

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
About This Section

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

Quality score for the ORGUL clustered with this gene is 4

Aliases
ATP-Binding Cassette, Sub-Family A (ABC1), Member 11, Pseudogene1 2
ABCA111 2 3
EST11335302

External Ids:    HGNC: 311   Entrez Gene: 799632   Ensembl: ENSG000002515957   UniProtKB: Q4W5N13   
ORGUL members:    fRNAdb10:FR285599      
H-InvDB12:HIT000096154    
NCBI13:BC040413    
NONCODE14:n405504 n335509 n333527      
RNAdb15:HIV2766    

Export aliases for ABCA11P gene to outside databases

Previous GC identifers: GC04U900972 GC04M000412


(According to Entrez Gene, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
About This Section

GeneCards Summary for ABCA11P Gene: 
ABCA11P (ATP-binding cassette, sub-family A (ABC1), member 11, pseudogene) is a pseudogene, and is affiliated with the lncRNA class.

fRNAdb sequence ontology for ABCA11P:
ncRNA - An RNA transcript that does not encode for a protein rather the RNA molecule is the gene product.

View fRNAdb secondary structures for ABCA11P

(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 73), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section
RefSeq DNA sequence:
NC_000004.11  NC_018915.2  NT_037622.5  
Regulatory elements:
   SABiosciences Regulatory transcription factor binding sites in the ABCA11P gene promoter:
         Ik-1   
         Other transcription factors

Browse SwitchGear Promoter luciferase reporter plasmids
   Search SABiosciences Chromatin IP Primers for ABCA11P

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat ABCA11P


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

Entrez Gene cytogenetic band: 4p16.3   Ensembl cytogenetic band:  4p16.3   HGNC cytogenetic band: 4p16.3

ABCA11P Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
ABCA11P gene location

GeneLoc information about chromosome 4         GeneLoc Exon Structure

GeneLoc location for GC04M000420:  view genomic region     (about GC identifiers)

Start:
419,224 bp from pter      End:
467,998 bp from pter
Size:
48,775 bases      Orientation:
minus strand
ORGUL member locations:
Legend (see complete legend)

ORGUL Member Locations for ABCA11P

(According to UniProtKB, HORDE, neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MAXQB 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., Ontologies according to Gene Ontology Consortium 01 Oct 2013 and Entrez Gene, Antibodies by EMD Millipore, R&D Systems, GenScript, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, and/or Cloud-Clone Corp.)
About This Section

UniProtKB/Swiss-Prot: ABCAB_HUMAN, Q4W5N1 (See protein sequence)
Recommended Name: Putative ATP-binding cassette sub-family A member 11  
Size: 156 amino acids; 17479 Da
Caution: In contrast to other members of the family, it is much shorter and lacks ABC transporter domains. Defined
as a pseudogene by HGNC. However, proteomic data on a specific peptide from PubMed:17924679 suggest the existence
of this protein
Secondary accessions: Q9H7T1

Explore the universe of human proteins at neXtProt for ABCA11P: NX_Q4W5N1

Post-translational modifications:

  • View modification sites using PhosphoSitePlus
  • View neXtProt modification sites for NX_Q4W5N1

  • ABCA11P Protein expression data from MOPED1, PaxDb2 and MAXQB3 : --

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    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
    About This Section
    HGNC Gene Families: 
    ABCA: ATP binding cassette transporters / subfamily A

    2 InterPro protein domains:
     IPR027417 P-loop_NTPase
     IPR026082 ABC_A

    Graphical View of Domain Structure for InterPro Entry Q4W5N1

    ProtoNet protein and cluster: Q4W5N1

    UniProtKB/Swiss-Prot: ABCAB_HUMAN, Q4W5N1
    Similarity: Belongs to the ABC transporter superfamily. ABCA family


