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] See more...

Aliases for LIN54 Gene

Aliases for LIN54 Gene

  • Lin-54 DREAM MuvB Core Complex Component 2 3 5
  • CXCDC1 2 3 4
  • CXC Domain-Containing Protein 1 3 4
  • Protein Lin-54 Homolog 3 4
  • MIP120 2 3
  • JC8.6 2 3
  • TCX1 2 3
  • Lin-54 Homolog (C. Elegans) 2
  • CXC Domain Containing 1 2
  • Lin-54 Homolog 3
  • DKFZp686L1814 2
  • KIAA2037 4
  • LIN54 5

External Ids for LIN54 Gene

Previous GeneCards Identifiers for LIN54 Gene

  • GC04M084066
  • GC04M083845
  • GC04M079586

Summaries for LIN54 Gene

Entrez Gene Summary for LIN54 Gene

  • 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]

GeneCards Summary for LIN54 Gene

LIN54 (Lin-54 DREAM MuvB Core Complex Component) is a Protein Coding gene. Diseases associated with LIN54 include Spondyloarthropathy 1 and Anemia Of Prematurity. Among its related pathways are Cell cycle Cell cycle (generic schema) and Regulation of PLK1 Activity at G2/M Transition. An important paralog of this gene is TESMIN.

UniProtKB/Swiss-Prot Summary for LIN54 Gene

  • Component of the DREAM complex, a multiprotein complex that can both act as a transcription activator or repressor depending on the context (PubMed:17671431, PubMed:17531812). In G0 phase, the complex binds to more than 800 promoters and is required for repression of E2F target genes (PubMed:17671431, PubMed:17531812). In S phase, the complex selectively binds to the promoters of G2/M genes whose products are required for mitosis and participates in their cell cycle dependent activation (PubMed:17671431, PubMed:17531812). In the complex, acts as a DNA-binding protein that binds the promoter of CDK1 in a sequence-specific manner (PubMed:19725879). Specifically recognizes the consensus motif 5'-TTYRAA-3' in target DNA (PubMed:27465258).

Additional gene information for LIN54 Gene

No data available for CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for LIN54 Gene

Genomics for LIN54 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for LIN54 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH04J083009 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE CraniofacialAtlas 600.7 +1.3 1321 5.7 BRCA1 SP1 HNRNPL CREB1 GATAD2A ATF7 TEAD4 PRDM10 REST ZNF629 LIN54 THAP9-AS1 HNRNPD HNRNPDL HELQ ENSG00000272677 RNU6-615P RF00026-800 SEC31A
GH04J082954 Enhancer 0.5 Ensembl 11.6 +58.0 57950 0.8 ZNF600 ZNF316 ZNF623 ZBTB11 ZNF121 THAP9-AS1 LIN54 piR-43325-066 RF00026-800 RNU6-615P SEC31A
GH04J083107 Promoter/Enhancer 2.4 EPDnew FANTOM5 Ensembl ENCODE CraniofacialAtlas dbSUPER 2.2 -98.9 -98947 9.3 HNRNPL CREB1 CTCF TEAD4 PRDM10 REST POLR2A BACH1 TARDBP FOXA1 PLAC8 HELQ THAP9 LIN54 COQ2 HPSE lnc-LIN54-3 lnc-COPS4-1 COPS4
GH04J082956 Enhancer 0.4 Ensembl 11.6 +55.9 55850 2.2 ZNF189 CREM MLLT1 THAP9-AS1 LIN54 piR-43325-066 RF00026-800 RNU6-615P SEC31A
GH04J083215 Enhancer 1.3 FANTOM5 ENCODE dbSUPER 2.1 -205.2 -205218 4.7 BACH1 LARP7 ZNF143 RELA TCF12 IKZF2 POLR2A SP1 TRIM22 PKNOX1 PLAC8 ENSG00000248401 THAP9 HPSE COQ2 LIN54 HELQ FJ601684-347 HSALNG0035565 ENSG00000250057
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around LIN54 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for LIN54

