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] See more...

Aliases for RALY Gene

Aliases for RALY Gene

  • RALY Heterogeneous Nuclear Ribonucleoprotein 2 3 5
  • HNRPCL2 2 3 4
  • P542 2 3 4
  • RNA-Binding Protein (Autoantigenic, HnRNP-Associated With Lethal Yellow) 2 3
  • HnRNP Associated With Lethal Yellow Protein Homolog 3 4
  • Heterogeneous Nuclear Ribonucleoprotein C-Like 2 3 4
  • HnRNP Core Protein C-Like 2 3 4
  • RNA-Binding Protein Raly 3 4
  • Autoantigen P542 3 4
  • RNA Binding Protein, Autoantigenic (HnRNP-Associated With Lethal Yellow Homolog (Mouse)) 2
  • RNA Binding Protein, Autoantigenic (HnRNP-Associated With Lethal Yellow Homolog) 3
  • RNA-Binding Protein (Autoantigenic) 3
  • RALY 5

External Ids for RALY Gene

Previous GeneCards Identifiers for RALY Gene

  • GC20P032340
  • GC20P033250
  • GC20P033297
  • GC20P032045
  • GC20P032581
  • GC20P029366

Summaries for RALY Gene

Entrez Gene Summary for RALY Gene

  • 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]

GeneCards Summary for RALY Gene

RALY (RALY Heterogeneous Nuclear Ribonucleoprotein) is a Protein Coding gene. Diseases associated with RALY include Skin Carcinoma In Situ and Dermatosis Papulosa Nigra. Gene Ontology (GO) annotations related to this gene include nucleic acid binding and RNA binding. An important paralog of this gene is RALYL.

UniProtKB/Swiss-Prot Summary for RALY Gene

  • RNA-binding protein that acts as a transcriptional cofactor for cholesterol biosynthetic genes in the liver. Binds the lipid-responsive non-coding RNA LeXis and is required for LeXis-mediated effect on cholesterogenesis (By similarity). May be a heterogeneous nuclear ribonucleoprotein (hnRNP) (PubMed:9376072).

Gene Wiki entry for RALY Gene

No data available for CIViC Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for RALY Gene

Genomics for RALY Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for RALY Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH20J033992 Promoter/Enhancer 2.4 EPDnew Ensembl ENCODE CraniofacialAtlas dbSUPER 605.3 +0.5 455 5 SP1 CREB1 GATAD2A ATF7 PRDM10 ZNF629 TFE3 IKZF1 NFKBIZ ZNF692 RALY RALY-AS1 CDK5RAP1 ENSG00000272945 PIGU MAP1LC3A AHCY EIF2S2
GH20J034036 Enhancer 1.3 Ensembl ENCODE dbSUPER 16 +59.3 59255 37 CREB1 GATAD2A CTCF TEAD4 PRDM10 REST IKZF1 ZNF300 RELA ZIC2 RALY MAP1LC3A AHCY GSS MYH7B MIR4755 lnc-ASIP-1 EIF2S2
GH20J034334 Enhancer 1.1 Ensembl ENCODE 11.8 +343.0 342955 5.2 HNRNPL CREB1 GATAD2A SOX13 IKZF1 NFKBIZ KDM1A RCOR2 RXRB NR2C1 MAP1LC3A ITCH RALY TRPC4AP ZNF341-AS1 TP53INP2 PROCR NCOA6 RF00017-3557 ENSG00000234087
GH20J034890 Enhancer 1.2 Ensembl ENCODE dbSUPER 10.1 +897.6 897554 5.2 LEF1 IKZF1 JUND PRDM1 MTA2 PKNOX1 MTA1 BRD9 ZNF24 DPF2 CPNE1 RBM39 RBM12 PIGU NCOA6 TRPC4AP RPL36P4 ERGIC3 RALY MAP1LC3A
GH20J034022 Enhancer 0.9 ENCODE dbSUPER 12.4 +28.9 28935 0.9 CTCF RXRB RAD21 IKZF2 TRIM22 PKNOX1 EED U2AF2 SMC3 RBM22 NCOA6 RALY CDK5RAP1 ZNF341-AS1 CBFA2T2 MAP1LC3A L13714-279 MIR4755 EIF2S2
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around RALY on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for RALY

Top Transcription factor binding sites by QIAGEN in the RALY gene promoter:
  • Nkx2-5
  • POU2F1a
  • Spz1
  • STAT3

Genomic Locations for RALY Gene

Genomic Locations for RALY Gene
chr20:33,993,646-34,108,308
(GRCh38/hg38)
Size:
114,663 bases
Orientation:
Plus strand
chr20:32,581,452-32,696,114
(GRCh37/hg19)
Size:
114,663 bases
Orientation:
Plus strand

