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

    Gene ID: 19383, updated on 2-Oct-2018

    Summary

    Official Symbol
    Ralyprovided by MGI
    Official Full Name
    hnRNP-associated with lethal yellowprovided by MGI
    Primary source
    MGI:MGI:97850
    See related
    Ensembl:ENSMUSG00000027593 Vega:OTTMUSG00000015980
    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; AI663842
    Expression
    Ubiquitous expression in ovary adult (RPKM 41.7), liver E14 (RPKM 41.0) and 28 other tissues See more
    Orthologs

    Genomic context

    See Raly in Genome Data Viewer
    Location:
    2 H1; 2 76.83 cM
    Exon count:
    12
    Annotation release Status Assembly Chr Location
    106 current GRCm38.p4 (GCF_000001635.24) 2 NC_000068.7 (154791097..154871010)
    Build 37.2 previous assembly MGSCv37 (GCF_000001635.18) 2 NC_000068.6 (154616846..154692997)

    Chromosome 2 - NC_000068.7Genomic Context describing neighboring genes Neighboring gene predicted gene 14216 Neighboring gene predicted gene, 38598 Neighboring gene ribosomal protein L7A pseudogene Neighboring gene eukaryotic translation initiation factor 2, subunit 2 (beta) Neighboring gene nonagouti Neighboring gene predicted gene, 39965

    Genomic regions, transcripts, and products

    Expression

    • 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

    Variation

    Alleles

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

    Pathways from BioSystems

    • mRNA processing, organism-specific biosystem (from WikiPathways)
      mRNA processing, organism-specific biosystemAdapted from Reactome, see: [http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_1675.1 REACT 1675.1] This process describes the conversion of precursor messenger RNA into mature messenge...

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Homology

    Gene Ontology Provided by MGI

    Function Evidence Code Pubs
    RNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    RNA binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    nucleic acid binding IEA
    Inferred from Electronic Annotation
    more info
     
    transcription coregulator activity IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    Process Evidence Code Pubs
    RNA splicing IEA
    Inferred from Electronic Annotation
    more info
     
    cholesterol homeostasis IDA
    Inferred from Direct Assay
    more info
    PubMed 
    mRNA processing IEA
    Inferred from Electronic Annotation
    more info
     
    regulation of nucleic acid-templated transcription IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    Component Evidence Code Pubs
    catalytic step 2 spliceosome ISO
    Inferred from Sequence Orthology
    more info
     
    nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    nucleus IDA
    Inferred from Direct Assay
    more info
    PubMed 
    nucleus ISO
    Inferred from Sequence Orthology
    more info
     
    spliceosomal complex IEA
    Inferred from Electronic Annotation
    more info
     

    General protein information

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

    NCBI Reference Sequences (RefSeq)

    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_001139511.1NP_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 long isoform.
      Source sequence(s)
      AK135386, CF424086, CO812619
      Consensus CDS
      CCDS16939.1
      UniProtKB/Swiss-Prot
      Q64012
      UniProtKB/TrEMBL
      Q3U3F6
      Related
      ENSMUSP00000105323.3, OTTMUSP00000017056, ENSMUST00000109701.9, OTTMUST00000038029
      Conserved Domains (2) summary
      COG0724
      Location:12106
      RRM; RNA recognition motif (RRM) domain [Translation, ribosomal structure and biogenesis]
      cd12604
      Location:2095
      RRM_RALY; RNA recognition motif in vertebrate RNA-binding protein Raly
    2. NM_001139512.1NP_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 long isoform.
      Source sequence(s)
      BY028715, CF424086, CO812619, L17076
      Consensus CDS
      CCDS16939.1
      UniProtKB/Swiss-Prot
      Q64012
      UniProtKB/TrEMBL
      Q3U3F6
      Conserved Domains (2) summary
      COG0724
      Location:12106
      RRM; RNA recognition motif (RRM) domain [Translation, ribosomal structure and biogenesis]
      cd12604
      Location:2095
      RRM_RALY; RNA recognition motif in vertebrate RNA-binding protein Raly
    3. NM_001139513.1NP_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 longer isoform.
      Source sequence(s)
      CF424086, CO812619, CX214615, L17076
      Consensus CDS
      CCDS50767.1
      UniProtKB/Swiss-Prot
      Q64012
      Related
      ENSMUSP00000112090.2, ENSMUST00000116389.8
      Conserved Domains (2) summary
      COG0724
      Location:12113
      RRM; RNA recognition motif (RRM) domain [Translation, ribosomal structure and biogenesis]
      cd12604
      Location:2095
      RRM_RALY; RNA recognition motif in vertebrate RNA-binding protein Raly
    4. NM_023130.3NP_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 long isoform.
      Source sequence(s)
      AK014356, CF424086, CO812619
      Consensus CDS
      CCDS16939.1
      UniProtKB/Swiss-Prot
      Q64012
      UniProtKB/TrEMBL
      Q3U3F6
      Related
      ENSMUSP00000058105.6, OTTMUSP00000017055, ENSMUST00000058089.12, OTTMUST00000038028
      Conserved Domains (2) summary
      COG0724
      Location:12106
      RRM; RNA recognition motif (RRM) domain [Translation, ribosomal structure and biogenesis]
      cd12604
      Location:2095
      RRM_RALY; RNA recognition motif in vertebrate RNA-binding protein Raly

