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    RBM6 RNA binding motif protein 6 [ Homo sapiens (human) ]

    Gene ID: 10180, updated on 27-Nov-2024

    Summary

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    Official Symbol
    RBM6provided by HGNC
    Official Full Name
    RNA binding motif protein 6provided by HGNC
    Primary source
    HGNC:HGNC:9903
    See related
    Ensembl:ENSG00000004534 MIM:606886; AllianceGenome:HGNC:9903
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    3G2; g16; DEF3; DEF-3; HLC-11; NY-LU-12
    Summary
    Enables RNA binding activity. Predicted to be involved in mRNA splicing, via spliceosome. Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Ubiquitous expression in endometrium (RPKM 33.9), lymph node (RPKM 31.2) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See RBM6 in Genome Data Viewer
    Location:
    3p21.31
    Exon count:
    26
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (49940150..50077249)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (49969226..50106392)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (49977583..50114682)

    Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:49934943-49935443 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:49939657-49940330 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:49940331-49941004 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14376 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19881 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:49941679-49942351 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19882 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19883 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:49949147-49949724 Neighboring gene macrophage stimulating 1 receptor Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14377 Neighboring gene MON1 homolog A, secretory trafficking associated Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:49977213-49977735 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:49977736-49978257 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14379 Neighboring gene NANOG hESC enhancer GRCh37_chr3:50050258-50050926 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:50119658-50120158 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr3:50120996-50121560 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:50126209-50126800 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:50126801-50127391 Neighboring gene MPRA-validated peak4650 silencer Neighboring gene RBM5 antisense RNA 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:50157731-50158609 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:50158610-50159487 Neighboring gene RNA binding motif protein 5 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:50160473-50160973 Neighboring gene SEMA3F antisense RNA 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:50162997-50163986 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:50170449-50170950 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:50172709-50173300 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:50177671-50178232 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:50178233-50178794 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:50188081-50188752 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14380 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14381 Neighboring gene basic proline-rich protein-like Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14382 Neighboring gene semaphorin 3F

    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
    • 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. RNA-binding protein RBM6 acts as a tumor suppressor gene to inhibit the progression of hepatocellular carcinoma. Ye Z, et al. J BUON, 2021 Mar-Apr. PMID 34076986
    2. RNA-Binding Motif Protein 6 is a Candidate Serum Biomarker for Pancreatic Cancer. Duan B, et al. Proteomics Clin Appl, 2019 Sep. PMID 31207145
    3. RNA-binding protein RBM6 as a tumor suppressor gene represses the growth and progression in laryngocarcinoma. Wang Q, et al. Gene, 2019 May 20. PMID 30772516
    4. RBM6 splicing factor promotes homologous recombination repair of double-strand breaks and modulates sensitivity to chemotherapeutic drugs. Machour FE, et al. Nucleic Acids Res, 2021 Nov 18. PMID 34718714, Free PMC Article
    5. Human lung cancer antigens recognized by autologous antibodies: definition of a novel cDNA derived from the tumor suppressor gene locus on chromosome 3p21.3. Güre AO, et al. Cancer Res, 1998 Mar 1. PMID 9500467