    ABCA11P 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,
    bound targets from SABiosciences, miRNA Gene Targets from miRTarBase, shRNA from OriGene, RNAi from EMD Millipore, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, Gene Editing from DNA2.0, Sirion Biotech, Clones from EMD Millipore, OriGene, SwitchGear Genomics, GenScript, Sino Biological, DNA2.0, Vector BioLabs, and Sirion Biotech, Cell Lines from GenScript, LifeMap BioReagents, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Oct 2013 via Entrez Gene.)
    About This Section

         Gene Ontology (GO): 2 molecular function terms (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005524ATP binding IEA--
    GO:0016887ATPase activity IEA--
         
    ABCA11P for ontologies           About GeneDecksing


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    (Pathways according to EMD Millipore, 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 SABiosciences, 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 Oct 2013 via Entrez Gene).
    About This Section



    Interactions:

        Search SABiosciences Gene Network CentralTM Interacting Genes and Proteins Networks for ABCA11P

    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB, with drugs/clinical trials/news search links to CenterWatch)
    About This Section
    Browse Small Molecules at EMD Millipore
    Browse drugs & compounds from Enzo Life Sciences

    Browse Tocris compounds for ABCA11P (ABCAB)

    Search CenterWatch for drugs/clinical trials and news about ABCA11P

    (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,
    RNAi Products from EMD Millipore,
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    About This Section
    1 fRNAdb Secondary structure:


    REFSEQ mRNAs for ABCA11P gene: 
    NM_024903.1  

    Unigene Cluster for ABCA11P:

    ATP-binding cassette, sub-family A (ABC1), member 11, pseudogene
    Hs.745030  [show with all ESTs]
    Unigene Representative Sequence: NM_133474
    4 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000451020(uc003gac.2 uc003gad.2) ENST00000504019 ENST00000514396
    ENST00000507854(uc010ibd.2)
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    Additional mRNA sequence: 

    AK024359.1 AK303674.1 BC040413.1 BC060316.1 BC065035.1 BC098116.1 BC098259.1 BC098291.1 
    BC099730.1 BC105084.1 BC112069.1 BC143677.1 NR_002451.2 

    18 DOTS entries:

    DT.99963003  DT.121227576  DT.121227695  DT.91815210  DT.100777106  DT.100777109  DT.411539  DT.121227760 
    DT.100029317  DT.121227765  DT.121227442  DT.100022745  DT.100029320  DT.91793452  DT.100777104  DT.100777107 
    DT.40210097  DT.97836999 

    24/107 AceView cDNA sequences (see all 107):

    BC040413 NM_024903 BU156411 AK024359 BU950945 F10161 CK300580 BU952399 
    AI202316 AA984609 T74151 BU146970 AA825833 AI366031 BF844274 BM476083 
    AI654478 BC060316 AI138991 AW513477 BF679533 AK127067 AK095558 NM_133474 

    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™, plus additional links to Genevestigator, and/or SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from SABiosciences, Primers from OriGene, SABiosciences, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
    About This Section

    ABCA11P expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: AAAGAGAAGA
    ABCA11P Expression
    About this image


    Genevestigator expression for ABCA11P

    SOURCE GeneReport for Unigene cluster: Hs.745030
        SABiosciences Custom PCR Arrays for ABCA11P
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    In Situ
    Assay Products:
     

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for ABCA11P

    (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)
    About This Section
      --

    ENSEMBL Gene Tree for ABCA11P (if available)
    TreeFam Gene Tree for ABCA11P (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
    About This Section
    Paralogs for ABCA11P gene
    5 SIMAP similar genes for ABCA11P using alignment to 1 protein entry:     ABCAB_HUMAN:
    ABCA10    ABCA6    ABCA8    ABCA9    ABCA5

    ABCA11P for paralogs           About GeneDecksing



    (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) and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers from QIAGEN, Cancer Mutation PCR Arrays and Assays and Copy Number PCR Arrays from SABiosciences)
    About This Section

