Human Gene ABCF1 (uc003nql.3) Description and Page Index
  Description: Homo sapiens ATP-binding cassette, sub-family F (GCN20), member 1 (ABCF1), transcript variant 1, mRNA.
RefSeq Summary (NM_001025091): 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, Jul 2008].
Transcript (Including UTRs)
   Position: hg19 chr6:30,539,170-30,559,309 Size: 20,140 Total Exon Count: 25 Strand: +
Coding Region
   Position: hg19 chr6:30,539,265-30,558,478 Size: 19,214 Coding Exon Count: 25 

Page IndexSequence and LinksUniProtKB CommentsGenetic AssociationsCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr6:30,539,170-30,559,309)mRNA (may differ from genome)Protein (845 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
BioGPSCGAPEnsemblEntrez GeneExonPrimerGeneCards
GeneNetworkH-INVHGNCHPRDLynxMGI
neXtProtOMIMPubMedReactomeStanford SOURCETreefam
UniProtKBWikipedia

-  Comments and Description Text from UniProtKB
  ID: ABCF1_HUMAN
DESCRIPTION: RecName: Full=ATP-binding cassette sub-family F member 1; AltName: Full=ATP-binding cassette 50; AltName: Full=TNF-alpha-stimulated ABC protein;
FUNCTION: Isoform 2 is required for efficient Cap- and IRES- mediated mRNA translation initiation. Isoform 2 is not involved in the ribosome biogenesis.
SUBUNIT: Isoform 2 interacts (via N-terminus) with EIF2S1; the interaction is independent of its phosphorylated status. Isoform 2 associates (via both ABC transporter domains) with the ribosomes.
SUBCELLULAR LOCATION: Isoform 2: Cytoplasm. Nucleus, nucleoplasm. Nucleus envelope.
TISSUE SPECIFICITY: Ubiquitous.
INDUCTION: By TNF in cultured synoviocytes.
PTM: Isoform 2 is phosphorylated at phosphoserine and phosphothreonine. Isoform 2 phosphorylation on Ser-109 and Ser-140 by CK2; inhibits association of EIF2 with ribosomes. Phosphorylated upon DNA damage, probably by ATM or ATR.
SIMILARITY: Belongs to the ABC transporter superfamily. ABCF family. EF3 subfamily.
SIMILARITY: Contains 2 ABC transporter domains.
WEB RESOURCE: Name=ABCMdb; Note=Database for mutations in ABC proteins; URL="http://abcmutations.hegelab.org/proteinDetails?uniprot_id=Q8NE71";

-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): ABCF1
CDC HuGE Published Literature: ABCF1
Positive Disease Associations: Graves Disease , Lupus Erythematosus, Systemic
Related Studies:
  1. Graves Disease
    Kazuhiko Nakabayashi et al. Journal of human genetics 2011, Identification of independent risk loci for Graves' disease within the MHC in the Japanese population., Journal of human genetics. [PubMed 21900946]
  2. Lupus Erythematosus, Systemic
    Geoffrey Hom et al. The New England journal of medicine 2008, Association of systemic lupus erythematosus with C8orf13-BLK and ITGAM-ITGAX., The New England journal of medicine. [PubMed 18204098]
    We identified and then confirmed through replication two new genetic loci for SLE: a promoter-region allele associated with reduced expression of BLK and increased expression of C8orf13 and variants in the ITGAM-ITGAX region.

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 34.23 RPKM in Testis
Total median expression: 927.45 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -31.5095-0.332 Picture PostScript Text
3' UTR -273.30831-0.329 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR003593 - AAA+_ATPase
IPR003439 - ABC_transporter-like
IPR017871 - ABC_transporter_CS

Pfam Domains:
PF00005 - ABC transporter
PF12848 - ABC transporter

SCOP Domains:
52540 - P-loop containing nucleoside triphosphate hydrolases
53795 - PEP carboxykinase-like

ModBase Predicted Comparative 3D Structure on Q8NE71
FrontTopSide
The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologGenome BrowserNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
Gene SorterGene Sorter    
 RGD    
 Protein Sequence    
 Alignment    

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0000166 nucleotide binding
GO:0003723 RNA binding
GO:0005515 protein binding
GO:0005524 ATP binding
GO:0008135 translation factor activity, RNA binding
GO:0008494 translation activator activity
GO:0016887 ATPase activity
GO:0043022 ribosome binding