    See all (86) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. RBM6 splicing factor promotes homologous recombination repair of double-strand breaks and modulates sensitivity to chemotherapeutic drugs.
      Title: RBM6 splicing factor promotes homologous recombination repair of double-strand breaks and modulates sensitivity to chemotherapeutic drugs.
    2. RNA-binding protein RBM6 acts as a tumor suppressor gene to inhibit the progression of hepatocellular carcinoma.
      Title: RNA-binding protein RBM6 acts as a tumor suppressor gene to inhibit the progression of hepatocellular carcinoma.
    3. RNA-Binding Motif Protein 6 is a Candidate Serum Biomarker for Pancreatic Cancer
      Title: RNA-Binding Motif Protein 6 is a Candidate Serum Biomarker for Pancreatic Cancer.
    4. Upregulation of RBM6 reduced the expression of EGFR, ERK and p-ERK in vitro and in vivo. Data suggest that RBM6 as a tumor suppressor represses the growth and progression in laryngocarcinoma.
      Title: RNA-binding protein RBM6 as a tumor suppressor gene represses the growth and progression in laryngocarcinoma.
    5. Antagonizes the effects of RBM5, RBM6, and RBM10 in cell colony formation.
      Title: RBM5, 6, and 10 differentially regulate NUMB alternative splicing to control cancer cell proliferation.
    6. RBM6 mRNA experiences altered co-transcriptional gene regulation in certain cancers. RBM6-RBM5 transcription-induced chimerism might be a process that is linked to the tumour-associated increased transcriptional activity of the RBM6 gene
      Title: RBM6-RBM5 transcription-induced chimeras are differentially expressed in tumours.
    7. identified a novel fusion of the RNA binding motif 6 (RBM6) gene to CSF1R gene generated presumably by a t(3;5)(p21;q33) translocation that induced a myeloid proliferative disease with features of megakaryoblastic leukemia in a murine transplant model
      Title: A novel fusion of RBM6 to CSF1R in acute megakaryoblastic leukemia.
    Submit: New GeneRIF Correction

    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
    Parent-of-origin-specific allelic associations among 106 genomic loci for age at menarche.
    EBI GWAS Catalog
    Thirty new loci for age at menarche identified by a meta-analysis of genome-wide association studies.
    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)

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • FLJ36517, FLJ39446, FLJ42036, DKFZp686B0877

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables DNA binding TAS
    Traceable Author Statement
    more info
    		 PubMed 
    enables RNA binding HDA PubMed 
    enables RNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in RNA processing TAS
    Traceable Author Statement
    more info
    		 PubMed 
    involved_in mRNA splicing, via spliceosome IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Component Evidence Code Pubs
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

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    Preferred Names
    RNA-binding protein 6
    Names
    RNA-binding protein DEF-3
    lung cancer antigen NY-LU-12
    lung cancer protooncogene 11

    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_001167582.2 → NP_001161054.1  RNA-binding protein 6 isoform 2

      See identical proteins and their annotated locations for NP_001161054.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) lacks several internal exons in the CDS, as compared to variant 1. This results in a downstream in-frame AUG start codon, and the resulting isoform (2) has a shorter N-terminus, as compared to isoform 1. Variants 2, 3, 4, 5, and 6 all encode the same isoform (2).
      Source sequence(s)
      AK291719, BC012112, BC046643
      Consensus CDS
      CCDS54586.1
      UniProtKB/TrEMBL
      B3KSK6
      Related
      ENSP00000393530.1, ENST00000442092.5
      Conserved Domains (3) summary
      cd12563
      Location:132 → 218
      RRM2_RBM6; RNA recognition motif 2 in vertebrate RNA-binding protein 6 (RBM6)
      cd16163
      Location:244 → 303
      OCRE_RBM6; OCRE domain found in RNA-binding protein 6 (RBM6) and similar proteins
      pfam01585
      Location:529 → 573
      G-patch; G-patch domain

    2. NM_001349190.2 → NP_001336119.1  RNA-binding protein 6 isoform 2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3), as well as variants 2, 4, 5, and 6, encodes isoform 2.
      Source sequence(s)
      AC104450, AC105935
      Consensus CDS
      CCDS54586.1
      UniProtKB/TrEMBL
      B3KSK6
      Related
      ENSP00000392939.1, ENST00000422955.5
      Conserved Domains (3) summary
      cd12563
      Location:132 → 218
      RRM2_RBM6; RNA recognition motif 2 in vertebrate RNA-binding protein 6 (RBM6)
      cd16163
      Location:244 → 303
      OCRE_RBM6; OCRE domain found in RNA-binding protein 6 (RBM6) and similar proteins
      pfam01585
      Location:529 → 573
      G-patch; G-patch domain

