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    RALY RALY heterogeneous nuclear ribonucleoprotein [ Homo sapiens (human) ]

    Gene ID: 22913, updated on 7-Apr-2024

    Summary

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    Official Symbol
    RALYprovided by HGNC
    Official Full Name
    RALY heterogeneous nuclear ribonucleoproteinprovided by HGNC
    Primary source
    HGNC:HGNC:15921
    See related
    Ensembl:ENSG00000125970 MIM:614663; AllianceGenome:HGNC:15921
    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
    P542; HNRPCL2
    Summary
    This gene encodes a member of the heterogeneous nuclear ribonucleoprotein (hnRNP) gene family. This protein may play a role in pre-mRNA splicing and in embryonic development. Alternate splicing results in multiple transcript variants. [provided by RefSeq, Sep 2011]
    Expression
    Ubiquitous expression in bone marrow (RPKM 18.7), testis (RPKM 18.3) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See RALY in Genome Data Viewer
    Location:
    20q11.22
    Exon count:
    12
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 20 NC_000020.11 (33993911..34084884)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 20 NC_060944.1 (35720262..35811292)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 20 NC_000020.10 (32581717..32672690)

    Chromosome 20 - NC_000020.11Genomic Context describing neighboring genes Neighboring gene ReSE screen-validated silencer GRCh37_chr20:32507904-32508103 Neighboring gene tropomyosin 3 pseudogene 2 Neighboring gene H3K27ac hESC enhancer GRCh37_chr20:32521004-32521504 Neighboring gene phosphatidylinositol glycan anchor biosynthesis class P pseudogene 3 Neighboring gene H3K27ac hESC enhancer GRCh37_chr20:32580634-32581160 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12828 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12829 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12831 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12830 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:32586597-32587097 Neighboring gene RALY antisense RNA 1 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr20:32598140-32598817 Neighboring gene Sharpr-MPRA regulatory region 13564 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr20:32633616-32634424 Neighboring gene microRNA 4755 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr20:32664206-32665405 Neighboring gene eukaryotic translation initiation factor 2 subunit beta Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:32698990-32699652 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:32699653-32700314 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17755 Neighboring gene ribosomal protein S2 pseudogene 1

    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. RALY regulate the proliferation and expression of immune/inflammatory response genes via alternative splicing of FOS. Liang Z, et al. Genes Immun, 2022 Dec. PMID 35941292, Free PMC Article
    2. RNA-binding protein RALY reprogrammes mitochondrial metabolism via mediating miRNA processing in colorectal cancer. Sun L, et al. Gut, 2021 Sep. PMID 33219048, Free PMC Article
    3. RALY may cause an aggressive biological behavior and a dismal prognosis in non-small-cell lung cancer. Song G, et al. Exp Cell Res, 2020 Apr 15. PMID 32014444
    4. Identification and dynamic changes of RNAs isolated from RALY-containing ribonucleoprotein complexes. Rossi A, et al. Nucleic Acids Res, 2017 Jun 20. PMID 28379492, Free PMC Article
    5. Proteome-wide characterization of the RNA-binding protein RALY-interactome using the in vivo-biotinylation-pulldown-quant (iBioPQ) approach. Tenzer S, et al. J Proteome Res, 2013 Jun 7. PMID 23614458