Top Transcription factor binding sites by QIAGEN in the LIN54 gene promoter:
  • CREB
  • deltaCREB
  • E47
  • Pax-4a
  • Tal-1beta

Genomic Locations for LIN54 Gene

Genomic Locations for LIN54 Gene
chr4:82,909,973-83,012,951
(GRCh38/hg38)
Size:
102,979 bases
Orientation:
Minus strand
chr4:83,831,126-83,934,079
(GRCh37/hg19)
Size:
102,954 bases
Orientation:
Minus strand

Genomic View for LIN54 Gene

Genes around LIN54 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
LIN54 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for LIN54 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for LIN54 Gene

Proteins for LIN54 Gene

  • Protein details for LIN54 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q6MZP7-LIN54_HUMAN
    Recommended name:
    Protein lin-54 homolog
    Protein Accession:
    Q6MZP7
    Secondary Accessions:
    • Q32M68
    • Q32M69
    • Q6N071
    • Q76B60

    Protein attributes for LIN54 Gene

    Size:
    749 amino acids
    Molecular mass:
    79494 Da
    Quaternary structure:
    • Component of the DREAM complex (also named LINC complex) at least composed of E2F4, E2F5, LIN9, LIN37, LIN52, LIN54, MYBL1, MYBL2, RBL1, RBL2, RBBP4, TFDP1 and TFDP2. The complex exists in quiescent cells where it represses cell cycle-dependent genes. It dissociates in S phase when LIN9, LIN37, LIN52 and LIN54 form a subcomplex that binds to MYBL2.
    SequenceCaution:
    • Sequence=BAC98377.1; Type=Erroneous initiation; Note=Extended N-terminus.; Evidence={ECO:0000305};

    Three dimensional structures from OCA and Proteopedia for LIN54 Gene

    Alternative splice isoforms for LIN54 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for LIN54 Gene

Post-translational modifications for LIN54 Gene

  • Ubiquitination at Lys357
  • Modification sites at PhosphoSitePlus

No data available for DME Specific Peptides for LIN54 Gene

Domains & Families for LIN54 Gene

Gene Families for LIN54 Gene

Human Protein Atlas (HPA):
  • Predicted intracellular proteins

Protein Domains for LIN54 Gene

Suggested Antigen Peptide Sequences for LIN54 Gene

GenScript: Design optimal peptide antigens:
  • CXC domain-containing protein 1 (LIN54_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q6MZP7

UniProtKB/Swiss-Prot:

LIN54_HUMAN :
  • The CRC domain mediates DNA-binding (PubMed:19725879, PubMed:27465258). It contains two CXC subdomains (joined by a flexible linker) which are both required for efficient association with target DNA (PubMed:27465258). Each CXC subdomain coordinates three Zn(2+) ions (PubMed:27465258).
  • Belongs to the lin-54 family.
Domain:
  • The CRC domain mediates DNA-binding (PubMed:19725879, PubMed:27465258). It contains two CXC subdomains (joined by a flexible linker) which are both required for efficient association with target DNA (PubMed:27465258). Each CXC subdomain coordinates three Zn(2+) ions (PubMed:27465258).
Family:
  • Belongs to the lin-54 family.
genes like me logo Genes that share domains with LIN54: view

Function for LIN54 Gene

Molecular function for LIN54 Gene

UniProtKB/Swiss-Prot Function:
Component of the DREAM complex, a multiprotein complex that can both act as a transcription activator or repressor depending on the context (PubMed:17671431, PubMed:17531812). In G0 phase, the complex binds to more than 800 promoters and is required for repression of E2F target genes (PubMed:17671431, PubMed:17531812). In S phase, the complex selectively binds to the promoters of G2/M genes whose products are required for mitosis and participates in their cell cycle dependent activation (PubMed:17671431, PubMed:17531812). In the complex, acts as a DNA-binding protein that binds the promoter of CDK1 in a sequence-specific manner (PubMed:19725879). Specifically recognizes the consensus motif 5'-TTYRAA-3' in target DNA (PubMed:27465258).