    3. NM_001349191.2 → NP_001336120.1  RNA-binding protein 6 isoform 2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (4), as well as variants 2, 3, 5, and 6, encodes isoform 2.
      Source sequence(s)
      AC104450, AC105935
      Consensus CDS
      CCDS54586.1
      UniProtKB/TrEMBL
      B3KSK6
      Conserved Domains (3) summary
      cd12563
      Location:132 → 218
      RRM2_RBM6; RNA recognition motif 2 in vertebrate RNA-binding protein 6 (RBM6)
      cd16163
      Location:244 → 303
      OCRE_RBM6; OCRE domain found in RNA-binding protein 6 (RBM6) and similar proteins
      pfam01585
      Location:529 → 573
      G-patch; G-patch domain

    4. NM_001349192.2 → NP_001336121.1  RNA-binding protein 6 isoform 2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (5), as well as variants 2, 3, 4, and 6, encodes isoform 2.
      Source sequence(s)
      AC104450, AC105935
      Consensus CDS
      CCDS54586.1
      UniProtKB/TrEMBL
      B3KSK6
      Conserved Domains (3) summary
      cd12563
      Location:132 → 218
      RRM2_RBM6; RNA recognition motif 2 in vertebrate RNA-binding protein 6 (RBM6)
      cd16163
      Location:244 → 303
      OCRE_RBM6; OCRE domain found in RNA-binding protein 6 (RBM6) and similar proteins
      pfam01585
      Location:529 → 573
      G-patch; G-patch domain

    5. NM_001349193.2 → NP_001336122.1  RNA-binding protein 6 isoform 2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (6), as well as variants 2, 3, 4, and 5, encodes isoform 2.
      Source sequence(s)
      AC104450, AC105935
      Consensus CDS
      CCDS54586.1
      UniProtKB/TrEMBL
      B3KSK6
      Conserved Domains (3) summary
      cd12563
      Location:132 → 218
      RRM2_RBM6; RNA recognition motif 2 in vertebrate RNA-binding protein 6 (RBM6)
      cd16163
      Location:244 → 303
      OCRE_RBM6; OCRE domain found in RNA-binding protein 6 (RBM6) and similar proteins
      pfam01585
      Location:529 → 573
      G-patch; G-patch domain

    6. NM_001349194.2 → NP_001336123.1  RNA-binding protein 6 isoform 3

      Status: VALIDATED

      Source sequence(s)
      AC104450, AC105935
      UniProtKB/TrEMBL
      B3KSK6
      Conserved Domains (4) summary
      cd12563
      Location:140 → 226
      RRM2_RBM6; RNA recognition motif 2 in vertebrate RNA-binding protein 6 (RBM6)
      cd16163
      Location:252 → 311
      OCRE_RBM6; OCRE domain found in RNA-binding protein 6 (RBM6) and similar proteins
      pfam01585
      Location:537 → 581
      G-patch; G-patch domain
      cl17169
      Location:1 → 19
      RRM_SF; RNA recognition motif (RRM) superfamily

    7. NM_005777.3 → NP_005768.1  RNA-binding protein 6 isoform 1

      See identical proteins and their annotated locations for NP_005768.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) encodes the longest isoform (1).
      Source sequence(s)
      AF091264, AK291719, BC012112
      Consensus CDS
      CCDS2809.1
      UniProtKB/Swiss-Prot
      B4E0G6, O60549, O75524, P78332, Q86SS3
      UniProtKB/TrEMBL
      A8K6Q4
      Related
      ENSP00000266022.4, ENST00000266022.9
      Conserved Domains (5) summary
      COG1357
      Location:92 → 237
      YjbI; Uncharacterized protein YjbI, contains pentapeptide repeats [Function unknown]
      cd16163
      Location:766 → 825
      OCRE_RBM6; OCRE domain found in RNA-binding protein 6 (RBM6) and similar proteins
      pfam01585
      Location:1051 → 1094
      G-patch; G-patch domain
      cd12314
      Location:456 → 533
      RRM1_RBM6; RNA recognition motif 1 (RRM1) found in vertebrate RNA-binding protein 6 (RBM6)
      cd12563
      Location:654 → 740
      RRM2_RBM6; RNA recognition motif 2 (RRM2) found in vertebrate RNA-binding protein 6 (RBM6)

    RNA

    1. NR_146071.2 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      AC104450, AK298108, BC012112
      Related
      ENST00000419610.5

