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LIN54 lin-54 DREAM MuvB core complex component [ Homo sapiens (human) ]

Gene ID: 132660, updated on 3-Apr-2024

Summary

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Official Symbol
LIN54provided by HGNC
Official Full Name
lin-54 DREAM MuvB core complex componentprovided by HGNC
Primary source
HGNC:HGNC:25397
See related
Ensembl:ENSG00000189308 MIM:613367; AllianceGenome:HGNC:25397
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
TCX1; JC8.6; CXCDC1; MIP120
Summary
LIN54 is a component of the LIN, or DREAM, complex, an essential regulator of cell cycle genes (Schmit et al., 2009 [PubMed 19725879]).[supplied by OMIM, Dec 2010]
Expression
Ubiquitous expression in thyroid (RPKM 5.1), esophagus (RPKM 4.0) and 25 other tissues See more
Orthologs
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Genomic context

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See LIN54 in Genome Data Viewer
Location:
4q21.22
Exon count:
14
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 4 NC_000004.12 (82924603..83012941, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 4 NC_060928.1 (86253801..86342186, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 4 NC_000004.11 (83845756..83934094, complement)

Chromosome 4 - NC_000004.12Genomic Context describing neighboring genes Neighboring gene SEC31 homolog A, COPII coat complex component Neighboring gene H3K27ac hESC enhancer GRCh37_chr4:83821333-83821852 Neighboring gene H3K27ac hESC enhancer GRCh37_chr4:83821853-83822372 Neighboring gene THAP9 antisense RNA 1 Neighboring gene small nucleolar RNA, C/D box 144 Neighboring gene THAP domain containing 9 Neighboring gene ReSE screen-validated silencer GRCh37_chr4:83887737-83887940 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21666 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21667 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21668 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15537 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:83933797-83934682 Neighboring gene RNA, U6 small nuclear 615, pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21670 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21671 Neighboring gene Sharpr-MPRA regulatory region 7954 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21673 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21674 Neighboring gene H3K27ac hESC enhancer GRCh37_chr4:83956719-83957224 Neighboring gene COP9 signalosome subunit 4 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21676 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15539 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21677 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21678 Neighboring gene placenta associated 8

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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Related articles in PubMed

  1. Structural basis for LIN54 recognition of CHR elements in cell cycle-regulated promoters. Marceau AH, et al. Nat Commun, 2016 Jul 28. PMID 27465258, Free PMC Article
  2. LIN54 harboring a mutation in CHC domain is localized to the cytoplasm and inhibits cell cycle progression. Matsuo T, et al. Cell Cycle, 2012 Sep 1. PMID 22895175, Free PMC Article
  3. A B-myb--DREAM complex is not critical to regulate the G2/M genes in HPV-transformed cell lines. Rashid NN, et al. Anticancer Res, 2014 Nov. PMID 25368258
  4. LIN54 is an essential core subunit of the DREAM/LINC complex that binds to the cdc2 promoter in a sequence-specific manner. Schmit F, et al. FEBS J, 2009 Oct. PMID 19725879
  5. DYRK1A protein kinase promotes quiescence and senescence through DREAM complex assembly. Litovchick L, et al. Genes Dev, 2011 Apr 15. PMID 21498570, Free PMC Article

See all (40) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. the DNA-binding properties of LIN54 and the structural basis for recognition of a cell cycle genes homology region sequence, are described.
    Title: Structural basis for LIN54 recognition of CHR elements in cell cycle-regulated promoters.
  2. LIN54 harboring a mutation in CHC domain is localized to the cytoplasm and inhibits cell cycle progression.
    Title: LIN54 harboring a mutation in CHC domain is localized to the cytoplasm and inhibits cell cycle progression.
  3. Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
    Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
  4. the cysteine-rich CXC domain of LIN54 is a novel DNA-binding domain that binds to the cdc2 promoter in a sequence-specific manner
    Title: LIN54 is an essential core subunit of the DREAM/LINC complex that binds to the cdc2 promoter in a sequence-specific manner.
Submit: New GeneRIF Correction

