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EIF6 eukaryotic translation initiation factor 6 [ Homo sapiens (human) ]

Gene ID: 3692, updated on 23-Apr-2019

Summary

Official Symbol
EIF6provided by HGNC
Official Full Name
eukaryotic translation initiation factor 6provided by HGNC
Primary source
HGNC:HGNC:6159
See related
Ensembl:ENSG00000242372 MIM:602912
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
CAB; EIF3A; eIF-6; p27BBP; ITGB4BP; b(2)gcn; p27(BBP)
Summary
Hemidesmosomes are structures which link the basal lamina to the intermediate filament cytoskeleton. An important functional component of hemidesmosomes is the integrin beta-4 subunit (ITGB4), a protein containing two fibronectin type III domains. The protein encoded by this gene binds to the fibronectin type III domains of ITGB4 and may help link ITGB4 to the intermediate filament cytoskeleton. The encoded protein, which is insoluble and found both in the nucleus and in the cytoplasm, can function as a translation initiation factor and prevent the association of the 40S and 60S ribosomal subunits. Multiple non-protein coding transcript variants and variants encoding two different isoforms have been found for this gene. [provided by RefSeq, Jun 2012]
Expression
Ubiquitous expression in esophagus (RPKM 55.8), duodenum (RPKM 45.2) and 25 other tissues See more
Orthologs

Genomic context

See EIF6 in Genome Data Viewer
Location:
20q11.22
Exon count:
8
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 20 NC_000020.11 (35278906..35284816, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 20 NC_000020.10 (33866709..33872619, complement)

Chromosome 20 - NC_000020.11Genomic Context describing neighboring genes Neighboring gene MMP24-AS1-EDEM2 readthrough Neighboring gene metallothionein 1 pseudogene 3 Neighboring gene matrix metallopeptidase 24 Neighboring gene FAM83C antisense RNA 1 Neighboring gene MMP24 opposite strand Neighboring gene family with sequence similarity 83 member C Neighboring gene ubiquinol-cytochrome c reductase complex assembly factor 1

Genomic regions, transcripts, and products

Expression

  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

Phenotypes

NHGRI GWAS Catalog

Description
Many sequence variants affecting diversity of adult human height.
NHGRI GWA Catalog
Web-based, participant-driven studies yield novel genetic associations for common traits.
NHGRI GWA Catalog

Pathways from BioSystems

  • Ribosome biogenesis in eukaryotes, organism-specific biosystem (from KEGG)
    Ribosome biogenesis in eukaryotes, organism-specific biosystemRibosomes are the cellular factories responsible for making proteins. In eukaryotes, ribosome biogenesis involves the production and correct assembly of four rRNAs and about 80 ribosomal proteins. It...
  • Ribosome biogenesis in eukaryotes, conserved biosystem (from KEGG)
    Ribosome biogenesis in eukaryotes, conserved biosystemRibosomes are the cellular factories responsible for making proteins. In eukaryotes, ribosome biogenesis involves the production and correct assembly of four rRNAs and about 80 ribosomal proteins. It...
  • Translation Factors, organism-specific biosystem (from WikiPathways)
    Translation Factors, organism-specific biosystemProtein synthesis is the ultimate step of gene expression and a key control point for regulation. In particular, it enables cells to rapidly manipulate protein production without new mRNA synthesis, ...

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
ribosome binding IDA
Inferred from Direct Assay
more info
PubMed 
translation initiation factor activity IEA
Inferred from Electronic Annotation
more info
 
Process Evidence Code Pubs
gene silencing by miRNA IMP
Inferred from Mutant Phenotype
more info
PubMed 
mature ribosome assembly IMP
Inferred from Mutant Phenotype
more info
PubMed 
miRNA mediated inhibition of translation IMP
Inferred from Mutant Phenotype
more info
PubMed 
positive regulation of translation ISS
Inferred from Sequence or Structural Similarity
more info
 
regulation of fatty acid biosynthetic process ISS
Inferred from Sequence or Structural Similarity
more info
 
regulation of glycolytic process ISS
Inferred from Sequence or Structural Similarity
more info
 
regulation of megakaryocyte differentiation ISS
Inferred from Sequence or Structural Similarity
more info
 
regulation of reactive oxygen species metabolic process ISS
Inferred from Sequence or Structural Similarity
more info
 
response to insulin ISS
Inferred from Sequence or Structural Similarity
more info
 
ribosomal large subunit biogenesis IEA
Inferred from Electronic Annotation
more info
 
translational initiation IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
cytoplasm IDA
Inferred from Direct Assay
more info
PubMed 
extracellular exosome HDA PubMed 
lamin filament IEA
Inferred from Electronic Annotation
more info
 
nucleoplasm IDA
Inferred from Direct Assay
more info
 
nucleus IDA
Inferred from Direct Assay
more info
PubMed 

General protein information

Preferred Names
eukaryotic translation initiation factor 6
Names
B4 integrin interactor
eukaryotic translation initiation factor 3A
p27 beta-4 integrin-binding protein
NP_001254739.1
NP_002203.1
NP_852131.1
NP_852133.1

