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

    Gene ID: 132660, updated on 2-Nov-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
    mouse all
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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_2024_08 current GRCh38.p14 (GCF_000001405.40) 4 NC_000004.12 (82924603..83012941, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 4 NC_060928.1 (86253801..86342186, complement)
    RS_2024_09 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 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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    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)

    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
    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_2024_08

    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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