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RBM17 RNA binding motif protein 17 [ Homo sapiens (human) ]

Gene ID: 84991, updated on 6-Jan-2019

Summary

Official Symbol
RBM17provided by HGNC
Official Full Name
RNA binding motif protein 17provided by HGNC
Primary source
HGNC:HGNC:16944
See related
Ensembl:ENSG00000134453 MIM:606935
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
SPF45
Summary
This gene encodes an RNA binding protein. The encoded protein is part of the spliceosome complex and functions in the second catalytic step of mRNA splicing. Alternatively spliced transcript variants have been described. Related pseudogenes exist on chromosomes 9 and 15. [provided by RefSeq, Mar 2009]
Expression
Ubiquitous expression in bone marrow (RPKM 17.7), lymph node (RPKM 15.8) and 25 other tissues See more
Orthologs

Genomic context

See RBM17 in Genome Data Viewer
Location:
10p15.1
Exon count:
13
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 10 NC_000010.11 (6088986..6117459)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 10 NC_000010.10 (6130949..6159422)

Chromosome 10 - NC_000010.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC107984201 Neighboring gene interleukin 2 receptor subunit alpha Neighboring gene ribosomal protein L32 pseudogene 23 Neighboring gene uncharacterized LOC101928080 Neighboring gene RNA, 7SK small nuclear pseudogene 78 Neighboring gene 6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 3

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
Genome-wide association analysis identifies 11 risk variants associated with the asthma with hay fever phenotype.
NHGRI GWA Catalog
Variant of TYR and autoimmunity susceptibility loci in generalized vitiligo.
NHGRI GWA Catalog

HIV-1 interactions

Replication interactions

Interaction Pubs
Knockdown of RNA binding motif protein 17 (RBM17) by siRNA inhibits the early stages of HIV-1 replication in 293T cells infected with VSV-G pseudotyped HIV-1 PubMed

Protein interactions

Protein Gene Interaction Pubs
Pr55(Gag) gag HIV-1 Gag is identified to have a physical interaction with RNA binding motif protein 17 (RBM17; SPF45) in human HEK293 and/or Jurkat cell lines by using affinity tagging and purification mass spectrometry analyses PubMed

Go to the HIV-1, Human Interaction Database

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...
  • 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...

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • MGC14439, DKFZp686F13131

Gene Ontology Provided by GOA

Function Evidence Code Pubs
RNA binding IEA
Inferred from Electronic Annotation
more info
 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
Process Evidence Code Pubs
DNA repair IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
alternative mRNA splicing, via spliceosome IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
alternative mRNA splicing, via spliceosome IMP
Inferred from Mutant Phenotype
more info
PubMed 
mRNA splicing, via spliceosome TAS
Traceable Author Statement
more info
 
regulation of alternative mRNA splicing, via spliceosome IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
Component Evidence Code Pubs
nucleoplasm IDA
Inferred from Direct Assay
more info
 
nucleoplasm TAS
Traceable Author Statement
more info
 
spliceosomal complex IEA
Inferred from Electronic Annotation
more info
 

General protein information

Preferred Names
splicing factor 45
Names
45 kDa-splicing factor
splicing factor 45kDa

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.

mRNA and Protein(s)

  1. NM_001145547.1NP_001139019.1  splicing factor 45

    See identical proteins and their annotated locations for NP_001139019.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) differs in the 5' UTR compared to variant 1. Both variants 1 and 2 encode the same protein.
    Source sequence(s)
    AA905075, AF542550, AL157395, BC039322, CN291330
    Consensus CDS
    CCDS7077.1
    UniProtKB/Swiss-Prot
    Q96I25
    UniProtKB/TrEMBL
    Q5W009
    Related
    ENSP00000388638.1, ENST00000446108.5
    Conserved Domains (2) summary
    cd12647
    Location:303397
    RRM_UHM_SPF45; RNA recognition motif in UHM domain of 45 kDa-splicing factor (SPF45) and similar proteins
    pfam01585
    Location:235275
    G-patch; G-patch domain
  2. NM_032905.5NP_116294.1  splicing factor 45

    See identical proteins and their annotated locations for NP_116294.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longer transcript. Both variants 1 and 2 encode the same protein.
    Source sequence(s)
    AA905075, AF542550, AL157395, CN291330, CV570433
    Consensus CDS
    CCDS7077.1
    UniProtKB/Swiss-Prot
    Q96I25
    UniProtKB/TrEMBL
    Q5W009
    Related
    ENSP00000369218.4, ENST00000379888.8
    Conserved Domains (2) summary
    cd12647
    Location:303397
    RRM_UHM_SPF45; RNA recognition motif in UHM domain of 45 kDa-splicing factor (SPF45) and similar proteins
    pfam01585
    Location:235275
    G-patch; G-patch domain

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_000010.11 Reference GRCh38.p12 Primary Assembly

    Range
    6088986..6117459
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

RNA

  1. XR_001747246.2 RNA Sequence

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