Genomic View for RALY Gene

Genes around RALY on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
RALY Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for RALY Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for RALY Gene

Proteins for RALY Gene

  • Protein details for RALY Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9UKM9-RALY_HUMAN
    Recommended name:
    RNA-binding protein Raly
    Protein Accession:
    Q9UKM9
    Secondary Accessions:
    • Q14621
    • Q2M365
    • Q5QPL8
    • Q9BQX6
    • Q9UJE3

    Protein attributes for RALY Gene

    Size:
    306 amino acids
    Molecular mass:
    32463 Da
    Quaternary structure:
    • Identified in the spliceosome C complex (PubMed:11991638). Interacts (through its RNA-binding domain) with FUS (through its RNA-binding domain); both are components of the same RNPs (PubMed:30354839).
    Miscellaneous:
    • Autoantigen found in infectious mononucleosis caused by Epstein-Barr virus. An epitope recognized by B-cells, which cross-react with the BKRF1 protein (EBNA-1 nuclear protein) of Epstein-Barr virus has been identified.

    Three dimensional structures from OCA and Proteopedia for RALY Gene

    Alternative splice isoforms for RALY Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for RALY Gene

Post-translational modifications for RALY Gene

  • Ubiquitination at Lys4, Lys44, Lys55, Lys165, Lys191, and Lys216
  • Modification sites at PhosphoSitePlus

No data available for DME Specific Peptides for RALY Gene

Domains & Families for RALY Gene

Gene Families for RALY Gene

HGNC:
Human Protein Atlas (HPA):
  • Plasma proteins
  • Predicted intracellular proteins

Protein Domains for RALY Gene

InterPro:
Blocks:
  • RNA-binding region RNP-1 (RNA recognition motif)
ProtoNet:

Suggested Antigen Peptide Sequences for RALY Gene

GenScript: Design optimal peptide antigens:
  • cDNA FLJ77422, highly similar to Homo sapiens RNA binding protein, autoantigenic (hnRNP-associated with lethal yellow homolog (mouse)), transcript variant 1, mRNA (Q53GL6_HUMAN)
  • hnRNP associated with lethal yellow protein homolog (RALY_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q9UKM9

UniProtKB/Swiss-Prot:

RALY_HUMAN :
  • Belongs to the RRM HNRPC family. RALY subfamily.
Family:
  • Belongs to the RRM HNRPC family. RALY subfamily.
genes like me logo Genes that share domains with RALY: view

Function for RALY Gene

Molecular function for RALY Gene

UniProtKB/Swiss-Prot Function:
RNA-binding protein that acts as a transcriptional cofactor for cholesterol biosynthetic genes in the liver. Binds the lipid-responsive non-coding RNA LeXis and is required for LeXis-mediated effect on cholesterogenesis (By similarity). May be a heterogeneous nuclear ribonucleoprotein (hnRNP) (PubMed:9376072).

Phenotypes From GWAS Catalog for RALY Gene

Gene Ontology (GO) - Molecular Function for RALY Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003676 nucleic acid binding IEA --
GO:0003712 transcription coregulator activity IEA,ISS --
GO:0003723 RNA binding IEA,IBA 21873635
GO:0005515 protein binding IPI 22365833
genes like me logo Genes that share ontologies with RALY: view
genes like me logo Genes that share phenotypes with RALY: view

Animal Model Products

CRISPR Products

miRNA for RALY Gene

miRTarBase miRNAs that target RALY

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for RALY

Clone Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for RALY Gene

Localization for RALY Gene

Subcellular locations from UniProtKB/Swiss-Prot for RALY Gene

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for RALY gene
Compartment Confidence
nucleus 5
plasma membrane 1
extracellular 1
cytoskeleton 1
mitochondrion 1
endoplasmic reticulum 1
cytosol 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Nucleoplasm (4)
  • Vesicles (4)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for RALY Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus TAS,IDA 22720776
GO:0005681 spliceosomal complex IEA --
GO:0071013 catalytic step 2 spliceosome IDA 11991638
genes like me logo Genes that share ontologies with RALY: view

Pathways & Interactions for RALY Gene

PathCards logo

SuperPathways for RALY Gene

No Data Available

Gene Ontology (GO) - Biological Process for RALY Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000398 mRNA splicing, via spliceosome IC 11991638
GO:0006397 mRNA processing IEA --
GO:0008380 RNA splicing IEA --
GO:0042632 cholesterol homeostasis IEA,ISS --
GO:1903506 regulation of nucleic acid-templated transcription IEA,ISS --
genes like me logo Genes that share ontologies with RALY: view