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

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

  • MGC129905, DKFZp686L1814

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables metal ion binding IEA
Inferred from Electronic Annotation
more info
  
enables minor groove of adenine-thymine-rich DNA binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables transcription regulatory region nucleic acid binding IDA
Inferred from Direct Assay
more info
 PubMed 
Process Evidence Code Pubs
involved_in cell cycle IEA
Inferred from Electronic Annotation
more info
  
acts_upstream_of_or_within nucleosome organization IDA
Inferred from Direct Assay
more info
 PubMed 
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 IDA
Inferred from Direct Assay
more info
 PubMed 
located_in nucleoplasm TAS
Traceable Author Statement
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
CXC domain-containing protein 1
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_001115007.3 → NP_001108479.1  protein lin-54 homolog isoform b

    See identical proteins and their annotated locations for NP_001108479.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) differs in the 5' UTR and uses an alternate in-frame splice site in the 5' coding region, compared to variant 1. Variants 2, 3 and 7 encode the same isoform (b) which is shorter than isoform a.
    Source sequence(s)
    AC021105
    Consensus CDS
    CCDS47089.1
    UniProtKB/TrEMBL
    Q7Z3G2
    Related
    ENSP00000421045.1, ENST00000510557.5
    Conserved Domains (2) summary
    pfam03154
    Location:5 → 240
    Atrophin-1; Atrophin-1 family
    pfam03638
    Location:375 → 410
    TCR; Tesmin/TSO1-like CXC domain, cysteine-rich domain

  2. NM_001115008.3 → NP_001108480.1  protein lin-54 homolog isoform b

    See identical proteins and their annotated locations for NP_001108480.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) uses an alternate in-frame splice site in the 5' coding region, compared to variant 1. Variants 2, 3 and 7 encode the same isoform (b) which is shorter than isoform a.
    Source sequence(s)
    AC021105
    Consensus CDS
    CCDS47089.1
    UniProtKB/TrEMBL
    Q7Z3G2
    Related
    ENSP00000398265.2, ENST00000442461.6
    Conserved Domains (2) summary
    pfam03154
    Location:5 → 240
    Atrophin-1; Atrophin-1 family
    pfam03638
    Location:375 → 410
    TCR; Tesmin/TSO1-like CXC domain, cysteine-rich domain

  3. NM_001288996.2 → NP_001275925.1  protein lin-54 homolog isoform c

    See identical proteins and their annotated locations for NP_001275925.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (4) lacks two consecutive alternate exons in the 5' coding region, compared to variant 1. It encodes isoform c, which lacks an internal in-frame segment and is shorter, compared to isoform a.
    Source sequence(s)
    AB111889, AC021105, AI208524, BC109278, BX108765, BX537919, BX640657, BX640966, CK819664, DC335927
    Consensus CDS
    CCDS75157.1
    UniProtKB/TrEMBL
    B4DFU0
    Related
    ENSP00000423475.1, ENST00000506560.5
    Conserved Domains (2) summary
    pfam03154
    Location:160 → 432
    Atrophin-1; Atrophin-1 family
    pfam03638
    Location:507 → 542
    TCR; Tesmin/TSO1-like CXC domain, cysteine-rich domain

  4. NM_001288997.1 → NP_001275926.1  protein lin-54 homolog isoform b

    See identical proteins and their annotated locations for NP_001275926.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (7) uses an alternate in-frame splice site in the 5' coding region, compared to variant 1. Variants 2, 3 and 7 encode the same isoform (b) which is shorter than isoform a.
    Source sequence(s)
    AB111889, AC021105, AI208524, BX108765, BX537919, BX640657, BX640966, CK819664, DC335927
    Consensus CDS
    CCDS47089.1
    UniProtKB/TrEMBL
    Q7Z3G2
    Related
    ENSP00000407139.2, ENST00000446851.6
    Conserved Domains (2) summary
    pfam03154
    Location:5 → 240
    Atrophin-1; Atrophin-1 family
    pfam03638
    Location:375 → 410
    TCR; Tesmin/TSO1-like CXC domain, cysteine-rich domain

