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ABCF1 Gene

protein-coding   GIFtS: 60

GC06P030647
ATP-binding cassette, sub-family F (GCN20), member 1
Symbol approved by the HUGO Gene Nomenclature Committee (HGNC) database
(Previous symbol: ABC50)
Services    
(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc , and/or 7Ensembl, 8miRBase)
About This Section

Aliases
ABC27 2
ABC50 2, 3, 5
EST123147 1
OTTHUMP00000029110 2
OTTHUMP00000029111 2
Descriptions
ATP-binding cassette 50 3
ATP-binding cassette 50 (TNF-alpha stimulated) 2
ATP-binding cassette, sub-family F (GCN20), member 1 2
ATP-binding cassette, sub-family F, member 1 2
TNF-alpha-stimulated ABC protein 3
TNFalpha-inducible ATP-binding protein 2
External Ids
HGNC: 701
Entrez Gene: 232
UniProtKB: Q8NE713
Ensembl: ENSG000002045747
Search outside databases for aliases for ABCF1 gene

Previous GC identifers: GC06P030594 GC06P030309 GC06P030645

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

EntrezGene summary for ABCF1:
The protein encoded by this gene is a member of the superfamily of ATP-binding cassette (ABC)
transporters. ABC proteins transport various molecules across extra- and intra-cellular membranes.
ABC genes are divided into seven distinct subfamilies (ABC1, MDR/TAP, MRP, ALD, OABP, GCN20,
White). This protein is a member of the GCN20 subfamily. Unlike other members of the superfamily,
this protein lacks the transmembrane domains which are characteristic of most ABC transporters.
This protein may be regulated by tumor necrosis factor-alpha and play a role in enhancement of
protein synthesis and the inflammation process. [provided by RefSeq]

UniProtKB/Swiss-Prot: ABCF1_HUMAN, Q8NE71
Function: May function in mRNA translation (By similarity)

Gene Wiki entry for ABCF1

(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 36),
and/or miRBase,
Genomic Views according to UCSC and Ensembl, Transcription factor binding sites according to SABiosciences)
About This Section

Genomic View:
UCSC Golden Path with GeneCards custom track

 Transcription factor binding sites upstream to the ABCF1 gene  

Entrez Gene cytogenetic band: 6p21.33   Ensembl cytogenetic band:  6p21.33   HGNC cytogenetic band: 6p21.33

ABCF1 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)

GeneLoc gene densities for chromosome 6         GeneLoc Exon Structure

GeneLoc location for GC06P030647:     (about GC identifiers)

Start:
30,647,149 bp from pter
End:
30,667,288 bp from pter
Size:
20,140 bases
Orientation:
plus strand

2 alternative locations:
Chr6+,c6_COX 30,676,254-30,696,406      Chr6+,c6_QBL 30,671,532-30,691,667     
RefSeq DNA sequence:
NC_000006.10  NT_007592.14  NT_113891.1  NT_113893.1  
(According to 1UniProtKB, and/or Ensembl, Phosphorylation sites according to 2Phosphosite, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from Invitrogen, Millipore, Sigma-Aldrich, R&D Systems, Enzo Life Sciences, Abnova, OriGene and/or, Abcam,
Biochemical Assays by Invitrogen, Millipore, R&D Systems, Cell Signaling Technology, and/or Enzo Life Sciences, Ontologies according to Gene Ontology Consortium 01 Apr 2009 and Entrez Gene, Antibodies by Invitrogen, Millipore, Sigma-Aldrich, R&D Systems, Cell Signaling Technology, Abcam, Abnova, and/or Novus Biologicals)
About This Section

UniProtKB/Swiss-Prot: ABCF1_HUMAN, Q8NE71 (See protein sequence)
Recommended Name: ATP-binding cassette sub-family F member 1  
Size: 845 amino acids; 95926 Da
Subunit: Interacts with eukaryotic initiation factor 2 (eIF2). Associates with the ribosomes (By
similarity)
Secondary accessions: O14897 Q69YP6
Alternative splicing: 2 isoforms:  Q8NE71-1   Q8NE71-2   

Post-translational modifications:

  • Phosphorylated upon DNA damage, probably by ATM or ATR1
  • View phosphorylation sites using PhosphoSite2


