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EFTUD2 elongation factor Tu GTP binding domain containing 2 [ Homo sapiens (human) ]

Gene ID: 9343, updated on 10-Oct-2019

Summary

Official Symbol
EFTUD2provided by HGNC
Official Full Name
elongation factor Tu GTP binding domain containing 2provided by HGNC
Primary source
HGNC:HGNC:30858
See related
Ensembl:ENSG00000108883 MIM:603892
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
MFDM; MFDGA; Snu114; Snrp116; SNRNP116; U5-116KD
Summary
This gene encodes a GTPase which is a component of the spliceosome complex which processes precursor mRNAs to produce mature mRNAs. Mutations in this gene are associated with mandibulofacial dysostosis with microcephaly. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Apr 2012]
Expression
Ubiquitous expression in testis (RPKM 15.7), appendix (RPKM 15.5) and 25 other tissues See more
Orthologs

Genomic context

See EFTUD2 in Genome Data Viewer
Location:
17q21.31
Exon count:
29
Annotation release Status Assembly Chr Location
109.20190905 current GRCh38.p13 (GCF_000001405.39) 17 NC_000017.11 (44849948..44899625, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 17 NC_000017.10 (42927655..42976993, complement)

Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene ADAM metallopeptidase domain 11 Neighboring gene gap junction protein gamma 1 Neighboring gene HIG1 hypoxia inducible domain family member 1B Neighboring gene RNA, 7SL, cytoplasmic 405, pseudogene Neighboring gene coiled-coil domain containing 103 Neighboring gene family with sequence similarity 187 member A Neighboring gene uncharacterized LOC105371793 Neighboring gene glial fibrillary acidic protein Neighboring gene kinesin family member 18B

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 Functions

What's a GeneRIF?

Phenotypes

Copy number response

Description
Copy number response
Triplosensitivity

No evidence available (Last evaluated (2013-05-23)

ClinGen Genome Curation Page
Haploinsufficency

Sufficient evidence for dosage pathogenicity (Last evaluated (2013-05-23)

ClinGen Genome Curation PagePubMed

Pathways from BioSystems

  • Gene Expression, organism-specific biosystem (from REACTOME)
    Gene Expression, organism-specific biosystemGene Expression covers the pathways by which genomic DNA is transcribed to yield RNA, the regulation of these transcription processes, and the pathways by which newly-made RNA Transcripts are process...
  • Processing of Capped Intron-Containing Pre-mRNA, organism-specific biosystem (from REACTOME)
    Processing of Capped Intron-Containing Pre-mRNA, organism-specific biosystemCo-transcriptional pre-mRNA splicing is not obligatory. Pre-mRNA splicing begins co-transcriptionally and often continues post-transcriptionally. Human genes contain an average of nine introns per ge...
  • Spliceosome, organism-specific biosystem (from KEGG)
    Spliceosome, organism-specific biosystemAfter transcription, eukaryotic mRNA precursors contain protein-coding exons and noncoding introns. In the following splicing, introns are excised and exons are joined by a macromolecular complex, th...
  • Spliceosome, conserved biosystem (from KEGG)
    Spliceosome, conserved biosystemAfter transcription, eukaryotic mRNA precursors contain protein-coding exons and noncoding introns. In the following splicing, introns are excised and exons are joined by a macromolecular complex, th...
  • Spliceosome, 35S U5-snRNP, organism-specific biosystem (from KEGG)
    Spliceosome, 35S U5-snRNP, organism-specific biosystemStructural complex; Genetic information processing; Spliceosome
  • Spliceosome, 35S U5-snRNP, conserved biosystem (from KEGG)
    Spliceosome, 35S U5-snRNP, conserved biosystemStructural complex; Genetic information processing; Spliceosome
  • Spliceosome, U4/U6.U5 tri-snRNP, organism-specific biosystem (from KEGG)
    Spliceosome, U4/U6.U5 tri-snRNP, organism-specific biosystemStructural complex; Genetic information processing; Spliceosome
  • Spliceosome, U4/U6.U5 tri-snRNP, conserved biosystem (from KEGG)
    Spliceosome, U4/U6.U5 tri-snRNP, conserved biosystemStructural complex; Genetic information processing; Spliceosome
  • mRNA Processing, organism-specific biosystem (from WikiPathways)
    mRNA Processing, organism-specific biosystemThis process describes the conversion of precursor messenger RNA into mature messenger RNA (mRNA). The pre-mRNA molecule undergoes three main modifications. These modifications are 5' capping, 3' po...
  • mRNA Splicing, organism-specific biosystem (from REACTOME)
    mRNA Splicing, organism-specific biosystemThe process in which excision of introns from the primary transcript of messenger RNA (mRNA) is followed by ligation of the two exon termini exposed by removal of each intron, is called mRNA splicing...
  • mRNA Splicing - Major Pathway, organism-specific biosystem (from REACTOME)
    mRNA Splicing - Major Pathway, organism-specific biosystemThe splicing of pre-mRNA occurs within a large, very dynamic complex, designated the 'spliceosome'. The 50-60S spliceosomes are estimated to be 40-60 nm in diameter, and have molecular weights in the...
  • mRNA Splicing - Minor Pathway, organism-specific biosystem (from REACTOME)
    mRNA Splicing - Minor Pathway, organism-specific biosystemThe splicing of a subset of pre-mRNA introns occurs by a second pathway, designated the AT-AC or U12-dependent splicing pathway. AT-AC introns have highly conserved, non-canonical splice sites that ...