    10/358 SNPs in ABCA11P are shown (see all 358)    About this table     
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 4 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs1822868311,2
    --418793(+) CCAAAC/TACAAC 1 -- ds50010--------
    rs788683791,2
    C,F--418815(+) TACATT/GAATAC 1 -- ds50011Minor allele frequency- G:0.02EA 120
    rs1850401211,2
    --418820(+) TAATAC/TAGCTA 1 -- ds50010--------
    rs76890191,2
    C,F,A,H--418834(+) CATTAG/ATGCAG 1 -- ds500126Minor allele frequency- A:0.50NS EA NA WA CSA 2484
    rs1890227411,2
    C--418872(+) GGACAA/TGGGAA 1 -- ds50010--------
    rs1817420991,2
    --418883(+) ATGTTC/TGTGAA 1 -- ds50010--------
    rs285947571,2
    C--418915(+) AAAATG/AACTAT 1 -- ds50012Minor allele frequency- A:0.25NA WA 4
    rs76761051,2
    C,F--418924(+) ATGCCC/TACTGA 1 -- ds50012Minor allele frequency- T:0.50WA CSA 4
    rs1855167251,2
    --418964(+) ATACAA/C/TTGAAT 1 -- ds50010--------
    rs730703391,2
    C,F--419040(+) ATAATT/GTCAAT 1 -- ds50013Minor allele frequency- G:0.08WA NA 240

    HapMap Linkage Disequilibrium report for ABCA11P (419224 - 467998 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 6 variations for ABCA11P:    About this table     
    Variant IDTypeSubtypePubMed ID
    nsv521895CNV Loss19592680
    nsv469736CNV Loss16826518
    nsv517948CNV Loss19592680
    nsv461144CNV Loss19166990
    nsv461145CNV Gain19166990
    esv4769CNV Complex18987735

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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.)
    About This Section

    ABCA11P for disorders           About MalaCards
    OMIM information: 601519 603663 605480 609456    

    ABCA11P for disorders           About GeneDecksing


    Export disorders for ABCA11P 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)
    About This Section

    PubMed articles for ABCA11P gene integrated from 9 sources:
    (articles sorted by number of sources associating them with ABCA11P)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1, 2 Ota T.... Sugano S. (2004)
    2. Diversification of transcriptional modulation: large-scale identification and characterization of putative alternative promoters of human genes. (PubMed id 16344560)1 Kimura K.... Sugano S. (2006)
    3. Generation and annotation of the DNA sequences of human chromosomes 2 and 4. (PubMed id 15815621)2 Hillier L.W....Wilson R.K. (2005)
    4. 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. (2002)
    5. (PubMed id 15103394)10 
    6. (PubMed id 18089548)10 
    7. (PubMed id 15608161)10 

    (in PubMed, OMIM, and NCBI Bookshelf)
    About This Section
     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)
    About This Section
    Entrez Gene: 79963 HGNC: 31 AceView: FLJ14297 Ensembl:ENSG00000251595 euGenes: HUgn79963
    ECgene: ABCA11P H-InvDB: ABCA11P

    (According to HUGE)
    About This Section
      --

    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
    Wikipedia and/or GeneReviews via UniProtKB/Swiss-Prot)
    About This Section
    NameDescription
    PharmGKB entry for ABCA11P Pharmacogenomics, SNPs, Pathways

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
    About This Section
    Patent Information for ABCA11P gene:
    Search GeneIP for patents involving ABCA11P

    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, SABiosciences, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Cloud-Clone Corp., Thermo Fisher Scientific, LSBio, Gene Editing from DNA2.0 and Sirion Biotech, Clones from EMD Millipore, OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Sirion Biotech, Cell lines from GenScript, and LifeMap BioReagents, PCR Arrays from SABiosciences, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, and/or Enzo Life Sciences, In Situ Hybridization Assays from
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    About This Section

     
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    GeneCards Homepage - Last full update: 23 Oct 2013 - Incrementals: 3 Nov 2013 , 7 Nov 2013 , 23 Jan 2014

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    (GIFtS: 73)
    transforming growth factor, beta 1
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