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    RBM38 RNA binding motif protein 38 [ Homo sapiens (human) ]

    Gene ID: 55544, updated on 27-Nov-2024

    Summary

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    Official Symbol
    RBM38provided by HGNC
    Official Full Name
    RNA binding motif protein 38provided by HGNC
    Primary source
    HGNC:HGNC:15818
    See related
    Ensembl:ENSG00000132819 MIM:612428; AllianceGenome:HGNC:15818
    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
    RNPC1; SEB4B; SEB4D; HSRNASEB; dJ800J21.2
    Summary
    Enables mRNA 3'-UTR binding activity. Involved in DNA damage response, signal transduction by p53 class mediator; negative regulation of cell population proliferation; and regulation of gene expression. Located in cytosol and nucleus. [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Broad expression in bone marrow (RPKM 68.1), lymph node (RPKM 23.9) and 18 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See RBM38 in Genome Data Viewer
    Location:
    20q13.31
    Exon count:
    6
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 20 NC_000020.11 (57391396..57409333)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 20 NC_060944.1 (59169162..59187091)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 20 NC_000020.10 (55966452..55984389)

    Chromosome 20 - NC_000020.11Genomic Context describing neighboring genes Neighboring gene nuclear-encoded mitochondrial tRNA-Leu (TAA) 5-1 Neighboring gene ribonucleic acid export 1 Neighboring gene MT-RNR2 like 3 (pseudogene) Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:55949536-55950533 Neighboring gene uncharacterized LOC124904938 Neighboring gene Sharpr-MPRA regulatory region 7479 Neighboring gene RBM38 antisense RNA 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13059 Neighboring gene H3K27ac hESC enhancer GRCh37_chr20:55966169-55966670 Neighboring gene H3K27ac hESC enhancer GRCh37_chr20:55966671-55967170 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18146 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:55970944-55971905 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:55973481-55973980 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:55975022-55975885 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18148 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:55984023-55984528 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18149 Neighboring gene ReSE screen-validated silencer GRCh37_chr20:55985201-55985370 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18150 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18151 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18152 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:55988977-55989746 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:55989747-55990514 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:55990515-55991283 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18153 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18154 Neighboring gene uncharacterized LOC124904939 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18155 Neighboring gene ReSE screen-validated silencer GRCh37_chr20:56012611-56012842 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:56014209-56014710 Neighboring gene VISTA enhancer hs1971 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18156 Neighboring gene H3K4me1 hESC enhancers GRCh37_chr20:56026537-56027036 and GRCh37_chr20:56027096-56027596 Neighboring gene uncharacterized LOC105372688 Neighboring gene Sharpr-MPRA regulatory region 5175

    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 RNPC1 Inhibits Breast Cancer Cell Metastasis via Activating STARD13-Correlated ceRNA Network. Zheng L, et al. Mol Pharm, 2018 Jun 4. PMID 29733656
    2. RBM38 is involved in TGF-β-induced epithelial-to-mesenchymal transition by stabilising zonula occludens-1 mRNA in breast cancer. Wu J, et al. Br J Cancer, 2017 Aug 22. PMID 28683467, Free PMC Article
    3. The expression of RNA-binding protein RBM38 decreased in renal cell carcinoma and represses renal cancer cell proliferation, migration, and invasion. Huang W, et al. Tumour Biol, 2017 May. PMID 28459215
    4. The RNA binding protein RBM38 (RNPC1) regulates splicing during late erythroid differentiation. Heinicke LA, et al. PLoS One, 2013. PMID 24250749, Free PMC Article
    5. Structural basis for mRNA recognition by human RBM38. Qian K, et al. Biochem J, 2020 Jan 17. PMID 31860021

    See all (66) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. TRIM17-mediated ubiquitination and degradation of RBM38 promotes cisplatin resistance in non-small cell lung cancer.
      Title: TRIM17-mediated ubiquitination and degradation of RBM38 promotes cisplatin resistance in non-small cell lung cancer.
    2. LncRNA CALML3-AS1 suppresses papillary thyroid cancer progression via sponging miR-20a-5p/RBM38 axis.
      Title: LncRNA CALML3-AS1 suppresses papillary thyroid cancer progression via sponging miR-20a-5p/RBM38 axis.
    3. RNA binding Motif protein-38 regulates myocardial hypertrophy in LXR-alpha-dependent lipogenesis pathway.
      Title: RNA binding Motif protein-38 regulates myocardial hypertrophy in LXR-α-dependent lipogenesis pathway.
    4. [RBM38 Mediates the Proliferation of Acute Myeloid Leukemia Cells HL-60 by Regulating FZD1 mRNA Stability].
      Title: [RBM38 Mediates the Proliferation of Acute Myeloid Leukemia Cells HL-60 by Regulating FZD1 mRNA Stability].
    5. RNA-binding protein RBM38 inhibits colorectal cancer progression by partly and competitively binding to PTEN 3'UTR with miR-92a-3p.
      Title: RNA-binding protein RBM38 inhibits colorectal cancer progression by partly and competitively binding to PTEN 3'UTR with miR-92a-3p.
    6. RNA-binding protein RNPC1 acts as an oncogene in gastric cancer by stabilizing aurora kinase B mRNA.
      Title: RNA-binding protein RNPC1 acts as an oncogene in gastric cancer by stabilizing aurora kinase B mRNA.
    7. Survivin Expression Is Differentially Regulated by a Selective Cross-talk between RBM38 and miRNAs let-7b or miR-203a.
      Title: Survivin Expression Is Differentially Regulated by a Selective Cross-talk between RBM38 and miRNAs let-7b or miR-203a.
    8. Rbm38 Reduces the Transcription Elongation Defect of the SMEK2 Gene Caused by Splicing Deficiency.
      Title: Rbm38 Reduces the Transcription Elongation Defect of the SMEK2 Gene Caused by Splicing Deficiency.
    9. RNA Binding Protein RNPC1 Suppresses the Stemness of Human Endometrial Cancer Cells via Stabilizing MST1/2 mRNA.
      Title: RNA Binding Protein RNPC1 Suppresses the Stemness of Human Endometrial Cancer Cells via Stabilizing MST1/2 mRNA.
    10. The authors report the crystal structure of the RNA-recognition motif domain of human RBM38 in complex with a single-stranded RNA, reveal the RNA-recognition mechanism of human RBM38 and provide structural information for understanding the RNA-binding property of RBM38.
      Title: Structural basis for mRNA recognition by human RBM38.
    Submit: New GeneRIF Correction See all GeneRIFs (41)