    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_000003.12 Reference GRCh38.p14 Primary Assembly

      Range
      49940150..50077249
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047447131.1 → XP_047303087.1  RNA-binding protein 6 isoform X1

      UniProtKB/Swiss-Prot
      B4E0G6, O60549, O75524, P78332, Q86SS3

    2. XM_047447132.1 → XP_047303088.1  RNA-binding protein 6 isoform X2

    3. XM_017005496.3 → XP_016860985.2  RNA-binding protein 6 isoform X4

      Conserved Domains (3) summary
      COG1357
      Location:92 → 237
      YjbI; Uncharacterized protein YjbI, contains pentapeptide repeats [Function unknown]
      cd12314
      Location:456 → 533
      RRM1_RBM6; RNA recognition motif 1 in vertebrate RNA-binding protein 6 (RBM6)
      cd12563
      Location:654 → 740
      RRM2_RBM6; RNA recognition motif 2 in vertebrate RNA-binding protein 6 (RBM6)

    4. XM_047447137.1 → XP_047303093.1  RNA-binding protein 6 isoform X8

    5. XM_047447136.1 → XP_047303092.1  RNA-binding protein 6 isoform X8

      Related
      ENSP00000408665.1, ENST00000425608.5

    6. XM_047447133.1 → XP_047303089.1  RNA-binding protein 6 isoform X5

    7. XM_006712916.2 → XP_006712979.1  RNA-binding protein 6 isoform X3

      See identical proteins and their annotated locations for XP_006712979.1

      UniProtKB/TrEMBL
      E9PGM9
      Related
      ENSP00000396466.1, ENST00000443081.5
      Conserved Domains (5) summary
      smart00443
      Location:917 → 963
      G_patch; glycine rich nucleic binding domain
      COG1357
      Location:11 → 127
      YjbI; Uncharacterized protein YjbI, contains pentapeptide repeats [Function unknown]
      cd12314
      Location:324 → 401
      RRM1_RBM6; RNA recognition motif 1 in vertebrate RNA-binding protein 6 (RBM6)
      cd12563
      Location:522 → 608
      RRM2_RBM6; RNA recognition motif 2 in vertebrate RNA-binding protein 6 (RBM6)
      cd16163
      Location:634 → 693
      OCRE_RBM6; OCRE domain found in RNA-binding protein 6 (RBM6) and similar proteins

    8. XM_017005497.2 → XP_016860986.1  RNA-binding protein 6 isoform X6

      UniProtKB/TrEMBL
      B3KSK6

    9. XM_047447134.1 → XP_047303090.1  RNA-binding protein 6 isoform X7

    10. XM_047447135.1 → XP_047303091.1  RNA-binding protein 6 isoform X7

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060927.1 Alternate T2T-CHM13v2.0

      Range
      49969226..50106392
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054344843.1 → XP_054200818.1  RNA-binding protein 6 isoform X8

    2. XM_054344834.1 → XP_054200809.1  RNA-binding protein 6 isoform X1

      UniProtKB/Swiss-Prot
      B4E0G6, O60549, O75524, P78332, Q86SS3

    3. XM_054344835.1 → XP_054200810.1  RNA-binding protein 6 isoform X2

    4. XM_054344837.1 → XP_054200812.1  RNA-binding protein 6 isoform X4

    5. XM_054344842.1 → XP_054200817.1  RNA-binding protein 6 isoform X8

    6. XM_054344838.1 → XP_054200813.1  RNA-binding protein 6 isoform X5

    7. XM_054344836.1 → XP_054200811.1  RNA-binding protein 6 isoform X3

      UniProtKB/TrEMBL
      E9PGM9

    8. XM_054344839.1 → XP_054200814.1  RNA-binding protein 6 isoform X6

    9. XM_054344840.1 → XP_054200815.1  RNA-binding protein 6 isoform X7

    10. XM_054344841.1 → XP_054200816.1  RNA-binding protein 6 isoform X7

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    P78332.5 GenPept UniProtKB/Swiss-Prot:P78332

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