Phenotypes From GWAS Catalog for LIN54 Gene

Gene Ontology (GO) - Molecular Function for LIN54 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000977 RNA polymerase II regulatory region sequence-specific DNA binding IBA 21873635
GO:0003677 DNA binding IEA --
GO:0005515 protein binding IPI 17531812
GO:0046872 metal ion binding IEA --
genes like me logo Genes that share ontologies with LIN54: view
genes like me logo Genes that share phenotypes with LIN54: view

Animal Model Products

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for LIN54

Clone Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for LIN54 Gene

Localization for LIN54 Gene

Subcellular locations from UniProtKB/Swiss-Prot for LIN54 Gene

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for LIN54 gene
Compartment Confidence
nucleus 5
cytosol 3
extracellular 1
cytoskeleton 1
peroxisome 0

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for LIN54 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IBA 21873635
GO:0005654 nucleoplasm TAS --
genes like me logo Genes that share ontologies with LIN54: view

Pathways & Interactions for LIN54 Gene

genes like me logo Genes that share pathways with LIN54: view

Pathways by source for LIN54 Gene

1 KEGG pathway for LIN54 Gene

Gene Ontology (GO) - Biological Process for LIN54 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006355 regulation of transcription, DNA-templated IBA 21873635
GO:0007049 cell cycle IEA --
GO:0051726 regulation of cell cycle TAS --
genes like me logo Genes that share ontologies with LIN54: view

No data available for SIGNOR curated interactions for LIN54 Gene

Drugs & Compounds for LIN54 Gene

No Compound Related Data Available

Transcripts for LIN54 Gene

mRNA/cDNA for LIN54 Gene

5 REFSEQ mRNAs :
15 NCBI additional mRNA sequence :
10 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for LIN54

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for LIN54 Gene

ExUns: 1a · 1b ^ 2 ^ 3 ^ 4 ^ 5 ^ 6a · 6b ^ 7 ^ 8 ^ 9a · 9b ^ 10a · 10b ^ 11 ^ 12 ^ 13 ^ 14 ^ 15
SP1: - - -
SP2: - - - -
SP3:
SP4:
SP5:
SP6: -

Relevant External Links for LIN54 Gene

GeneLoc Exon Structure for
LIN54

Expression for LIN54 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for LIN54 Gene

Protein differential expression in normal tissues from HIPED for LIN54 Gene

This gene is overexpressed in Heart (27.2), CD8 Tcells (22.4), and Peripheral blood mononuclear cells (13.9).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for LIN54 Gene



Protein tissue co-expression partners for LIN54 Gene

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for LIN54

SOURCE GeneReport for Unigene cluster for LIN54 Gene:

Hs.96952

Evidence on tissue expression from TISSUES for LIN54 Gene

  • Nervous system(4.3)
genes like me logo Genes that share expression patterns with LIN54: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for LIN54 Gene

Orthologs for LIN54 Gene

This gene was present in the common ancestor of animals.