  • REFSEQ proteins (2 alternative transcripts): 
    NP_001020262.1  NP_001081.1  


    ENSEMBL proteins: 
    ENSP00000313603 ENSP00000365728 ENSP00000379772 


    Human Recombinant Proteins 
    Browse Drug Discovery Central at Invitrogen for human recombinant proteins
    Browse Purified and Recombinant Proteins at Millipore
    Browse Human Recombinant Proteins at Sigma-Aldrich  
    Browse R&D Systems for human recombinant proteins
    Browse recombinant and purified proteins available from Enzo Life Sciences
    Recombinant Proteins from Abcam (ABCF1)
    Human Recombinant Proteins from Abnova (ABCF1)
                    Browse Origene for full length recombinant human proteins expressed in human HEK293 cells 


    Antibodies for ABCF1: 
    Browse Antibodies Central at Invitrogen
    Browse Millipore's Extensive Line of Mono- and Polyclonal Antibodies
    Sigma-Aldrich Antibodies for ABCF1
    Browse R&D Systems for Antibodies
    Antibodies from Abcam (ABCF1), each with their AbpromiseSM
    Monoclonal and Polyclonal Antibodies from Abnova (ABCF1)
    Novus Biologicals Antibodies for ABCF1

    Assays for ABCF1: 
    Browse Invitrogen for biochemical assays
    Browse Kits and Assays available from Millipore
    Browse R&D Systems for biochemical assays
    Browse biochemical assays available from Enzo Life Sciences

    (According to InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
    About This Section

    3 InterPro domains/families:
     IPR003439 ABC_transporter-like
     IPR003593 ATPase_AAA+_core
     IPR017871 ABC_transporter_CS


       GeneDecks  ABCF1 for the domains selected above  
    About GeneDecksing

    Graphical View of Domain Structure for InterPro Entry Q8NE71

    ProtoNet protein and cluster: Q8NE71

    UniProtKB/Swiss-Prot: ABCF1_HUMAN, Q8NE71
    Similarity: Belongs to the ABC transporter family. EF3 subfamily
    Similarity: Contains 2 ABC transporter domains

    (According to MGI Jun 06 2009, UniProtKB, IUBMB,and/or Genatlas,
    shRNA from OriGene, Sigma-Aldrich, RNAi from Sigma-Aldrich,
    RNAi Products, Clones, and Q-PCR Products from Invitrogen, Millipore, OriGene, and/or Abnova, siRNAs from Applied Biosystems, SYBR primers from OriGene, Cell-based Assays from Millipore, Ontologies according to Gene Ontology Consortium 01 Apr 2009 via Entrez Gene.)
    About This Section

    Inhib.
    RNA:
    Invitrogen RNAi Products for gene knock-down (ABCF1)
    Browse for Gene Knock-down Tools from Millipore
    Abnova Chimera RNAi Products for Gene knock-down (ABCF1)
                   OriGene 29mer shRNA kit in GFP-retroviral vectors (see all 2): NM_001090

                  Applied Biosystems Silencer® siRNAs for ABCF1

                  Sigma-Aldrich siRNA for ABCF1  
                         Sigma-Aldrich shRNA for ABCF1  
                         Explore Sigma-Aldrich super-pooled esiRNAs  

    Clones:Invitrogen Clones for ABCF1
    Browse Clones for the Expression of Recombinant Proteins Available from Millipore
                   OriGene GFP tagged cDNA clones in CMV expression vector (see all 2): NM_001025091
                                     Myc/DDK tagged cDNA clones in CMV expression vector (see all 2): NM_001025091
                                     untagged cDNA clones in CMV expression vector (see all 2): NM_001025091 

    Primers: Browse Quantitative PCR Central at Invitrogen for Q-PCR LUX™ Primers
                  OriGene genome-wide validated SYBR primer pairs: NM_001025091

    UniProtKB/Swiss-Prot: ABCF1_HUMAN, Q8NE71
    Function: May function in mRNA translation (By similarity)
    Induction: By TNF (in cultured synoviocytes)

    Genatlas biochemistry entry for ABCF1:
    ATP binding cassette superfamily,subfamily F (GCN20) member 1,widely expressed,putative ribosomal
    protein,involved in translation of mRNA,present in synoviocytes after TNFA induction,potentially
    involved in inflammatory process

