U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

Links from GEO Profiles

    • Showing Current items.

    Lin54 lin-54 DREAM MuvB core complex component [ Mus musculus (house mouse) ]

    Gene ID: 231506, updated on 27-Nov-2024

    Summary

    Go to the top of the page Help
    Official Symbol
    Lin54provided by MGI
    Official Full Name
    lin-54 DREAM MuvB core complex componentprovided by MGI
    Primary source
    MGI:MGI:2140902
    See related
    Ensembl:ENSMUSG00000118665 AllianceGenome:MGI:2140902
    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
    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, Nov 2024]
    Expression
    Ubiquitous expression in placenta adult (RPKM 4.3), liver E14 (RPKM 4.0) and 28 other tissues See more
    Orthologs
    human all
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    Go to the top of the page Help
    See Lin54 in Genome Data Viewer
    Location:
    5 E4; 5 48.48 cM
    Exon count:
    16
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCm39 (GCF_000001635.27) 5 NC_000071.7 (100589892..100648506, complement)
    108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 5 NC_000071.6 (100442033..100500639, complement)

    Chromosome 5 - NC_000071.7Genomic Context describing neighboring genes Neighboring gene SEC31 homolog A, COPII coat complex component Neighboring gene RIKEN cDNA 5430416N02 gene Neighboring gene STARR-positive B cell enhancer ABC_E2162 Neighboring gene STARR-seq mESC enhancer starr_13725 Neighboring gene STARR-seq mESC enhancer starr_13727 Neighboring gene STARR-positive B cell enhancer ABC_E2163 Neighboring gene predicted gene, 19620 Neighboring gene COP9 signalosome subunit 4

    Genomic regions, transcripts, and products

    Go to the top of the page Help

    Go to nucleotide: Graphics FASTA GenBank

    Expression

    Go to the top of the page Help
    • 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

    Go to the top of the pageHelp

    Related articles in PubMed

    1. The polycomb group protein L3mbtl2 assembles an atypical PRC1-family complex that is essential in pluripotent stem cells and early development. Qin J, et al. Cell Stem Cell, 2012 Sep 7. PMID 22770845, Free PMC Article
    2. TWIST1 and chromatin regulatory proteins interact to guide neural crest cell differentiation. Fan X, et al. Elife, 2021 Feb 8. PMID 33554859, Free PMC Article
    3. Proximity-dependent biotin identification (BioID) reveals a dynamic LSD1-CoREST interactome during embryonic stem cell differentiation. Barnes CE, et al. Mol Omics, 2022 Jan 17. PMID 34709266, Free PMC Article
    4. Mapping the NPHP-JBTS-MKS protein network reveals ciliopathy disease genes and pathways. Sang L, et al. Cell, 2011 May 13. PMID 21565611, Free PMC Article
    5. Systematic analysis of human protein complexes identifies chromosome segregation proteins. Hutchins JR, et al. Science, 2010 Apr 30. PMID 20360068, Free PMC Article

    See all (20) citations in PubMed

    GeneRIFs: Gene References Into Functions

    Variation

    Go to the top of the page Help

    Alleles

    Alleles of this type are documented at Mouse Genome Informatics  (MGI)
    • Endonuclease-mediated (4) 

    Pathways from PubChem

    Go to the top of the page

    Interactions

    Go to the top of the page Help
    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Go to the top of the page Help

    Markers

    Homology

    Clone Names

    • KIAA2037, 4832414L08

    Gene Ontology Provided by MGI

    Function Evidence Code Pubs
    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
    		  

    General protein information

    Go to the top of the page Help
    Preferred Names
    protein lin-54 homolog
    Names
    lin-54 homolog

    NCBI Reference Sequences (RefSeq)

    Go to the top of the page Help

    NEW Try the new Transcript table

    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_001115010.1 → NP_001108482.1  protein lin-54 homolog isoform 1

      See identical proteins and their annotated locations for NP_001108482.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1). Variants 1, 2 and 5 encode the same isoform (1).
      Source sequence(s)
      AC107744, AK030894, AK134320, AK220225
      Consensus CDS
      CCDS19462.2
      UniProtKB/Swiss-Prot
      A0JLY2, Q3KQN0, Q3UYW5, Q571G4, Q8BMU8, Q8C107
      Related
      ENSMUSP00000159392.2, ENSMUST00000239513.1
      Conserved Domains (2) summary
      PHA03247
      Location:165 → 499
      PHA03247; large tegument protein UL36; Provisional
      pfam03638
      Location:597 → 631
      TCR; Tesmin/TSO1-like CXC domain, cysteine-rich domain

