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Raly hnRNP-associated with lethal yellow [ Mus musculus (house mouse) ]

Gene ID: 19383, updated on 2-Nov-2024

Summary

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Official Symbol
Ralyprovided by MGI
Official Full Name
hnRNP-associated with lethal yellowprovided by MGI
Primary source
MGI:MGI:97850
See related
Ensembl:ENSMUSG00000027593 AllianceGenome:MGI:97850
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Mus musculus
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Also known as
Merc
Summary
Enables RNA binding activity and transcription coregulator activity. Involved in cholesterol homeostasis and negative regulation of transcription by RNA polymerase II. Located in nucleus. Is expressed in central nervous system and sensory organ. Orthologous to human RALY (RALY heterogeneous nuclear ribonucleoprotein). [provided by Alliance of Genome Resources, Nov 2024]
Expression
Ubiquitous expression in ovary adult (RPKM 41.7), liver E14 (RPKM 41.0) and 28 other tissues See more
Orthologs
human all
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Genomic context

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See Raly in Genome Data Viewer
Location:
2 H1; 2 76.83 cM
Exon count:
14
Annotation release Status Assembly Chr Location
RS_2024_02 current GRCm39 (GCF_000001635.27) 2 NC_000068.8 (154632989..154712930)
108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 2 NC_000068.7 (154790920..154871010)

Chromosome 2 - NC_000068.8Genomic Context describing neighboring genes Neighboring gene predicted gene, 57835 Neighboring gene STARR-seq mESC enhancer starr_06133 Neighboring gene predicted gene, 38598 Neighboring gene STARR-positive B cell enhancer ABC_E1013 Neighboring gene ribosomal protein L7A pseudogene Neighboring gene STARR-positive B cell enhancer ABC_E7874 Neighboring gene eukaryotic translation initiation factor 2 subunit 2 beta Neighboring gene STARR-seq mESC enhancer starr_06136 Neighboring gene STARR-seq mESC enhancer starr_06137 Neighboring gene nonagouti Neighboring gene predicted gene, 39965

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: Mouse ENCODE transcriptome data Mouse ENCODE transcriptome data
  • Description: RNA profiling data sets generated by the Mouse ENCODE project.
  • BioProject: PRJNA66167
  • Publication: PMID 25409824
  • Analysis date: n/a

Bibliography

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Related articles in PubMed

  1. Collaborative interactions of heterogenous ribonucleoproteins contribute to transcriptional regulation of sterol metabolism in mice. Zhang Z, et al. Nat Commun, 2020 Feb 20. PMID 32080181, Free PMC Article
  2. Progressive obesity alters the steroidogenic response to ovulatory stimulation and increases the abundance of mRNAs stored in the ovulated oocyte. Pohlmeier WE, et al. Mol Reprod Dev, 2014 Aug. PMID 24824196
  3. Pleiotropic effects of the mouse lethal yellow (Ay) mutation explained by deletion of a maternally expressed gene and the simultaneous production of agouti fusion RNAs. Duhl DM, et al. Development, 1994 Jun. PMID 8050375
  4. A molecular model for the genetic and phenotypic characteristics of the mouse lethal yellow (Ay) mutation. Michaud EJ, et al. Proc Natl Acad Sci U S A, 1994 Mar 29. PMID 8146154, Free PMC Article
  5. Downregulation of a Dorsal Root Ganglion-Specifically Enriched Long Noncoding RNA is Required for Neuropathic Pain by Negatively Regulating RALY-Triggered Ehmt2 Expression. Pan Z, et al. Adv Sci (Weinh), 2021 Jul. PMID 34383386, Free PMC Article

See all (37) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Effects of the Combination of the C1473G Mutation in the Tph2 Gene and Lethal Yellow Mutations in the Raly-Agouti Locus on Behavior, Brain 5-HT and Melanocortin Systems in Mice.
    Title: Effects of the Combination of the C1473G Mutation in the Tph2 Gene and Lethal Yellow Mutations in the Raly-Agouti Locus on Behavior, Brain 5-HT and Melanocortin Systems in Mice.
  2. Downregulation of a Dorsal Root Ganglion-Specifically Enriched Long Noncoding RNA is Required for Neuropathic Pain by Negatively Regulating RALY-Triggered Ehmt2 Expression.
    Title: Downregulation of a Dorsal Root Ganglion-Specifically Enriched Long Noncoding RNA is Required for Neuropathic Pain by Negatively Regulating RALY-Triggered Ehmt2 Expression.
  3. Liver-specific deletion of RALY alters hepatic lipid content and serum cholesterol level. RALY binds the promoter region of the master metabolic regulator Srebp2 and show that it directly interacts with coactivator Nuclear Transcription Factor Y (NFY) to influence cholesterogenic gene expression.
    Title: Collaborative interactions of heterogenous ribonucleoproteins contribute to transcriptional regulation of sterol metabolism in mice.
Submit: New GeneRIF Correction