    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 of lipid-lowering response to statins in combined study populations.
    EBI GWAS Catalog
    Genome-wide association study identifies a novel locus contributing to type 2 diabetes susceptibility in Sikhs of Punjabi origin from India.
    EBI GWAS Catalog
    Genome-wide association study of hematological and biochemical traits in a Japanese population.
    EBI GWAS Catalog
    Seventy-five genetic loci influencing the human red blood cell.
    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

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables RNA binding HDA PubMed 
    enables mRNA 3'-UTR binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables mRNA 3'-UTR binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables mRNA binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in 3'-UTR-mediated mRNA stabilization IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in RNA splicing IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in cell differentiation IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in mRNA processing IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in negative regulation of cell population proliferation IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in regulation of RNA splicing IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in regulation of RNA splicing IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    NOT involved_in regulation of cell cycle IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in regulation of cell cycle IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in regulation of myotube differentiation IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    is_active_in cytosol IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in cytosol IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in nucleus IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    RNA-binding protein 38
    Names
    CLL-associated antigen KW-5
    RNA-binding region (RNP1, RRM) containing 1
    RNA-binding region-containing protein 1
    ssDNA-binding protein SEB4

    NCBI Reference Sequences (RefSeq)

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    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_001291780.2 → NP_001278709.1  RNA-binding protein 38 isoform c

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) represents the longest transcript and encodes the longest isoform (c).
      Source sequence(s)
      AL109955
      UniProtKB/Swiss-Prot
      Q9H0Z9
      Conserved Domains (2) summary
      TIGR01628
      Location:46 → 269
      PABP-1234; polyadenylate binding protein, human types 1, 2, 3, 4 family
      cd12384
      Location:34 → 141
      RRM_RBM24_RBM38_like; RNA recognition motif (RRM) found in eukaryotic RNA-binding protein RBM24, RBM38 and similar proteins

    2. NM_017495.6 → NP_059965.2  RNA-binding protein 38 isoform a

      See identical proteins and their annotated locations for NP_059965.2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) lacks an alternate in-frame exon in the 5' coding region, compared to variant 3, resulting in an isoform (a) that is shorter than isoform c.
      Source sequence(s)
      AL109955
      Consensus CDS
      CCDS46617.1
      UniProtKB/Swiss-Prot
      A6NDK1, A6NMU6, Q15350, Q15351, Q9BYK3, Q9BYK4, Q9H0Z9
      Related
      ENSP00000348538.5, ENST00000356208.10
      Conserved Domains (2) summary
      TIGR01628
      Location:46 → 237
      PABP-1234; polyadenylate binding protein, human types 1, 2, 3, 4 family
      cd12384
      Location:34 → 109
      RRM_RBM24_RBM38_like; RNA recognition motif (RRM) found in eukaryotic RNA-binding protein RBM24, RBM38 and similar proteins

    3. NM_183425.3 → NP_906270.1  RNA-binding protein 38 isoform b

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) lacks an alternate in-frame exon in the 5' coding region, and also lacks another exon that results in a frameshift in the 3' coding region, compared to variant 3. The encoded isoform (b) has a distinct C-terminus and is shorter than isoform c.
      Source sequence(s)
      AL109955
      Consensus CDS
      CCDS46618.1
      UniProtKB/Swiss-Prot
      Q9H0Z9
      Related
      ENSP00000407848.2, ENST00000440234.6
      Conserved Domains (1) summary
      cd12384
      Location:34 → 109
      RRM_RBM24_RBM38_like; RNA recognition motif (RRM) found in eukaryotic RNA-binding protein RBM24, RBM38 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_000020.11 Reference GRCh38.p14 Primary Assembly

      Range
      57391396..57409333
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011528885.4 → XP_011527187.1  RNA-binding protein 38 isoform X1

      Conserved Domains (1) summary
      cd12384
      Location:34 → 141
      RRM_RBM24_RBM38_like; RNA recognition motif in eukaryotic RNA-binding protein RBM24, RBM38 and similar proteins

    2. XM_005260446.5 → XP_005260503.1  RNA-binding protein 38 isoform X3

      Conserved Domains (1) summary
      cd12384
      Location:34 → 141
      RRM_RBM24_RBM38_like; RNA recognition motif in eukaryotic RNA-binding protein RBM24, RBM38 and similar proteins

    3. XM_047440258.1 → XP_047296214.1  RNA-binding protein 38 isoform X2

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060944.1 Alternate T2T-CHM13v2.0

      Range
      59169162..59187091
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054323628.1 → XP_054179603.1  RNA-binding protein 38 isoform X1

    2. XM_054323630.1 → XP_054179605.1  RNA-binding protein 38 isoform X3

    3. XM_054323629.1 → XP_054179604.1  RNA-binding protein 38 isoform X2

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9H0Z9.2 GenPept UniProtKB/Swiss-Prot:Q9H0Z9

    Gene LinkOut

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

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