U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

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

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

Summary

Go to the top of the page Help
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
NEW
Try the new Gene table
Try the new Transcript table

Genomic context

Go to the top of the page Help
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

Go to the top of the page Help

Go to nucleotide: Graphics FASTA GenBank

Expression

Go to the top of the page Help
  • 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

Go to the top of the pageHelp

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

Go to the top of the page Help

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

Go to the top of the page Help

See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Interactions

Go to the top of the page Help
Products Interactant Other Gene Complex Source Pubs Description

General gene information

Go to the top of the page Help

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

Go to the top of the page Help
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)

Go to the top of the page Help

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.

Chemical Information
Molecular Biology Databases
Research Materials
Tools
Miscellaneous