Variation

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Alleles

Alleles of this type are documented at Mouse Genome Informatics  (MGI)
  • Endonuclease-mediated (1) 
  • Gene trapped (1)  1 citation

Pathways from PubChem

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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 MGI

Function Evidence Code Pubs
enables RNA binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables RNA binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables transcription coregulator activity IMP
Inferred from Mutant Phenotype
more info
 PubMed 
Process Evidence Code Pubs
involved_in RNA splicing IEA
Inferred from Electronic Annotation
more info
  
involved_in cholesterol homeostasis IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in mRNA processing IEA
Inferred from Electronic Annotation
more info
  
involved_in negative regulation of transcription by RNA polymerase II IMP
Inferred from Mutant Phenotype
more info
 PubMed 
Component Evidence Code Pubs
part_of catalytic step 2 spliceosome IEA
Inferred from Electronic Annotation
more info
  
part_of catalytic step 2 spliceosome ISO
Inferred from Sequence Orthology
more info
  
is_active_in nucleus IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in nucleus IDA
Inferred from Direct Assay
more info
 PubMed 
located_in nucleus ISO
Inferred from Sequence Orthology
more info
  

General protein information

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Preferred Names
RNA-binding protein Raly
Names
hnRNP associated with lethal yellow protein
maternally-expressed hnRNP C-related protein

NCBI Reference Sequences (RefSeq)

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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_001139511.2 → NP_001132983.1  RNA-binding protein Raly short isoform

    See identical proteins and their annotated locations for NP_001132983.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) lacks an exon in the 5' coding region, compared to variant 1. It encodes a protein that is 16 amino acids shorter than the longest isoform.
    Source sequence(s)
    AL929024
    Consensus CDS
    CCDS16939.1
    UniProtKB/TrEMBL
    Q3TGD3, Q3U3F6
    Related
    ENSMUSP00000105323.4, ENSMUST00000109701.10
    Conserved Domains (1) summary
    cd12604
    Location:20 → 95
    RRM_RALY; RNA recognition motif (RRM) found in vertebrate RNA-binding protein Raly

  2. NM_001139512.2 → NP_001132984.1  RNA-binding protein Raly short isoform

    See identical proteins and their annotated locations for NP_001132984.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (4) has multiple differences in the 5' UTR and lacks an exon in the 5' coding region, compared to variant 1. It encodes a protein that is 16 amino acids shorter than the longest isoform.
    Source sequence(s)
    AL929024
    Consensus CDS
    CCDS16939.1
    UniProtKB/TrEMBL
    Q3TGD3, Q3U3F6
    Conserved Domains (1) summary
    cd12604
    Location:20 → 95
    RRM_RALY; RNA recognition motif (RRM) found in vertebrate RNA-binding protein Raly

  3. NM_001139513.2 → NP_001132985.1  RNA-binding protein Raly long isoform

    See identical proteins and their annotated locations for NP_001132985.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) encodes the longest isoform.
    Source sequence(s)
    AL929024
    Consensus CDS
    CCDS50767.1
    UniProtKB/Swiss-Prot
    A2AU63, Q64012, Q99K76, Q9CXH8, Q9QZX6
    UniProtKB/TrEMBL
    A2AU62
    Related
    ENSMUSP00000112090.3, ENSMUST00000116389.9
    Conserved Domains (1) summary
    cd12604
    Location:20 → 95
    RRM_RALY; RNA recognition motif (RRM) found in vertebrate RNA-binding protein Raly

  4. NM_001420806.1 → NP_001407735.1  RNA-binding protein Raly long isoform

    Status: VALIDATED

    Source sequence(s)
    AL929024
    UniProtKB/Swiss-Prot
    A2AU63, Q64012, Q99K76, Q9CXH8, Q9QZX6