    5 Gene Ontology (GO) molecular function terms (links to tree view):

    GO IDQualified GO termEvidencePubMed IDs
    GO:0000166 nucleotide binding IEA--
    GO:0005524 ATP binding TAS9790762
    GO:0008135 translation factor activity, nucleic acid binding TAS9790762
    GO:0016887 ATPase activity IEA--
    GO:0042626 ATPase activity, coupled to transmembrane movement of substances TAS9790762
    About this table

    (Pathways according to Invitrogen (maps by GeneGo), Millipore, Cell Signaling Technology, Sigma-Aldrich, KEGG and/or UniProtKB,
    Sets of similar genes according to GeneDecks, Proteins Network according to SABiosciences, Interactions according to 1UniProtKB, 2MINT, and/or 3STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Apr 2009 via Entrez Gene.)
    About This Section


     Gene Network CentralTM Interacting Genes and Proteins Network for  ABCF1 


    1 Interacting protein for ABCF1 (Q8NE712) via UniProtKB, MINT, and/or STRING
    InteractantInteraction Details
    GeneCardExternal ID(s)
    --Q5JWN52MINT-64421
    About this table

    2 Gene Ontology (GO) biological process terms (links to tree view):

    GO IDQualified GO termEvidencePubMed IDs
    GO:0006412 translation TAS9790762
    GO:0006954 inflammatory response TAS9790762
    About this table
    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, Sigma-Aldrich, Tocris Bioscience, and/or Novoseek and Drugs according to Enzo Life Sciences and/or PharmGKB)
    About This Section

    Browse drugs & compounds from Enzo Life Sciences
    Browse Small Molecules at Sigma-Aldrich

    Browse Tocris compounds for ABCF1

    (GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 219 Homo sapiens; Jun 2 2009) or GenBank,
    RefSeq according to Entrez Gene,
    DOTS (version 10), and/or AceView,
    non coding RNAs according to RNAdb,
    ESTs according to GeneTide,
    exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
    RNAi Products from Invitrogen, Millipore, and/or Abnova,
    siRNAs from Applied Biosystems, Sigma-Aldrich,
    shRNA from Sigma-Aldrich, OriGene,
    Tagged/untagged cDNA clones from OriGene,
    Expression Assays from Applied Biosystems)
    About This Section

    Inhib.
    RNA:
    Invitrogen RNAi Products for gene knock-down (ABCF1)
    Browse for Gene Knock-down Tools from Millipore
    Abnova Chimera RNAi Products for Gene knock-down (ABCF1)
                   OriGene 29mer shRNA kit in GFP-retroviral vectors (see all 2): NM_001090

                  Sigma-Aldrich siRNA for ABCF1  
                         Sigma-Aldrich shRNA for ABCF1  
                         Explore Sigma-Aldrich super-pooled esiRNAs  

    Applied Biosystems Silencer® siRNAs: 

    NM_001025091  NM_001090  

    REFSEQ mRNAs for ABCF1 gene (2 alternative transcripts): 

    NM_001025091.1   NM_001090.2   

    Applied Biosystems TaqMan ® Gene Expression Assays: 

    NM_001025091  NM_001090  

                   OriGene GFP tagged cDNA clones in CMV expression vector (see all 2): NM_001025091
                                     Myc/DDK tagged cDNA clones in CMV expression vector (see all 2): NM_001025091
                                     untagged cDNA clones in CMV expression vector (see all 2): NM_001025091 

    Additional cDNA sequence: 

    AB209564.1 AF027302.1 AF075071.1 AK298061.1 AK307551.1 AL832430.1 BC016772.1 BC034488.2 
    BC112923.1 CR591008.1 CR606523.1 U66677.1 

    16 DOTS entries:

    DT.100815058  DT.101984925  DT.217889  DT.92442036  DT.100815063  DT.95108905  DT.121360162  DT.97769090 
    DT.100815055  DT.95258527  DT.40190068  DT.100815060  DT.121360120  DT.121360366  DT.95189966  DT.97855263 

    24/391 AceView cDNA sequences (see all 391 ):

    BQ951527 CB243302 BU620927 AA237011 BQ001284 BM666238 BQ054175 AI167633 
    BQ954679 BM762693 BE698513 F07368 AA339120 BM468644 AA197173 BM893863 
    BQ678264 BQ962497 BQ060931 AA486482 C02340 BQ073631 BU187212 CR591008 

    highest scoring ESTs for ABCF1:

    R49296 AF027302 AW860237 BE698504 BE698513 BE764997 BF086911 BQ315622 BQ315625 BQ315723 

    Unigene Cluster for ABCF1:

    ATP-binding cassette, sub-family F (GCN20), member 1
    Hs.655285  [show with all ESTs]
    Unigene Representative Sequence: NM_001025091


    GeneLoc Exon Structure

    3 Ensembl transcripts including schematic representations:
    ENST00000326195  ENST00000376545  ENST00000396515  
    (Experimental results according to 1GeneNote and GNF BioGPS,
    probe sets-to-genes annotations according to 2GeneAnnot , 3GeneTide , Sets of similar genes according to GeneDecks, Electronic Northern calculations according to data from UniGene (Build 219 Homo sapiens), SAGE tags according to CGAP, plus additional links to SOURCE, and/or GNF BioGPS, and/or EXPOLDB, and/or UniProtKB,
    Expression Assays from Applied Biosystems )
    About This Section

    ABCF1 expression in normal and diseased human tissues

     Applied Biosystems TaqMan ® Gene Expression Assays for ABCF1

    1 / 2 / 3

    3 probe-sets matching ABCF1 gene


    Affymetrix
    probe-set
    Array  GeneAnnot data GeneNote data GeneTide data
    # genes Sensitivity Specificity Correlation Length Gb_Accession Consensus Uniqueness Score Rank

    39141_at2, 3 U95-A 2 1.00 0.53 1.00 1.00 AF027302 0.80 0.80 0.80 1

    200045_at2, 3 U133-B 2 1.00 0.50 -- -- NM_001090 0.40 0.67 0.55 1

    200045_at2 U133Plus2 2 1.00 0.50 -- -- -- -- -- -- --
    About this table
    Data from (Publications) and GNF BioGPS
        About these images
    About these images

    CGAP SAGE TAG: AAGGTGGAGT

    SOURCE GeneReport for Unigene cluster: Hs.655285

    Expression variation in blood from EXPOLDB for ABCF1

    UniProtKB/Swiss-Prot: ABCF1_HUMAN, Q8NE71
    Tissue specificity: Ubiquitous

    (Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD and/or 5MGI Jun 06 2009, with possible further links to Flybase and/or WormBase, Gene Trees according to Ensembl)
    About This Section


    Orthologs for ABCF1 gene from 5/15 species (see all 15 )
    Organism Gene Locus Description Human
    Similarity
    NCBI accessions
    dog
    (Canis familiaris)
    ABCF11   -- ATP-binding cassette, sub-family F (GCN20), member more 91.1(n)
    96.64(a)
    474826  XM_532056.2  XP_532056.2 
    chimpanzee
    (Pan troglodytes)
    ABCF11   -- ATP-binding cassette, sub-family F (GCN20), member more 99.38(n)
    99.5(a)
    462543  NM_001042379.1  NP_001035838.1 
    cow
    (Bos taurus)
    ABCF11   -- ATP-binding cassette, sub-family F (GCN20), member more 90.96(n)
    97.86(a)
    525343  XM_603695.3  XP_603695.3 
    rat
    (Rattus norvegicus)
    Abcf11   -- ATP-binding cassette, sub-family F (GCN20), member more 86.87(n)
    92.84(a)
    85493  XM_001062137.1  XP_001062137.1 
    mouse
    (Mus musculus)
    Abcf11, 5 17 (20.50 cM)5
    ATP-binding cassette, sub-family F (GCN20), member more1, 5 86.52(n)1
    91.87(a)1
    2247421  NM_013854.11  NP_038882.11 
     AA1443985  AA4083565  (see all 26)
    About this table        Species with no ortholog for ABCF1

    ENSEMBL Gene Tree for ABCF1
    (Paralogs according to 1HomoloGene
    and 2Ensembl, Pseudogenes according to 3Pseudogene.org)
    About This Section

    Paralogs for ABCF1 gene
    ABCF32  ABCF22  

    (According to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, and UniProtKB, Linkage Disequilibrium by HapMap, Genotyping Reagents from Applied Biosystems)
    About This Section