    See all (152) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. SUMOylation of RALY promotes vasculogenic mimicry in glioma cells via the FOXD1/DKK1 pathway.
      Title: SUMOylation of RALY promotes vasculogenic mimicry in glioma cells via the FOXD1/DKK1 pathway.
    2. The RNA binding protein RALY suppresses p53 activity and promotes lung tumorigenesis.
      Title: The RNA binding protein RALY suppresses p53 activity and promotes lung tumorigenesis.
    3. RALY regulate the proliferation and expression of immune/inflammatory response genes via alternative splicing of FOS.
      Title: RALY regulate the proliferation and expression of immune/inflammatory response genes via alternative splicing of FOS.
    4. RNA binding protein RALY activates the cholesterol synthesis pathway through an MTA1 splicing switch in hepatocellular carcinoma.
      Title: RNA binding protein RALY activates the cholesterol synthesis pathway through an MTA1 splicing switch in hepatocellular carcinoma.
    5. RNA-binding protein RALY reprogrammes mitochondrial metabolism via mediating miRNA processing in colorectal cancer.
      Title: RNA-binding protein RALY reprogrammes mitochondrial metabolism via mediating miRNA processing in colorectal cancer.
    6. RALYL increases hepatocellular carcinoma stemness by sustaining the mRNA stability of TGF-beta2.
      Title: RALYL increases hepatocellular carcinoma stemness by sustaining the mRNA stability of TGF-β2.
    7. RALY may cause an aggressive biological behavior and a dismal prognosis in non-small-cell lung cancer.
      Title: RALY may cause an aggressive biological behavior and a dismal prognosis in non-small-cell lung cancer.
    8. RALY regulates PRMT1 expression and interacts with the amyotrophic lateral sclerosis-linked protein FUS.
      Title: The hnRNP RALY regulates PRMT1 expression and interacts with the ALS-linked protein FUS: implication for reciprocal cellular localization.
    9. hnRNP RALY regulates
      Title: The hnRNP RALY regulates transcription and cell proliferation by modulating the expression of specific factors including the proliferation marker E2F1.
    10. RALY promotes Protein Arginine Methyltransferase 1 alternatively spliced isoform v2 relative expression and metastatic potential in breast cancer cells
      Title: RNA binding protein RALY promotes Protein Arginine Methyltransferase 1 alternatively spliced isoform v2 relative expression and metastatic potential in breast cancer cells.
    Submit: New GeneRIF Correction See all GeneRIFs (13)

    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
    A meta-analysis of genome-wide association studies of breast cancer identifies two novel susceptibility loci at 6q14 and 20q11.
    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)

    Genotypes

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • MGC117312

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    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 
    enables transcription coregulator activity ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    Process Evidence Code Pubs
    involved_in cholesterol homeostasis ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in mRNA splicing, via spliceosome IC
    Inferred by Curator
    more info
    		 PubMed 
    involved_in negative regulation of transcription by RNA polymerase II ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    Component Evidence Code Pubs
    part_of catalytic step 2 spliceosome 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 Raly
    Names
    RNA binding protein, autoantigenic (hnRNP-associated with lethal yellow homolog)
    RNA-binding protein (autoantigenic)
    RNA-binding protein (autoantigenic, hnRNP-associated with lethal yellow)
    autoantigen p542
    heterogeneous nuclear ribonucleoprotein C-like 2
    hnRNP associated with lethal yellow protein homolog
    hnRNP core protein C-like 2

    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_007367.4 → NP_031393.2  RNA-binding protein Raly isoform 2

      See identical proteins and their annotated locations for NP_031393.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) lacks an in-frame exon in the coding region, compared to variant 1. The encoded isoform (2) is shorter than isoform 1. This isoform is also known as short isoform.
      Source sequence(s)
      AK226085, AL031668, BM680768
      Consensus CDS
      CCDS13229.1
      UniProtKB/TrEMBL
      A8K4T9
      Related
      ENSP00000364255.3, ENST00000375114.7
      Conserved Domains (2) summary
      COG0724
      Location:12 → 106
      RRM; RNA recognition motif (RRM) domain [Translation, ribosomal structure and biogenesis]
      cd12604
      Location:20 → 95
      RRM_RALY; RNA recognition motif in vertebrate RNA-binding protein Raly

