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    Lin54 lin-54 DREAM MuvB core complex component [ Rattus norvegicus (Norway rat) ]

    Gene ID: 305171, updated on 9-Dec-2024

    Summary

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    Official Symbol
    Lin54provided by RGD
    Official Full Name
    lin-54 DREAM MuvB core complex componentprovided by RGD
    Primary source
    RGD:1311361
    See related
    EnsemblRapid:ENSRNOG00000002203 AllianceGenome:RGD:1311361
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Rattus norvegicus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
    Also known as
    RGD1311361
    Summary
    Predicted to enable minor groove of adenine-thymine-rich DNA binding activity and transcription regulatory region nucleic acid binding activity. Predicted to be involved in regulation of DNA-templated transcription. Predicted to act upstream of or within nucleosome organization. Predicted to be part of RNA polymerase II transcription repressor complex. Predicted to be active in nucleus. Orthologous to human LIN54 (lin-54 DREAM MuvB core complex component). [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Biased expression in Thymus (RPKM 88.5), Spleen (RPKM 65.8) and 9 other tissues See more
    Orthologs
    human mouse all
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    Genomic context

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    See Lin54 in Genome Data Viewer
    Location:
    14p22
    Exon count:
    20
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 14 NC_086032.1 (9434093..9514091)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 14 NC_051349.1 (9129775..9188244)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 14 NC_005113.4 (10770072..10828115)

    Chromosome 14 - NC_086032.1Genomic Context describing neighboring genes Neighboring gene COP9 signalosome subunit 4 Neighboring gene uncharacterized LOC102550950 Neighboring gene SEC31 homolog A, COPII coat complex component Neighboring gene transfer RNA serine (anticodon AGA) 37

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
    • Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
    • BioProject: PRJNA238328
    • Publication: PMID 24510058
    • Analysis date: Mon Jun 6 17:44:12 2016

    Bibliography

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    Related articles in PubMed

    1. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Strausberg RL, et al. Proc Natl Acad Sci U S A, 2002 Dec 24. PMID 12477932, Free PMC Article
    2. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, et al. Brief Bioinform, 2011 Sep. PMID 21873635, Free PMC Article

    GeneRIFs: Gene References Into Functions

    Pathways from PubChem

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    General gene information

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    Markers

    Homology

    Gene Ontology Provided by RGD

    Function Evidence Code Pubs
    enables DNA binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables minor groove of adenine-thymine-rich DNA binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables minor groove of adenine-thymine-rich DNA binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables transcription regulatory region nucleic acid binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables transcription regulatory region nucleic acid binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    Process Evidence Code Pubs
    involved_in nucleosome organization IEA
    Inferred from Electronic Annotation
    more info
    		  
    acts_upstream_of_or_within nucleosome organization ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in regulation of DNA-templated transcription IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Component Evidence Code Pubs
    part_of RNA polymerase II transcription repressor complex IEA
    Inferred from Electronic Annotation
    more info
    		  
    part_of RNA polymerase II transcription repressor complex ISO
    Inferred from Sequence Orthology
    more info
    		  
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in nucleus IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    protein lin-54 homolog

    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_001100564.2 → NP_001094034.1  protein lin-54 homolog isoform 1

      See identical proteins and their annotated locations for NP_001094034.1

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000014
      UniProtKB/Swiss-Prot
      Q4FZV6, Q641Z1
      UniProtKB/TrEMBL
      A0A8L2Q0T4, A6K5Z8
      Related
      ENSRNOP00000096414.2, ENSRNOT00000102075.2
      Conserved Domains (1) summary
      pfam03638
      Location:596 → 631
      TCR; Tesmin/TSO1-like CXC domain, cysteine-rich domain

    2. NM_001428575.1 → NP_001415504.1  protein lin-54 homolog isoform 2

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000014
      UniProtKB/TrEMBL
      A0A8I6G8M1

    3. NM_001428576.1 → NP_001415505.1  protein lin-54 homolog isoform 3

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000014
      UniProtKB/TrEMBL
      A6K600

    4. NM_001428577.1 → NP_001415506.1  protein lin-54 homolog isoform 4

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000014
      UniProtKB/TrEMBL
      A0A8I5ZJ81, A0A8L2Q0T4

    5. NM_001428578.1 → NP_001415507.1  protein lin-54 homolog isoform 1

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000014
      UniProtKB/Swiss-Prot
      Q4FZV6, Q641Z1
      UniProtKB/TrEMBL
      A0A8L2Q0T4, A6K5Z8

    6. NM_001428579.1 → NP_001415508.1  protein lin-54 homolog isoform 2

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000014
      UniProtKB/TrEMBL
      A0A8I6G8M1

    RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

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

    Reference GRCr8

    Genomic

    1. NC_086032.1 Reference GRCr8

      Range
      9434093..9514091
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006250658.5 → XP_006250720.1  protein lin-54 homolog isoform X2

      See identical proteins and their annotated locations for XP_006250720.1

      UniProtKB/Swiss-Prot
      Q4FZV6, Q641Z1
      UniProtKB/TrEMBL
      A0A8L2Q0T4, A6K5Z8
      Conserved Domains (1) summary
      pfam03638
      Location:596 → 631
      TCR; Tesmin/TSO1-like CXC domain, cysteine-rich domain

    2. XM_006250661.5 → XP_006250723.1  protein lin-54 homolog isoform X4

      UniProtKB/TrEMBL
      A0A8I6G8M1
      Conserved Domains (1) summary
      pfam03638
      Location:375 → 410
      TCR; Tesmin/TSO1-like CXC domain, cysteine-rich domain

    3. XM_006250657.5 → XP_006250719.1  protein lin-54 homolog isoform X1

      UniProtKB/TrEMBL
      A0A8I5ZJ81, A0A8L2Q0T4
      Related
      ENSRNOP00000083208.2, ENSRNOT00000119980.2
      Conserved Domains (1) summary
      pfam03638
      Location:614 → 649
      TCR; Tesmin/TSO1-like CXC domain, cysteine-rich domain

    4. XM_008770022.4 → XP_008768244.1  protein lin-54 homolog isoform X3

      Conserved Domains (1) summary
      pfam03638
      Location:393 → 428
      TCR; Tesmin/TSO1-like CXC domain, cysteine-rich domain

    5. XM_006250659.5 → XP_006250721.1  protein lin-54 homolog isoform X2

      See identical proteins and their annotated locations for XP_006250721.1

      UniProtKB/Swiss-Prot
      Q4FZV6, Q641Z1
      UniProtKB/TrEMBL
      A0A8L2Q0T4, A6K5Z8
      Conserved Domains (1) summary
      pfam03638
      Location:596 → 631
      TCR; Tesmin/TSO1-like CXC domain, cysteine-rich domain

    6. XM_017599168.3 → XP_017454657.1  protein lin-54 homolog isoform X4

      UniProtKB/TrEMBL
      A0A8I6G8M1
      Conserved Domains (1) summary
      pfam03638
      Location:375 → 410
      TCR; Tesmin/TSO1-like CXC domain, cysteine-rich domain

    7. XM_039091835.2 → XP_038947763.1  protein lin-54 homolog isoform X5

      UniProtKB/TrEMBL
      A6K600
      Conserved Domains (2) summary
      pfam03638
      Location:266 → 301
      TCR; Tesmin/TSO1-like CXC domain, cysteine-rich domain
      NF033645
      Location:4 → 172
      pilus_FilE; putative pilus assembly protein FilE
    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q641Z1.2 GenPept UniProtKB/Swiss-Prot:Q641Z1

    Gene LinkOut

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