No data available for Pathways by source and SIGNOR curated interactions for RALY Gene

Drugs & Compounds for RALY Gene

No Compound Related Data Available

Transcripts for RALY Gene

mRNA/cDNA for RALY Gene

2 REFSEQ mRNAs :
12 NCBI additional mRNA sequence :
10 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for RALY

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for RALY Gene

ExUns: 1a · 1b · 1c ^ 2 ^ 3 ^ 4 ^ 5a · 5b ^ 6a · 6b ^ 7a · 7b · 7c ^ 8a · 8b · 8c ^ 9a · 9b ^ 10a · 10b · 10c ^ 11a · 11b · 11c · 11d · 11e ^
SP1: - - - - - - -
SP2: - - - - -
SP3: - - - - - - - -
SP4: - - - - - - - - -
SP5: - -
SP6: - -
SP7: - - - - - - - - - -
SP8: - - - - -
SP9: - - -
SP10: - - - - - - -
SP11: - - -
SP12:
SP13:
SP14:

ExUns: 12a · 12b ^ 13 ^ 14 ^ 15
SP1:
SP2:
SP3:
SP4:
SP5:
SP6:
SP7:
SP8:
SP9:
SP10:
SP11:
SP12:
SP13:
SP14:

Relevant External Links for RALY Gene

GeneLoc Exon Structure for
RALY

Expression for RALY Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for RALY Gene

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for RALY Gene



Protein tissue co-expression partners for RALY Gene

- Elite partner

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for RALY

SOURCE GeneReport for Unigene cluster for RALY Gene:

Hs.136947

mRNA Expression by UniProt/SwissProt for RALY Gene:

Q9UKM9-RALY_HUMAN
Tissue specificity: Expressed in heart, brain, lung, liver, skeletal muscle, kidney and pancreas. Weakly expressed in placenta.

Evidence on tissue expression from TISSUES for RALY Gene

  • Nervous system(4.8)
  • Liver(4.5)
  • Blood(4.4)
  • Skin(3.1)
  • Lung(2.8)
  • Intestine(2.6)
  • Muscle(2.4)
  • Eye(2.3)
  • Lymph node(2.3)
  • Heart(2.3)
  • Kidney(2.1)
  • Spleen(2)
genes like me logo Genes that share expression patterns with RALY: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues , Protein differential expression in normal tissues and Phenotype-based relationships between genes and organs from Gene ORGANizer for RALY Gene

Orthologs for RALY Gene

This gene was present in the common ancestor of animals.

Orthologs for RALY Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
Mammalia RALY 30 31
  • 98.58 (n)
OneToOne
Dog
(Canis familiaris)
Mammalia RALY 30 31
  • 91.24 (n)
OneToOne
Cow
(Bos Taurus)
Mammalia RALY 30 31
  • 88.46 (n)
OneToOne
Rat
(Rattus norvegicus)
Mammalia Raly 30
  • 85.75 (n)
Mouse
(Mus musculus)
Mammalia Raly 30 17 31
  • 83.99 (n)
OneToOne
Oppossum
(Monodelphis domestica)
Mammalia -- 31
  • 73 (a)
OneToMany
-- 31
  • 69 (a)
OneToMany
Platypus
(Ornithorhynchus anatinus)
Mammalia -- 31
  • 26 (a)
ManyToMany
Chicken
(Gallus gallus)
Aves RALY 30 31
  • 74.07 (n)
OneToOne
Lizard
(Anolis carolinensis)
Reptilia RALY 31
  • 65 (a)
OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia raly 30
  • 73.68 (n)
African clawed frog
(Xenopus laevis)
Amphibia Xl.20815 30
Zebrafish
(Danio rerio)
Actinopterygii raly 30 31
  • 72.17 (n)
OneToOne
Fruit Fly
(Drosophila melanogaster)
Insecta CG42458 31
  • 12 (a)
OneToMany
Species where no ortholog for RALY was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • Alpha proteobacteria (Wolbachia pipientis)
  • Amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • Baker's yeast (Saccharomyces cerevisiae)
  • Barley (Hordeum vulgare)
  • Beta proteobacteria (Neisseria meningitidis)
  • Bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • Common water flea (Daphnia pulex)
  • Corn (Zea mays)
  • E. coli (Escherichia coli)
  • Filamentous fungi (Aspergillus nidulans)
  • Firmicute Bacteria (Streptococcus pneumoniae)
  • Fission Yeast (Schizosaccharomyces pombe)
  • Green Algae (Chlamydomonas reinhardtii)
  • Honey Bee (Apis mellifera)
  • K. Lactis Yeast (Kluyveromyces lactis)
  • Loblloly Pine (Pinus taeda)
  • Malaria Parasite (Plasmodium falciparum)
  • Medicago Trunc (Medicago Truncatula)
  • Moss (Physcomitrella patens)
  • Orangutan (Pongo pygmaeus)
  • Pig (Sus scrofa)
  • Rainbow Trout (Oncorhynchus mykiss)
  • Rice (Oryza sativa)
  • Rice Blast Fungus (Magnaporthe grisea)
  • Schistosome Parasite (Schistosoma mansoni)
  • Sea Anemone (Nematostella vectensis)
  • Sea Vase (Ciona intestinalis)
  • Sea Squirt (Ciona savignyi)
  • Sea Urchin (Strongylocentrotus purpuratus)
  • Sorghum (Sorghum bicolor)
  • Soybean (Glycine max)
  • Stem Rust Fungus (Puccinia graminis)
  • Sugarcane (Saccharum officinarum)
  • Thale Cress (Arabidopsis thaliana)
  • Tomato (Lycopersicon esculentum)
  • Toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • Wheat (Triticum aestivum)
  • Worm (Caenorhabditis elegans)