  5. NM_194282.4 → NP_919258.2  protein lin-54 homolog isoform a

    See identical proteins and their annotated locations for NP_919258.2

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (a).
    Source sequence(s)
    AC021105
    Consensus CDS
    CCDS3599.1
    UniProtKB/Swiss-Prot
    Q32M68, Q32M69, Q6MZP7, Q6N071, Q76B60
    UniProtKB/TrEMBL
    B4DFU0
    Related
    ENSP00000341947.3, ENST00000340417.8
    Conserved Domains (2) summary
    pfam03154
    Location:211 → 461
    Atrophin-1; Atrophin-1 family
    pfam03638
    Location:596 → 631
    TCR; Tesmin/TSO1-like CXC domain, cysteine-rich domain

RNA

  1. NR_110253.2 RNA Sequence

    Status: VALIDATED

    Description
    Transcript Variant: This variant (5) lacks two internal exons compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AB111889, AC021105, AI208524, BC109277, BX108765, BX537919, BX640657, BX640966, CK819664, DC335927

  2. NR_110254.2 RNA Sequence

    Status: VALIDATED

    Description
    Transcript Variant: This variant (6) uses an alternate splice site in the 5' region, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AC021105
    Related
    ENST00000510877.5

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000004.12 Reference GRCh38.p14 Primary Assembly

    Range
    82924603..83012941 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017007728.2 → XP_016863217.1  protein lin-54 homolog isoform X2

    UniProtKB/TrEMBL
    B4DFU0
    Conserved Domains (2) summary
    pfam03154
    Location:160 → 432
    Atrophin-1; Atrophin-1 family
    pfam03638
    Location:507 → 542
    TCR; Tesmin/TSO1-like CXC domain, cysteine-rich domain

  2. XM_005262750.5 → XP_005262807.1  protein lin-54 homolog isoform X1

    See identical proteins and their annotated locations for XP_005262807.1

    UniProtKB/Swiss-Prot
    Q32M68, Q32M69, Q6MZP7, Q6N071, Q76B60
    UniProtKB/TrEMBL
    B4DFU0
    Related
    ENSP00000425844.1, ENST00000505397.1
    Conserved Domains (2) summary
    pfam03154
    Location:211 → 461
    Atrophin-1; Atrophin-1 family
    pfam03638
    Location:596 → 631
    TCR; Tesmin/TSO1-like CXC domain, cysteine-rich domain

  3. XM_006714081.4 → XP_006714144.1  protein lin-54 homolog isoform X1

    See identical proteins and their annotated locations for XP_006714144.1

    UniProtKB/Swiss-Prot
    Q32M68, Q32M69, Q6MZP7, Q6N071, Q76B60
    UniProtKB/TrEMBL
    B4DFU0
    Conserved Domains (2) summary
    pfam03154
    Location:211 → 461
    Atrophin-1; Atrophin-1 family
    pfam03638
    Location:596 → 631
    TCR; Tesmin/TSO1-like CXC domain, cysteine-rich domain

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060928.1 Alternate T2T-CHM13v2.0

    Range
    86253801..86342186 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054348915.1 → XP_054204890.1  protein lin-54 homolog isoform X2

  2. XM_054348913.1 → XP_054204888.1  protein lin-54 homolog isoform X1

    UniProtKB/Swiss-Prot
    Q32M68, Q32M69, Q6MZP7, Q6N071, Q76B60

  3. XM_054348914.1 → XP_054204889.1  protein lin-54 homolog isoform X1

    UniProtKB/Swiss-Prot
    Q32M68, Q32M69, Q6MZP7, Q6N071, Q76B60
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q6MZP7.3 GenPept UniProtKB/Swiss-Prot:Q6MZP7

Gene LinkOut

The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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