    2. NM_016732.3 → NP_057951.1  RNA-binding protein Raly isoform 1

      See identical proteins and their annotated locations for NP_057951.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1). This isoform is also known as long isoform.
      Source sequence(s)
      AK222915, AL031668, BG751407, BM680768
      Consensus CDS
      CCDS13230.1
      UniProtKB/Swiss-Prot
      Q14621, Q2M365, Q5QPL8, Q9BQX6, Q9UJE3, Q9UKM9
      UniProtKB/TrEMBL
      A8K4T9
      Related
      ENSP00000246194.3, ENST00000246194.8
      Conserved Domains (1) summary
      cd12604
      Location:20 → 95
      RRM_RALY; RNA recognition motif in vertebrate RNA-binding protein Raly

    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_000020.11 Reference GRCh38.p14 Primary Assembly

      Range
      33993911..34084884
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011528695.4 → XP_011526997.1  RNA-binding protein Raly isoform X1

      See identical proteins and their annotated locations for XP_011526997.1

      UniProtKB/Swiss-Prot
      Q14621, Q2M365, Q5QPL8, Q9BQX6, Q9UJE3, Q9UKM9
      UniProtKB/TrEMBL
      A8K4T9
      Conserved Domains (1) summary
      cd12604
      Location:20 → 95
      RRM_RALY; RNA recognition motif in vertebrate RNA-binding protein Raly

    2. XM_005260334.6 → XP_005260391.1  RNA-binding protein Raly isoform X1

      See identical proteins and their annotated locations for XP_005260391.1

      UniProtKB/Swiss-Prot
      Q14621, Q2M365, Q5QPL8, Q9BQX6, Q9UJE3, Q9UKM9
      UniProtKB/TrEMBL
      A8K4T9
      Conserved Domains (1) summary
      cd12604
      Location:20 → 95
      RRM_RALY; RNA recognition motif in vertebrate RNA-binding protein Raly

    3. XM_017027731.3 → XP_016883220.1  RNA-binding protein Raly isoform X1

      UniProtKB/Swiss-Prot
      Q14621, Q2M365, Q5QPL8, Q9BQX6, Q9UJE3, Q9UKM9
      UniProtKB/TrEMBL
      A8K4T9
      Conserved Domains (1) summary
      cd12604
      Location:20 → 95
      RRM_RALY; RNA recognition motif in vertebrate RNA-binding protein Raly

    4. XM_005260336.6 → XP_005260393.1  RNA-binding protein Raly isoform X2

      See identical proteins and their annotated locations for XP_005260393.1

      UniProtKB/TrEMBL
      A8K4T9
      Conserved Domains (2) summary
      COG0724
      Location:12 → 106
      RRM; RNA recognition motif (RRM) domain [Translation, ribosomal structure and biogenesis]
      cd12604
      Location:20 → 95
      RRM_RALY; RNA recognition motif in vertebrate RNA-binding protein Raly

    5. XM_047440016.1 → XP_047295972.1  RNA-binding protein Raly isoform X2

      Related
      ENSP00000415973.1, ENST00000442805.1

    6. XM_047440015.1 → XP_047295971.1  RNA-binding protein Raly isoform X1

      UniProtKB/Swiss-Prot
      Q14621, Q2M365, Q5QPL8, Q9BQX6, Q9UJE3, Q9UKM9

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060944.1 Alternate T2T-CHM13v2.0

      Range
      35720262..35811292
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054323201.1 → XP_054179176.1  RNA-binding protein Raly isoform X1

      UniProtKB/TrEMBL
      Q53GL6

    2. XM_054323199.1 → XP_054179174.1  RNA-binding protein Raly isoform X1

      UniProtKB/TrEMBL
      Q53GL6

    3. XM_054323200.1 → XP_054179175.1  RNA-binding protein Raly isoform X1

      UniProtKB/TrEMBL
      Q53GL6

    4. XM_054323203.1 → XP_054179178.1  RNA-binding protein Raly isoform X2

    5. XM_054323202.1 → XP_054179177.1  RNA-binding protein Raly isoform X1

      UniProtKB/TrEMBL
      Q53GL6
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9UKM9.1 GenPept UniProtKB/Swiss-Prot:Q9UKM9

    Gene LinkOut

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

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