    2. NM_001346583.2 → NP_001333512.1  protein lin-54 homolog isoform 2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) differs in the 5' UTR and uses an alternate in-frame splice site in the 5' coding region, compared to variant 1. It encodes isoform 2, which lacks an internal in-frame segment and is shorter, compared to isoform 1.
      Source sequence(s)
      AC107744, AC109196, MG954270
      Consensus CDS
      CCDS84919.1
      UniProtKB/TrEMBL
      E9PV28
      Conserved Domains (2) summary
      PHA03247
      Location:5 → 278
      PHA03247; large tegument protein UL36; Provisional
      pfam03638
      Location:376 → 410
      TCR; Tesmin/TSO1-like CXC domain, cysteine-rich domain

    3. NM_001359914.2 → NP_001346843.1  protein lin-54 homolog isoform 3

      Status: VALIDATED

      Description
      Transcript Variant: This variant (4) differs in the 5' UTR and coding sequence compared to variant 1. The resulting isoform (3) is shorter at the N-terminus compared to isoform 1.
      Source sequence(s)
      AC107744, AC109196, MG954270
      UniProtKB/TrEMBL
      B7ZN58
      Conserved Domains (1) summary
      pfam03638
      Location:266 → 301
      TCR; Tesmin/TSO1-like CXC domain, cysteine-rich domain

    4. NM_001425849.1 → NP_001412778.1  protein lin-54 homolog isoform 1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (5) differs in the 5' UTR compared to variant 1. Variants 1, 2 and 5 encode the same isoform (1).
      Source sequence(s)
      AC107744, AC109196
      UniProtKB/Swiss-Prot
      A0JLY2, Q3KQN0, Q3UYW5, Q571G4, Q8BMU8, Q8C107

    5. NM_001425850.1 → NP_001412779.1  protein lin-54 homolog isoform 2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (6) differs in the 5' UTR and uses an alternate in-frame splice site in the 5' coding region, compared to variant 1. It encodes isoform 2, which lacks an internal in-frame segment and is shorter, compared to isoform 1.
      Source sequence(s)
      AC107744, AC109196

    6. NM_172714.5 → NP_766302.2  protein lin-54 homolog isoform 1

      See identical proteins and their annotated locations for NP_766302.2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) differs in the 5' UTR compared to variant 1. Variants 1, 2 and 5 encode the same isoform (1).
      Source sequence(s)
      AC107744, AC109196, MG954270
      Consensus CDS
      CCDS19462.2
      UniProtKB/Swiss-Prot
      A0JLY2, Q3KQN0, Q3UYW5, Q571G4, Q8BMU8, Q8C107
      Related
      ENSMUSP00000159391.2, ENSMUST00000239512.1
      Conserved Domains (2) summary
      PHA03247
      Location:165 → 499
      PHA03247; large tegument protein UL36; Provisional
      pfam03638
      Location:597 → 631
      TCR; Tesmin/TSO1-like CXC domain, cysteine-rich domain

    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_000071.7 Reference GRCm39 C57BL/6J

      Range
      100589892..100648506 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006534883.5 → XP_006534946.1  protein lin-54 homolog isoform X1

      Conserved Domains (2) summary
      PHA03247
      Location:183 → 517
      PHA03247; large tegument protein UL36; Provisional
      pfam03638
      Location:615 → 649
      TCR; Tesmin/TSO1-like CXC domain, cysteine-rich domain

    2. XM_017320848.3 → XP_017176337.1  protein lin-54 homolog isoform X3

      Conserved Domains (2) summary
      PHA03247
      Location:23 → 296
      PHA03247; large tegument protein UL36; Provisional
      pfam03638
      Location:394 → 428
      TCR; Tesmin/TSO1-like CXC domain, cysteine-rich domain

    3. XM_011249429.4 → XP_011247731.1  protein lin-54 homolog isoform X4

      See identical proteins and their annotated locations for XP_011247731.1

      UniProtKB/TrEMBL
      E9PV28
      Conserved Domains (2) summary
      PHA03247
      Location:5 → 278
      PHA03247; large tegument protein UL36; Provisional
      pfam03638
      Location:376 → 410
      TCR; Tesmin/TSO1-like CXC domain, cysteine-rich domain
    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q571G4.2 GenPept UniProtKB/Swiss-Prot:Q571G4

    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
    Miscellaneous