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • FLJ44695, KIAA0031, DKFZp686E24196

Gene Ontology Provided by GOA

Function Evidence Code Pubs
GTP binding IEA
Inferred from Electronic Annotation
more info
 
GTPase activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
RNA binding HDA PubMed 
U5 snRNA binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
Process Evidence Code Pubs
cellular response to drug IEA
Inferred from Electronic Annotation
more info
 
mRNA splicing, via spliceosome IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
mRNA splicing, via spliceosome IDA
Inferred from Direct Assay
more info
PubMed 
mRNA splicing, via spliceosome TAS
Traceable Author Statement
more info
 
response to cocaine IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
Cajal body IDA
Inferred from Direct Assay
more info
PubMed 
U2-type catalytic step 2 spliceosome IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
U2-type catalytic step 2 spliceosome IDA
Inferred from Direct Assay
more info
PubMed 
U2-type precatalytic spliceosome IDA
Inferred from Direct Assay
more info
PubMed 
U4/U6 x U5 tri-snRNP complex IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
U4/U6 x U5 tri-snRNP complex IDA
Inferred from Direct Assay
more info
PubMed 
catalytic step 2 spliceosome IDA
Inferred from Direct Assay
more info
PubMed 
cytosol IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
cytosol IDA
Inferred from Direct Assay
more info
 
intracellular membrane-bounded organelle IDA
Inferred from Direct Assay
more info
 
membrane HDA PubMed 
nuclear speck IDA
Inferred from Direct Assay
more info
PubMed 
nucleoplasm IDA
Inferred from Direct Assay
more info
 
nucleoplasm TAS
Traceable Author Statement
more info
 
nucleus IDA
Inferred from Direct Assay
more info
PubMed 
ribonucleoprotein complex IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 

General protein information

Preferred Names
116 kDa U5 small nuclear ribonucleoprotein component
Names
SNU114 homolog
U5 snRNP-specific protein, 116 kDa
elongation factor Tu GTP-binding domain-containing protein 2
hSNU114

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_032674.1 RefSeqGene

    Range
    5181..54678
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001142605.1NP_001136077.1  116 kDa U5 small nuclear ribonucleoprotein component isoform b

    See identical proteins and their annotated locations for NP_001136077.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) differs in the 5' UTR and in the 5' coding region, compared to variant 1. These differences causes translation initiation at a downstream AUG and results an isoform (b) with a shorter N-terminus compared to isoform a.
    Source sequence(s)
    AC015936, AK126464, BC002360, DC353274
    Consensus CDS
    CCDS45707.1
    UniProtKB/Swiss-Prot
    Q15029
    UniProtKB/TrEMBL
    B3KX19
    Related
    ENSP00000385873.2, ENST00000402521.7
    Conserved Domains (2) summary
    pfam16004
    Location:1975
    EFTUD2; 116 kDa U5 small nuclear ribonucleoprotein component N-terminus
    cl27769
    Location:87919
    GTP_EFTU; Elongation factor Tu GTP binding domain
  2. NM_001258353.1NP_001245282.1  116 kDa U5 small nuclear ribonucleoprotein component isoform a

    See identical proteins and their annotated locations for NP_001245282.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) differs in the 5' UTR compared to variant 1. Both variants 1 and 3 encode the same protein.
    Source sequence(s)
    AC015936, AK128148
    Consensus CDS
    CCDS11489.1
    UniProtKB/Swiss-Prot
    Q15029
    Related
    ENSP00000467805.1, ENST00000591382.5
    Conserved Domains (2) summary
    pfam16004
    Location:4110
    EFTUD2; 116 kDa U5 small nuclear ribonucleoprotein component N-terminus
    cl30786
    Location:122954
    FusA; Translation elongation factor EF-G, a GTPase [Translation, ribosomal structure and biogenesis]
  3. NM_001258354.1NP_001245283.1  116 kDa U5 small nuclear ribonucleoprotein component isoform c

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) uses an alternate in-frame splice site in the 5' coding region compared to variant 1. The resulting protein (isoform c) is shorter compared to isoform a.
    Source sequence(s)
    AC015936, AK297392
    Consensus CDS
    CCDS59295.1
    UniProtKB/Swiss-Prot
    Q15029
    Related
    ENSP00000465058.1, ENST00000592576.5
    Conserved Domains (2) summary
    pfam16004
    Location:4110
    EFTUD2; 116 kDa U5 small nuclear ribonucleoprotein component N-terminus
    cl27769
    Location:122944
    GTP_EFTU; Elongation factor Tu GTP binding domain
  4. NM_004247.4NP_004238.3  116 kDa U5 small nuclear ribonucleoprotein component isoform a

    See identical proteins and their annotated locations for NP_004238.3

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) encodes the longest isoform (a). Both variants 1 and 3 encode the same protein.
    Source sequence(s)
    AC015936, AK126464, BC002360, DC353274
    Consensus CDS
    CCDS11489.1
    UniProtKB/Swiss-Prot
    Q15029
    UniProtKB/TrEMBL
    B3KX19
    Related
    ENSP00000392094.1, ENST00000426333.7
    Conserved Domains (2) summary
    pfam16004
    Location:4110
    EFTUD2; 116 kDa U5 small nuclear ribonucleoprotein component N-terminus
    cl30786
    Location:122954
    FusA; Translation elongation factor EF-G, a GTPase [Translation, ribosomal structure and biogenesis]

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109.20190905

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000017.11 Reference GRCh38.p13 Primary Assembly

    Range
    44849948..44899625 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

RNA

  1. XR_934602.3 RNA Sequence

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