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

    Gene ID: 19383, updated on 27-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
    • 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
    Molecular Biology Databases
    Research Materials
    Tools