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Aliases for RALY Gene

Aliases for RALY Gene

  • RALY Heterogeneous Nuclear Ribonucleoprotein 2 3 5
  • 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
  • Autoantigen P542 3 4
  • HNRPCL2 3 4
  • 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
  • RNA-Binding Protein Raly 3

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. 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 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

Additional gene information for RALY Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for RALY Gene

Genomics for RALY Gene

GeneHancer (GH) Regulatory Elements for RALY Gene

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
GH20J033991 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE dbSUPER 655.4 +0.4 401 4.5 HDGF PKNOX1 CLOCK SMAD1 MLX ZFP64 ARID4B SIN3A DMAP1 ZNF2 RALY RALY-AS1 ENSG00000228386 ENSG00000229188 BPIFB5P BPIFA3 ENSG00000224876 RPL12P3 SUN5 RPS2P1
GH20J033992 Enhancer 0.5 ENCODE 650.7 -1.9 -1936 0.2 POLR2A NFYB ELF1 SPI1 RALY RALY-AS1 PIGPP3
GH20J033731 Promoter/Enhancer 2.4 EPDnew FANTOM5 Ensembl ENCODE 18.9 -260.4 -260391 4 HDGF FOXA2 ARNT ARID4B SIN3A DMAP1 YBX1 ZNF2 YY1 SLC30A9 ZNF341 PIR41069 ENSG00000229188 CBFA2T2 RALY ZNF341-AS1 CDK5RAP1 ASIP
GH20J034110 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE dbSUPER 13.2 +118.2 118156 3.4 DMAP1 YY1 SLC30A9 ZNF213 E2F8 ZNF143 SP3 NFYC ZNF610 GLIS1 EIF2S2 ZNF341-AS1 NCOA6 TRPC4AP RALY CDK5RAP1 GGT7 CBFA2T2 MAP1LC3A MIR4755
GH20J033810 Promoter/Enhancer 2.6 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 10.6 -180.7 -180738 4.6 HDGF PKNOX1 FOXA2 MLX ARNT ZFP64 ARID4B SIN3A FEZF1 DMAP1 ZNF341-AS1 CHMP4B CDK5RAP1 RALY CBFA2T2 TPM3P2
- 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 UCSC Golden Path with GeneCards custom track

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

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.
    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 Lys216, Lys191, Lys165, posLast=5555, Lys44, and posLast=44
  • 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

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 --
GO:0005515 protein binding IPI 22720776
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

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

Subcellular locations from the

Human Protein Atlas (HPA)

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

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:0006351 transcription, DNA-templated IEA --
GO:0006355 regulation of transcription, DNA-templated IEA --
GO:0006397 mRNA processing IEA --
GO:0008380 RNA splicing IEA --
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

Unigene Clusters for RALY Gene

RNA binding protein, autoantigenic (hnRNP-associated with lethal yellow homolog (mouse)):
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

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

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
ECgene alternative splicing isoforms for
RALY

Expression for RALY Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP 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

NURSA nuclear receptor signaling pathways regulating expression of RALY Gene:

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(4.7)
  • Liver(4.3)
  • Blood(4.2)
  • Lung(2.8)
  • Skin(2.5)
  • Eye(2.3)
  • Intestine(2)
  • Muscle(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 34 33
  • 98.58 (n)
OneToOne
dog
(Canis familiaris)
Mammalia RALY 34 33
  • 91.24 (n)
OneToOne
cow
(Bos Taurus)
Mammalia RALY 34 33
  • 88.46 (n)
OneToOne
rat
(Rattus norvegicus)
Mammalia Raly 33
  • 85.75 (n)
mouse
(Mus musculus)
Mammalia Raly 16 34 33
  • 83.99 (n)
oppossum
(Monodelphis domestica)
Mammalia -- 34
  • 73 (a)
OneToMany
-- 34
  • 69 (a)
OneToMany
platypus
(Ornithorhynchus anatinus)
Mammalia -- 34
  • 26 (a)
ManyToMany
chicken
(Gallus gallus)
Aves RALY 34 33
  • 74.07 (n)
OneToOne
lizard
(Anolis carolinensis)
Reptilia RALY 34
  • 65 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia raly 33
  • 73.68 (n)
African clawed frog
(Xenopus laevis)
Amphibia Xl.20815 33
zebrafish
(Danio rerio)
Actinopterygii raly 34 33
  • 72.17 (n)
OneToOne
fruit fly
(Drosophila melanogaster)
Insecta CG42458 34
  • 12 (a)
OneToMany
Species where no ortholog for RALY was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya 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 squirt (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 from dbSNP and Humsavar for RALY Gene

SNP ID Clin Chr 20 pos Variation AA Info Type
rs1000008406 -- 33,994,227(+) A/G genic_upstream_transcript_variant, intron_variant
rs1000029934 -- 34,046,706(+) T/C intron_variant
rs1000063431 -- 34,063,153(+) C/T intron_variant
rs1000071032 -- 34,071,468(+) G/A intron_variant
rs1000124309 -- 34,072,490(+) T/C intron_variant

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

Additional Disease Information for RALY

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology

No disorders were found for RALY Gene.

No data available for MalaCards , 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 58
  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 22 58
  3. 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 58
  4. 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 44 58
  5. Global, in vivo, and site-specific phosphorylation dynamics in signaling networks. (PMID: 17081983) Olsen JV … Mann M (Cell 2006) 3 4 58

Products for RALY Gene

Sources for RALY Gene

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