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

Gene ID: 19383, updated on 6-Jun-2024

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 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 regulation of nucleic acid-templated transcription. 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, Apr 2022]
Expression
Ubiquitous expression in ovary adult (RPKM 41.7), liver E14 (RPKM 41.0) and 28 other tissues See more
Orthologs
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Genomic context

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

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

Bibliography

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Variation

Alleles

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

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

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 nucleic acid binding IEA
Inferred from Electronic Annotation
more info
 
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
acts_upstream_of_or_within RNA splicing IEA
Inferred from Electronic Annotation
more info
 
involved_in cholesterol homeostasis IDA
Inferred from Direct Assay
more info
PubMed 
acts_upstream_of_or_within 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 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
 
part_of ribonucleoprotein complex IEA
Inferred from Electronic Annotation
more info
 
part_of 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)

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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_001139511.2NP_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:2095
    RRM_RALY; RNA recognition motif (RRM) found in vertebrate RNA-binding protein Raly
  2. NM_001139512.2NP_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:2095
    RRM_RALY; RNA recognition motif (RRM) found in vertebrate RNA-binding protein Raly
  3. NM_001139513.2NP_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:2095
    RRM_RALY; RNA recognition motif (RRM) found in vertebrate RNA-binding protein Raly
  4. NM_001420806.1NP_001407735.1  RNA-binding protein Raly long isoform

    Status: VALIDATED

    Source sequence(s)
    AL929024
    UniProtKB/Swiss-Prot
    A2AU63, Q64012, Q99K76, Q9CXH8, Q9QZX6
    UniProtKB/TrEMBL
    A2AU62
  5. NM_001420807.1NP_001407736.1  RNA-binding protein Raly long isoform

    Status: VALIDATED

    Source sequence(s)
    AL929024
    UniProtKB/Swiss-Prot
    A2AU63, Q64012, Q99K76, Q9CXH8, Q9QZX6
    UniProtKB/TrEMBL
    A2AU62
  6. NM_001420808.1NP_001407737.1  RNA-binding protein Raly long isoform

    Status: VALIDATED

    Source sequence(s)
    AL929024
    UniProtKB/Swiss-Prot
    A2AU63, Q64012, Q99K76, Q9CXH8, Q9QZX6
    UniProtKB/TrEMBL
    A2AU62
    Related
    ENSMUSP00000029120.8, ENSMUST00000029120.14
  7. NM_001420809.1NP_001407738.1  RNA-binding protein Raly long isoform

    Status: VALIDATED

    Source sequence(s)
    AL929024
    UniProtKB/Swiss-Prot
    A2AU63, Q64012, Q99K76, Q9CXH8, Q9QZX6
    UniProtKB/TrEMBL
    A2AU62
  8. NM_001420810.1NP_001407739.1  RNA-binding protein Raly short isoform

    Status: VALIDATED

    Source sequence(s)
    AL929024
    UniProtKB/TrEMBL
    Q3TGD3, Q3U3F6
  9. NM_001420811.1NP_001407740.1  RNA-binding protein Raly short isoform

    Status: VALIDATED

    Source sequence(s)
    AL929024
    UniProtKB/TrEMBL
    Q3TGD3, Q3U3F6
  10. NM_001420812.1NP_001407741.1  RNA-binding protein Raly short isoform

    Status: VALIDATED

    Source sequence(s)
    AL929024
    UniProtKB/TrEMBL
    Q3TGD3, Q3U3F6
  11. NM_001420813.1NP_001407742.1  RNA-binding protein Raly short isoform

    Status: VALIDATED

    Source sequence(s)
    AL929024
    UniProtKB/TrEMBL
    Q3TGD3, Q3U3F6
  12. NM_001420814.1NP_001407743.1  RNA-binding protein Raly short isoform

    Status: VALIDATED

    Source sequence(s)
    AL929024
    UniProtKB/TrEMBL
    Q3TGD3, Q3U3F6
  13. NM_001420815.1NP_001407744.1  RNA-binding protein Raly isoform 3

    Status: VALIDATED

    Source sequence(s)
    AL929024
  14. NM_001420816.1NP_001407745.1  RNA-binding protein Raly isoform 3

    Status: VALIDATED

    Source sequence(s)
    AL929024
  15. NM_023130.4NP_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:2095
    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_036159726.1XP_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:2095
    RRM_RALY; RNA recognition motif (RRM) found in vertebrate RNA-binding protein Raly