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

    Gene ID: 84991, updated on 5-May-2024

    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; AllianceGenome:HGNC:16944
    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
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See RBM17 in Genome Data Viewer
    Location:
    10p15.1
    Exon count:
    13
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 10 NC_000010.11 (6089034..6117447)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 10 NC_060934.1 (6089199..6117608)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 10 NC_000010.10 (6130997..6159410)

    Chromosome 10 - NC_000010.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC107984201 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2095 Neighboring gene interleukin 2 receptor subunit alpha Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2947 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2948 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2949 Neighboring gene CRISPRi-FlowFISH-validated IL2RA regulatory element GRCh37_chr10:6094489-6094989 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2950 Neighboring gene CRISPRi-FlowFISH-validated IL2RA regulatory element GRCh37_chr10:6104083-6104713 Neighboring gene MPRA-validated peak860 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2096 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2951 Neighboring gene CRISPRi-FlowFISH-validated IL2RA regulatory element GRCh37_chr10:6125624-6126124 Neighboring gene ribosomal protein L32 pseudogene 23 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2098 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2097 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2952 Neighboring gene H3K27ac hESC enhancer GRCh37_chr10:6131655-6132493 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:6138283-6138782 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:6137781-6138282 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:6138886-6139486 Neighboring gene H3K27ac hESC enhancer GRCh37_chr10:6149773-6150468 Neighboring gene MPRA-validated peak861 silencer Neighboring gene uncharacterized LOC101928080 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2953 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2954 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2955 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2956 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:6176097-6176645 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:6176646-6177193 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2957 Neighboring gene uncharacterized LOC124902369 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2958 Neighboring gene CRISPRi-FlowFISH-validated PFKFB3 regulatory elements GRCh37_chr10:6186610-6187110 and GRCh37_chr10:6186666-6187166 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2959 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2960 Neighboring gene RN7SK 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 Functions

    What's a GeneRIF?

    Phenotypes

    EBI GWAS Catalog

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

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Clone Names

    • MGC14439, DKFZp686F13131

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables RNA binding IEA
    Inferred from Electronic Annotation
    more info
     
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    Process Evidence Code Pubs
    involved_in alternative mRNA splicing, via spliceosome IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in alternative mRNA splicing, via spliceosome IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in mRNA cis splicing, via spliceosome IEA
    Inferred from Electronic Annotation
    more info
     
    Component Evidence Code Pubs
    located_in nucleoplasm IDA
    Inferred from Direct Assay
    more info
     
    located_in nucleoplasm TAS
    Traceable Author Statement
    more info
     
    part_of 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)

    NEW Try the new Transcript table

    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_001145547.2NP_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
      Q96GY6, Q96I25
      UniProtKB/TrEMBL
      Q5W009
      Related
      ENSP00000388638.1, ENST00000446108.5
      Conserved Domains (2) summary
      pfam01585
      Location:235279
      G-patch; G-patch domain
      cd12647
      Location:303397
      RRM_UHM_SPF45; RNA recognition motif (RRM) found in UHM domain of 45 kDa-splicing factor (SPF45) and similar proteins
    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
      Q96GY6, Q96I25
      UniProtKB/TrEMBL
      Q5W009
      Related
      ENSP00000369218.4, ENST00000379888.9
      Conserved Domains (2) summary
      pfam01585
      Location:235279
      G-patch; G-patch domain
      cd12647
      Location:303397
      RRM_UHM_SPF45; RNA recognition motif (RRM) found in UHM domain of 45 kDa-splicing factor (SPF45) and similar proteins

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000010.11 Reference GRCh38.p14 Primary Assembly

      Range
      6089034..6117447
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060934.1 Alternate T2T-CHM13v2.0

      Range
      6089199..6117608
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)