Biological Process:
GO:0006412 translation
GO:0006413 translational initiation
GO:0006954 inflammatory response
GO:0045727 positive regulation of translation
GO:0055085 transmembrane transport
GO:0042254 ribosome biogenesis

Cellular Component:
GO:0005634 nucleus
GO:0005635 nuclear envelope
GO:0005654 nucleoplasm
GO:0005737 cytoplasm
GO:0005829 cytosol
GO:0005840 ribosome
GO:0016020 membrane
GO:0042788 polysomal ribosome


-  Descriptions from all associated GenBank mRNAs
  AF027302 - Homo sapiens TNF-alpha stimulated ABC protein (ABC50) mRNA, complete cds.
AK307551 - Homo sapiens cDNA, FLJ97499.
BC034488 - Homo sapiens ATP-binding cassette, sub-family F (GCN20), member 1, mRNA (cDNA clone MGC:26501 IMAGE:4826422), complete cds.
AK298061 - Homo sapiens cDNA FLJ56536 complete cds, highly similar to ATP-binding cassette sub-family F member 1.
BC112923 - Homo sapiens ATP-binding cassette, sub-family F (GCN20), member 1, mRNA (cDNA clone MGC:131563 IMAGE:7470309), complete cds.
BC016772 - Homo sapiens ATP-binding cassette, sub-family F (GCN20), member 1, mRNA (cDNA clone IMAGE:4092495), partial cds.
DQ891255 - Synthetic construct clone IMAGE:100003885; FLH178752.01X; RZPDo839G09128D ATP-binding cassette, sub-family F (GCN20), member 1 (ABCF1) gene, encodes complete protein.
DQ894817 - Synthetic construct Homo sapiens clone IMAGE:100009277; FLH178748.01L; RZPDo839G09127D ATP-binding cassette, sub-family F (GCN20), member 1 (ABCF1) gene, encodes complete protein.
JD128580 - Sequence 109604 from Patent EP1572962.
AL832430 - Homo sapiens mRNA; cDNA DKFZp762E013 (from clone DKFZp762E013).
AB209564 - Homo sapiens mRNA for ATP-binding cassette, sub-family F, member 1 variant protein.
U66677 - Homo sapiens clone EST123147 mRNA sequence.
DQ601208 - Homo sapiens piRNA piR-39274, complete sequence.
JD561768 - Sequence 542792 from Patent EP1572962.
JD233182 - Sequence 214206 from Patent EP1572962.
JD530134 - Sequence 511158 from Patent EP1572962.
JD526801 - Sequence 507825 from Patent EP1572962.
JD268148 - Sequence 249172 from Patent EP1572962.
JD263513 - Sequence 244537 from Patent EP1572962.
JD166229 - Sequence 147253 from Patent EP1572962.
JD236258 - Sequence 217282 from Patent EP1572962.
JD040109 - Sequence 21133 from Patent EP1572962.
JD437062 - Sequence 418086 from Patent EP1572962.
JD071762 - Sequence 52786 from Patent EP1572962.
JD510281 - Sequence 491305 from Patent EP1572962.
JD456444 - Sequence 437468 from Patent EP1572962.
JD309332 - Sequence 290356 from Patent EP1572962.
JD222126 - Sequence 203150 from Patent EP1572962.
JD262416 - Sequence 243440 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  Reactome (by CSHL, EBI, and GO)

Protein Q8NE71 (Reactome details) participates in the following event(s):

R-HSA-5227009 ABCF1 binds EIF2
R-HSA-382556 ABC-family proteins mediated transport
R-HSA-382551 Transport of small molecules

-  Other Names for This Gene
  Alternate Gene Symbols: A2BF75, ABC50, ABCF1_HUMAN, NM_001025091, NP_001020262, O14897, Q69YP6, Q8NE71
UCSC ID: uc003nql.3
RefSeq Accession: NM_001025091
Protein: Q8NE71 (aka ABCF1_HUMAN)
CCDS: CCDS34380.1, CCDS34381.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_001025091.1
exon count: 25CDS single in 3' UTR: no RNA size: 3474
ORF size: 2538CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 4484.00frame shift in genome: no % Coverage: 99.71
has start codon: yes stop codon in genome: no # of Alignments: 7
has end codon: yes retained intron: no # AT/AC introns 0
selenocysteine: no end bleed into intron: 0# strange splices: 0
Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.