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

    Gene ID: 84991, updated on 3-Nov-2024

    Summary

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    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
    mouse all
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    Genomic context

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    See RBM17 in Genome Data Viewer
    Location:
    10p15.1
    Exon count:
    13
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 10 NC_000010.11 (6089034..6117447)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 10 NC_060934.1 (6089199..6117608)
    RS_2024_09 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

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: HPA RNA-seq normal tissues 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

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    Related articles in PubMed

    1. The splicing factor RBM17 drives leukemic stem cell maintenance by evading nonsense-mediated decay of pro-leukemic factors. Liu L, et al. Nat Commun, 2022 Jul 4. PMID 35781533, Free PMC Article
    2. SPF45/RBM17-dependent, but not U2AF-dependent, splicing in a distinct subset of human short introns. Fukumura K, et al. Nat Commun, 2021 Aug 13. PMID 34389706, Free PMC Article
    3. A 5'-tRNA halve, tiRNA-Gly promotes cell proliferation and migration via binding to RBM17 and inducing alternative splicing in papillary thyroid cancer. Han L, et al. J Exp Clin Cancer Res, 2021 Jul 5. PMID 34225773, Free PMC Article
    4. Human SPF45, a splicing factor, has limited expression in normal tissues, is overexpressed in many tumors, and can confer a multidrug-resistant phenotype to cells. Sampath J, et al. Am J Pathol, 2003 Nov. PMID 14578179, Free PMC Article
    5. Exploration of the effects of the CYCLOPS gene RBM17 in hepatocellular carcinoma. Li C, et al. PLoS One, 2020. PMID 32497093, Free PMC Article

    See all (136) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. SAP30BP interacts with RBM17/SPF45 to promote splicing in a subset of human short introns.
      Title: SAP30BP interacts with RBM17/SPF45 to promote splicing in a subset of human short introns.
    2. AKT1 phosphorylates RBM17 to promote Sox2 transcription by modulating alternative splicing of FOXM1 to enhance cancer stem cell properties in colorectal cancer cells.
      Title: AKT1 phosphorylates RBM17 to promote Sox2 transcription by modulating alternative splicing of FOXM1 to enhance cancer stem cell properties in colorectal cancer cells.
    3. The splicing factor RBM17 drives leukemic stem cell maintenance by evading nonsense-mediated decay of pro-leukemic factors.
      Title: The splicing factor RBM17 drives leukemic stem cell maintenance by evading nonsense-mediated decay of pro-leukemic factors.
    4. A 5'-tRNA halve, tiRNA-Gly promotes cell proliferation and migration via binding to RBM17 and inducing alternative splicing in papillary thyroid cancer.
      Title: A 5'-tRNA halve, tiRNA-Gly promotes cell proliferation and migration via binding to RBM17 and inducing alternative splicing in papillary thyroid cancer.
    5. SPF45/RBM17-dependent, but not U2AF-dependent, splicing in a distinct subset of human short introns.
      Title: SPF45/RBM17-dependent, but not U2AF-dependent, splicing in a distinct subset of human short introns.
    6. Exploration of the effects of the CYCLOPS gene RBM17 in hepatocellular carcinoma.
      Title: Exploration of the effects of the CYCLOPS gene RBM17 in hepatocellular carcinoma.
    7. Also our presented results indicate that splicing factors hnRNP A1 and SPF45, previously shown to regulate Fas alternative splicing in normoxic cells, are not involved in hypoxia dependent alternative Fas pre-mRNA splicing regulation in an amount dependent manner. Our observations on hypoxia dependent alternative Fas pre-mRNA splicing regulation indicate a probable involvement of other, yet unidentified splicing factors.
      Title: Hypoxia alters splicing of the cancer associated Fas gene.
    8. Data show that RNA binding motif protein 17 (RBM17) overexpressed in glioma patients and resulted in the poor prognosis.
      Title: RBM17 controls apoptosis and proliferation to promote Glioma progression.
    9. this work provides the structural and molecular basis of the interaction between RBM17 and the phosphorylated form of ATXN1.
      Title: Structural basis of the phosphorylation dependent complex formation of neurodegenerative disease protein Ataxin-1 and RBM17.
    10. identify SPF45 as the first splicing factor regulated by multiple MAP kinase pathways and show effects of both SPF45 overexpression and phosphorylation
      Title: Mitogen-activated protein kinase phosphorylation of splicing factor 45 (SPF45) regulates SPF45 alternative splicing site utilization, proliferation, and cell adhesion.
    Submit: New GeneRIF Correction See all GeneRIFs (15)

    Phenotypes

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    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    Review eQTL and phenotype association data in this region using PheGenI

    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

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    HIV-1 interactions

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    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

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    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    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

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

    NCBI Reference Sequences (RefSeq)

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    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_001145547.2 → NP_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:235 → 279
      G-patch; G-patch domain
      cd12647
      Location:303 → 397
      RRM_UHM_SPF45; RNA recognition motif (RRM) found in UHM domain of 45 kDa-splicing factor (SPF45) and similar proteins

    2. NM_032905.5 → NP_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:235 → 279
      G-patch; G-patch domain
      cd12647
      Location:303 → 397
      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_2024_08

    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)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q96I25.1 GenPept UniProtKB/Swiss-Prot:Q96I25

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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