  5. NM_001420807.1 → NP_001407736.1  RNA-binding protein Raly long isoform

    Status: VALIDATED

    Source sequence(s)
    AL929024
    UniProtKB/Swiss-Prot
    A2AU63, Q64012, Q99K76, Q9CXH8, Q9QZX6

  6. NM_001420808.1 → NP_001407737.1  RNA-binding protein Raly long isoform

    Status: VALIDATED

    Source sequence(s)
    AL929024
    UniProtKB/Swiss-Prot
    A2AU63, Q64012, Q99K76, Q9CXH8, Q9QZX6
    Related
    ENSMUSP00000029120.8, ENSMUST00000029120.14

  7. NM_001420809.1 → NP_001407738.1  RNA-binding protein Raly long isoform

    Status: VALIDATED

    Source sequence(s)
    AL929024
    UniProtKB/Swiss-Prot
    A2AU63, Q64012, Q99K76, Q9CXH8, Q9QZX6

  8. NM_001420810.1 → NP_001407739.1  RNA-binding protein Raly short isoform

    Status: VALIDATED

    Source sequence(s)
    AL929024
    UniProtKB/TrEMBL
    Q3U3F6

  9. NM_001420811.1 → NP_001407740.1  RNA-binding protein Raly short isoform

    Status: VALIDATED

    Source sequence(s)
    AL929024
    UniProtKB/TrEMBL
    Q3U3F6

  10. NM_001420812.1 → NP_001407741.1  RNA-binding protein Raly short isoform

    Status: VALIDATED

    Source sequence(s)
    AL929024
    UniProtKB/TrEMBL
    Q3U3F6

  11. NM_001420813.1 → NP_001407742.1  RNA-binding protein Raly short isoform

    Status: VALIDATED

    Source sequence(s)
    AL929024
    UniProtKB/TrEMBL
    Q3U3F6

  12. NM_001420814.1 → NP_001407743.1  RNA-binding protein Raly short isoform

    Status: VALIDATED

    Source sequence(s)
    AL929024
    UniProtKB/TrEMBL
    Q3U3F6

  13. NM_001420815.1 → NP_001407744.1  RNA-binding protein Raly isoform 3

    Status: VALIDATED

    Source sequence(s)
    AL929024

  14. NM_001420816.1 → NP_001407745.1  RNA-binding protein Raly isoform 3

    Status: VALIDATED

    Source sequence(s)
    AL929024

  15. NM_023130.4 → NP_075619.2  RNA-binding protein Raly short isoform

    See identical proteins and their annotated locations for NP_075619.2

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) has an additional exon in the 5' UTR and lacks an exon in the 5' coding region, compared to variant 1. It encodes a protein that is 16 amino acids shorter than the longest isoform.
    Source sequence(s)
    AL929024
    Consensus CDS
    CCDS16939.1
    UniProtKB/TrEMBL
    Q3TGD3, Q3U3F6
    Related
    ENSMUSP00000058105.7, ENSMUST00000058089.13
    Conserved Domains (1) summary
    cd12604
    Location:20 → 95
    RRM_RALY; RNA recognition motif (RRM) found in vertebrate RNA-binding protein Raly

RNA

  1. NR_185198.1 RNA Sequence

    Status: VALIDATED

    Source sequence(s)
    AL929024

  2. NR_185199.1 RNA Sequence

    Status: VALIDATED

    Source sequence(s)
    AL929024

RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCm39 C57BL/6J

Genomic

  1. NC_000068.8 Reference GRCm39 C57BL/6J

    Range
    154632989..154712930
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_036159726.1 → XP_036015619.1  RNA-binding protein Raly isoform X1

    UniProtKB/Swiss-Prot
    A2AU63, Q64012, Q99K76, Q9CXH8, Q9QZX6
    UniProtKB/TrEMBL
    A2AU62
    Conserved Domains (1) summary
    cd12604
    Location:20 → 95
    RRM_RALY; RNA recognition motif (RRM) found in vertebrate RNA-binding protein Raly
Nucleotide Protein Strain
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q64012.3 GenPept UniProtKB/Swiss-Prot:Q64012

Gene LinkOut

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

Chemical Information
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