    10/128 NCBI SNPs in ABCF1 are shown (see all 128 )
    (Click for Applied Biosystems TaqMan ® Genotyping Assay)  (see all 55)
    ABGenomic DataTranscription DataAllele Frequencies
    SNP IDValidChr 6 posSequenceRecsAA
    Chg
    TypeMoreRecsAllele
    freq
    PopTotal
    sample
    More
    ------------
    --
    rs31326131,2
    A,C,F,H,O30645585(-) gATTAC/GGTTTC 2 -- ng5111Minor allele frequency- N:0.00EA WA NA EU 934
    rs31302431,2
    A,C,F,H30645832(+) acaggA/Ctttag 2 -- ng514Minor allele frequency- C:0.32EU EA WA 402
    rs96711,2
    C,F,H30667013(+) GCTGCT/CGAACT 2 -- ut31 ese37Minor allele frequency- C:0.05NA EU EA WA 560
    rs69025441,2
    C,H30656189(+) TGGACA/GATGAA 2 N/D mis1 ese34Minor allele frequency- G:0.00EU EA WA 418
    rs41482471,2
    F,H30647184(+) GTTCCC/TCGCCG 2 -- ut51 ese34Minor allele frequency- T:0.04EU EA WA 416
    --
    rs31302421,2
    C30645318(+) CACTCA/GTGCCA 2 -- ng510--------
    rs94687901,2
    H30665955(+) AACCTG/CATGTC 2 H/D mis1 ese34Minor allele frequency- C:0.00EU EA WA 412
    --
    rs41482521,2
    C30666457(+) AGTGA-/AGCTTT 2 -- ut310--------
    rs31300421,2
    H30647106(+) AGATGA/GCGGCG 2 -- ng514Minor allele frequency- G:0.00EU EA WA 416
    rs117589601,2
    H30662406(+) CATTGT/AGGGCC 2 E/V mis14Minor allele frequency- A:0.00EU EA WA 418
    About this table

    HapMap Linkage Disequilibrium images for ABCF1 (up to first 250kb)

    (in which this Gene is Involved, According to OMIM, UniProtKB, PharmGKB, Genatlas, GeneTests, Blood group antigen gene mutations by BGMUT, HGMD, GAD, HuGE Navigator, BCGD, and/or TGDB.)
    About This Section

    OMIM: 603429

    Human Genome Epidemiology Navigator: ABCF1 (2 documents)

    (Possibly Related Articles in Doctor's Guide)
    About This Section

      --

    (in PubMed. Associations of this gene to articles via 1Novoseek, 2HGNC, 3Entrez Gene, 4UniProtKB/Swiss-Prot, 5UniProtKB/TrEMBL, 6GAD, and/or 7PharmGKB)
    About This Section

    10/25 PubMed articles for ABCF1 gene (see all 25 ):
    (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, and/or H-InvDB)
    About This Section

    Entrez Gene: 23 HGNC: 70 AceView: ABCF1 Ensembl:ENSG00000204574 euGenes: HUgn23
    ECgene: ABCF1 H-InvDB: ABCF1
    (According to HUGE)
    About This Section

      --
    (According to ATLAS, HORDE, IMGT, MTDB, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
    Wikipedia and/or GeneReviews via UniProtKB/Swiss-Prot)
    About This Section

    NameDescription
    ATLAS Chromosomes in Cancer entry for ABCF1 Genetics and Cytogenetics in Oncology and Haematology
    (Available from WIS Yeda, Salk, Tufts)
    About This Section

      --
    (Reagents available from Applied Biosystems, Antibodies and assays by Cell Signaling Technology, Abcam, Novus Biologicals,
    Sigma-Aldrich, R&D Systems, Millipore, Abnova, and/or Invitrogen, Clones available from OriGene,and/or Invitrogen, Drugs and/or compounds by Sigma-Aldrich,
    Enzo Life Sciences, and/or Tocris Bioscience)
    About This Section



    Products for ABCF1:
     TaqMan ® Gene Expression Assays
     TaqMan ® Genotyping Assays
      Free SNP selection tool



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     Predesigned and custom siRNAs for ABCF1 Antibodies for ABCF1
     Explore super-pooled esiRNAs Browse proteins at Sigma-Aldrich
     Lentivirus-delivered shRNAs for ABCF1 Browse small molecules at Sigma-Aldrich
     "Your Favorite Gene" Pathwaysfeedback


      
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     Antibodies for ABCF1

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