NCBI Reference Sequences (RefSeq)

RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

  1. NG_023238.1 RefSeqGene

    Range
    4976..10886
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001267810.1NP_001254739.1  eukaryotic translation initiation factor 6 isoform a

    See identical proteins and their annotated locations for NP_001254739.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (6) differs in the 5' UTR compared to variant 1. Variants 1, 2, and 6 all encode the same isoform (a).
    Source sequence(s)
    BC001119, BM851166, BQ222221, CN265282
    Consensus CDS
    CCDS13249.1
    UniProtKB/Swiss-Prot
    P56537
    Conserved Domains (1) summary
    PTZ00136
    Location:1244
    PTZ00136; eukaryotic translation initiation factor 6-like protein; Provisional
  2. NM_002212.4NP_002203.1  eukaryotic translation initiation factor 6 isoform a

    See identical proteins and their annotated locations for NP_002203.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) encodes the longer isoform (a). Variants 1, 2, and 6 all encode isoform a.
    Source sequence(s)
    BC001119, BM851166
    Consensus CDS
    CCDS13249.1
    UniProtKB/Swiss-Prot
    P56537
    Related
    ENSP00000363574.3, ENST00000374450.8
    Conserved Domains (1) summary
    PTZ00136
    Location:1244
    PTZ00136; eukaryotic translation initiation factor 6-like protein; Provisional
  3. NM_181466.2NP_852131.1  eukaryotic translation initiation factor 6 isoform c

    See identical proteins and their annotated locations for NP_852131.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) contains an alternate segment compared to variant 1, which causes a frameshift, and lacks an alternate exon, which corrects the frameshift, compared to variant 1. The resulting isoform (c) lacks an internal segment compared to isoform a.
    Source sequence(s)
    BC001119, BM794263, BM851166, DB448068
    Consensus CDS
    CCDS13250.1
    UniProtKB/Swiss-Prot
    P56537
    Related
    ENSP00000363566.3, ENST00000374443.7
    Conserved Domains (1) summary
    cl00241
    Location:1225
    IF6; Ribosome anti-association factor IF6 binds the large ribosomal subunit and prevents the two subunits from associating during translation initiation. IF6 comprises a family of translation factors that includes both eukaryotic (eIF6) and archeal (aIF6) ...
  4. NM_181468.2NP_852133.1  eukaryotic translation initiation factor 6 isoform a

    See identical proteins and their annotated locations for NP_852133.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) differs in the 5' UTR compared to variant 1. Variants 1, 2, and 6 all encode isoform a.
    Source sequence(s)
    AF022229, BC001119, BM851166, CN265282
    Consensus CDS
    CCDS13249.1
    UniProtKB/Swiss-Prot
    P56537
    Related
    ENSP00000363559.3, ENST00000374436.7
    Conserved Domains (1) summary
    PTZ00136
    Location:1244
    PTZ00136; eukaryotic translation initiation factor 6-like protein; Provisional

RNA

  1. NR_052022.1 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (7) lacks an alternate coding exon compared to variant 1, that causes a frameshift. This transcript is a candidate for nonsense-mediated mRNA decay (NMD) and is not thought to be protein-coding.
    Source sequence(s)
    AK296076, BM851166, DB448068
    Related
    ENST00000447927.6
  2. NR_052023.1 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (8) uses an alternate splice junction at the 5' end of a coding exon compared to variant 1, that causes a frameshift. This transcript is a candidate for nonsense-mediated mRNA decay (NMD) and is not thought to be protein-coding.
    Source sequence(s)
    BC001119, BM851166, CT002623, DB448068
  3. NR_052024.1 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (9) uses an alternate first exon and lacks two alternate coding exons compared to variant 1, that causes a frameshift. This transcript is a candidate for nonsense-mediated mRNA decay (NMD) and is not thought to be protein-coding.
    Source sequence(s)
    BC001119, BG283650, BM851166, CN265282
    Related
    ENST00000440766.5

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p12 Primary Assembly

Genomic

  1. NC_000020.11 Reference GRCh38.p12 Primary Assembly

    Range
    35278906..35284816 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

  1. NM_181467.1: Suppressed sequence

    Description
    NM_181467.1: This RefSeq was permanently suppressed because it is a nonsense-mediated mRNA decay (NMD) candidate.
  2. NM_181469.1: Suppressed sequence

    Description
    NM_181469.1: This RefSeq was permanently suppressed because it is a nonsense-mediated mRNA decay (NMD) candidate.
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