Evolution for RALY Gene

ENSEMBL:
Gene Tree for RALY (if available)
TreeFam:
Gene Tree for RALY (if available)
Aminode:
Evolutionary constrained regions (ECRs) for RALY: view image

Paralogs for RALY Gene

Paralogs for RALY Gene

(16) SIMAP similar genes for RALY Gene using alignment to 7 proteins:

  • RALY_HUMAN
  • L8E7Y8_HUMAN
  • Q53GL6_HUMAN
  • Q5QPL9_HUMAN
  • Q5QPM0_HUMAN
  • Q5QPM1_HUMAN
  • Q5QPM2_HUMAN
genes like me logo Genes that share paralogs with RALY: view

Variants for RALY Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for RALY Gene

SNP ID Clinical significance and condition Chr 20 pos Variation AA Info Type
747105 Benign: not provided 34,077,074(+) T/C SYNONYMOUS_VARIANT
786970 Benign: not provided 34,075,911(+) G/A MISSENSE_VARIANT
rs2281209 - p.Gly251Ser
rs3180568 - p.Gln215Arg
rs35191085 - p.Val139Met

Additional dbSNP identifiers (rs#s) for RALY Gene

Structural Variations from Database of Genomic Variants (DGV) for RALY Gene

Variant ID Type Subtype PubMed ID
nsv979429 CNV duplication 23825009

Variation tolerance for RALY Gene

Residual Variation Intolerance Score: 76.4% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 5.17; 69.57% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for RALY Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
RALY

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for RALY Gene

Disorders for RALY Gene

MalaCards: The human disease database

(3) MalaCards diseases for RALY Gene - From: DISEASES

Disorder Aliases PubMed IDs
skin carcinoma in situ
  • carcinoma in situ of skin
dermatosis papulosa nigra
fanconi anemia, complementation group a
  • fanca
- elite association - COSMIC cancer census association via MalaCards
Search RALY in MalaCards View complete list of genes associated with diseases

Additional Disease Information for RALY

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
Open Targets Platform
genes like me logo Genes that share disorders with RALY: view

No data available for UniProtKB/Swiss-Prot and Genatlas for RALY Gene

Publications for RALY Gene

  1. Alternative processing of the human and mouse raly genes(1). (PMID: 10500250) Khrebtukova I … Michaud EJ (Biochimica et biophysica acta 1999) 2 3 4
  2. The p542 gene encodes an autoantigen that cross-reacts with EBNA-1 of the Epstein Barr virus and which may be a heterogeneous nuclear ribonucleoprotein. (PMID: 9376072) Rhodes GH … Vaughan JH (Journal of autoimmunity 1997) 3 4 23
  3. The hnRNP RALY regulates PRMT1 expression and interacts with the ALS-linked protein FUS: implication for reciprocal cellular localization. (PMID: 30354839) Gasperini L … Macchi P (Molecular biology of the cell 2018) 3 4
  4. Proteome-wide characterization of the RNA-binding protein RALY-interactome using the in vivo-biotinylation-pulldown-quant (iBioPQ) approach. (PMID: 23614458) Tenzer S … Macchi P (Journal of proteome research 2013) 2 3
  5. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. (PMID: 20379614) Rose JE … Uhl GR (Molecular medicine (Cambridge, Mass.) 2010) 3 41

Products for RALY Gene

Sources for RALY Gene