    RefSeqs of Annotated Genomes: Mus musculus Annotation Release 106

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

    Reference GRCm38.p4 C57BL/6J

    Genomic

    1. NC_000068.7 Reference GRCm38.p4 C57BL/6J

      Range
      154791097..154871010
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006499015.2XP_006499078.1  RNA-binding protein Raly isoform X1

      See identical proteins and their annotated locations for XP_006499078.1

      UniProtKB/Swiss-Prot
      Q64012
      Conserved Domains (2) summary
      COG0724
      Location:12113
      RRM; RNA recognition motif (RRM) domain [Translation, ribosomal structure and biogenesis]
      cd12604
      Location:2095
      RRM_RALY; RNA recognition motif in vertebrate RNA-binding protein Raly
    2. XM_006499014.3XP_006499077.1  RNA-binding protein Raly isoform X1

      See identical proteins and their annotated locations for XP_006499077.1

      UniProtKB/Swiss-Prot
      Q64012
      Conserved Domains (2) summary
      COG0724
      Location:12113
      RRM; RNA recognition motif (RRM) domain [Translation, ribosomal structure and biogenesis]
      cd12604
      Location:2095
      RRM_RALY; RNA recognition motif in vertebrate RNA-binding protein Raly
    3. XM_006499016.2XP_006499079.1  RNA-binding protein Raly isoform X2

      See identical proteins and their annotated locations for XP_006499079.1

      UniProtKB/Swiss-Prot
      Q64012
      UniProtKB/TrEMBL
      Q3U3F6
      Conserved Domains (2) summary
      COG0724
      Location:12106
      RRM; RNA recognition motif (RRM) domain [Translation, ribosomal structure and biogenesis]
      cd12604
      Location:2095
      RRM_RALY; RNA recognition motif in vertebrate RNA-binding protein Raly
    4. XM_006499013.3XP_006499076.1  RNA-binding protein Raly isoform X1

      See identical proteins and their annotated locations for XP_006499076.1

      UniProtKB/Swiss-Prot
      Q64012
      Related
      ENSMUSP00000029120.7, OTTMUSP00000017057, ENSMUST00000029120.13, OTTMUST00000038030
      Conserved Domains (2) summary
      COG0724
      Location:12113
      RRM; RNA recognition motif (RRM) domain [Translation, ribosomal structure and biogenesis]
      cd12604
      Location:2095
      RRM_RALY; RNA recognition motif in vertebrate RNA-binding protein Raly
    5. XM_017316631.1XP_017172120.1  RNA-binding protein Raly isoform X2

      UniProtKB/Swiss-Prot
      Q64012
      UniProtKB/TrEMBL
      Q3U3F6
      Conserved Domains (2) summary
      COG0724
      Location:12106
      RRM; RNA recognition motif (RRM) domain [Translation, ribosomal structure and biogenesis]
      cd12604
      Location:2095
      RRM_RALY; RNA recognition motif in vertebrate RNA-binding protein Raly
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