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

Gene ID: 231506, updated on 11-Apr-2024

Summary

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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 transcription, DNA-templated. Predicted to be active in nucleus. Orthologous to human LIN54 (lin-54 DREAM MuvB core complex component). [provided by Alliance of Genome Resources, Apr 2022]
Expression
Ubiquitous expression in placenta adult (RPKM 4.3), liver E14 (RPKM 4.0) and 28 other tissues See more
Orthologs
human all
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Genomic context

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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

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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. 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. 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
  3. 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
  4. Systematic analysis of human protein complexes identifies chromosome segregation proteins. Hutchins JR, et al. Science, 2010 Apr 30. PMID 20360068, Free PMC Article
  5. Database resources of the National Center for Biotechnology Information. Wheeler DL, et al. Nucleic Acids Res, 2001 Jan 1. PMID 11125038, Free PMC Article

See all (19) citations in PubMed

GeneRIFs: Gene References Into Functions

Variation

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Alleles

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

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

Clone Names

  • KIAA2037, 4832414L08

Gene Ontology Provided by MGI

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 ISO
Inferred from Sequence Orthology
more info
  
enables transcription regulatory region nucleic acid binding ISO
Inferred from Sequence Orthology
more info
  
Process Evidence Code Pubs
acts_upstream_of_or_within cell cycle 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 ISO
Inferred from Sequence Orthology
more info
  
is_active_in nucleus IBA
Inferred from Biological aspect of Ancestor
more info
  

General protein information

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Preferred Names
protein lin-54 homolog
Names
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_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

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