Orthologs for LIN54 Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
Mammalia LIN54 30 31
  • 99.82 (n)
OneToOne
Dog
(Canis familiaris)
Mammalia LIN54 30 31
  • 96.53 (n)
OneToOne
Cow
(Bos Taurus)
Mammalia LIN54 30 31
  • 95.19 (n)
OneToOne
Platypus
(Ornithorhynchus anatinus)
Mammalia -- 31
  • 93 (a)
OneToMany
-- 31
  • 92 (a)
OneToMany
-- 31
  • 83 (a)
OneToMany
-- 31
  • 60 (a)
OneToMany
Mouse
(Mus musculus)
Mammalia Lin54 30 17 31
  • 92.52 (n)
OneToOne
Rat
(Rattus norvegicus)
Mammalia Lin54 30
  • 90.25 (n)
Oppossum
(Monodelphis domestica)
Mammalia LIN54 31
  • 89 (a)
OneToOne
Chicken
(Gallus gallus)
Aves LIN54 30 31
  • 81.32 (n)
OneToOne
Lizard
(Anolis carolinensis)
Reptilia LIN54 31
  • 79 (a)
OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia lin54 30
  • 71.35 (n)
Str.16976 30
Zebrafish
(Danio rerio)
Actinopterygii lin54 30 31
  • 62.36 (n)
OneToOne
Fruit Fly
(Drosophila melanogaster)
Insecta mip120 31
  • 15 (a)
OneToMany
Worm
(Caenorhabditis elegans)
Secernentea lin-54 31
  • 29 (a)
OneToMany
Sea Squirt
(Ciona savignyi)
Ascidiacea -- 31
  • 49 (a)
OneToOne
Sea Vase
(Ciona intestinalis)
Ascidiacea Cin.8963 30
Species where no ortholog for LIN54 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • Alpha proteobacteria (Wolbachia pipientis)
  • Amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • Baker's yeast (Saccharomyces cerevisiae)
  • Barley (Hordeum vulgare)
  • Beta proteobacteria (Neisseria meningitidis)
  • Bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • Common water flea (Daphnia pulex)
  • Corn (Zea mays)
  • E. coli (Escherichia coli)
  • Filamentous fungi (Aspergillus nidulans)
  • Firmicute Bacteria (Streptococcus pneumoniae)
  • Fission Yeast (Schizosaccharomyces pombe)
  • Green Algae (Chlamydomonas reinhardtii)
  • Honey Bee (Apis mellifera)
  • K. Lactis Yeast (Kluyveromyces lactis)
  • Loblloly Pine (Pinus taeda)
  • Malaria Parasite (Plasmodium falciparum)
  • Medicago Trunc (Medicago Truncatula)
  • Moss (Physcomitrella patens)
  • Orangutan (Pongo pygmaeus)
  • Pig (Sus scrofa)
  • Rainbow Trout (Oncorhynchus mykiss)
  • Rice (Oryza sativa)
  • Rice Blast Fungus (Magnaporthe grisea)
  • Schistosome Parasite (Schistosoma mansoni)
  • Sea Anemone (Nematostella vectensis)
  • Sea Urchin (Strongylocentrotus purpuratus)
  • Sorghum (Sorghum bicolor)
  • Soybean (Glycine max)
  • Stem Rust Fungus (Puccinia graminis)
  • Sugarcane (Saccharum officinarum)
  • Thale Cress (Arabidopsis thaliana)
  • Tomato (Lycopersicon esculentum)
  • Toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • Wheat (Triticum aestivum)

Evolution for LIN54 Gene

ENSEMBL:
Gene Tree for LIN54 (if available)
TreeFam:
Gene Tree for LIN54 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for LIN54: view image

Paralogs for LIN54 Gene

Paralogs for LIN54 Gene

(2) SIMAP similar genes for LIN54 Gene using alignment to 2 proteins:

  • LIN54_HUMAN
  • D6REW4_HUMAN
genes like me logo Genes that share paralogs with LIN54: view

Variants for LIN54 Gene

Additional dbSNP identifiers (rs#s) for LIN54 Gene

Structural Variations from Database of Genomic Variants (DGV) for LIN54 Gene

Variant ID Type Subtype PubMed ID
esv2663118 CNV deletion 23128226
esv2668069 CNV deletion 23128226
esv3564154 CNV deletion 23714750
esv3601185 CNV loss 21293372
esv3601186 CNV loss 21293372
esv3601187 CNV loss 21293372
esv3601188 CNV loss 21293372
nsv1136882 CNV deletion 24896259

Variation tolerance for LIN54 Gene

Residual Variation Intolerance Score: 13.1% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 1.38; 27.20% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for LIN54 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
LIN54

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot and Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for LIN54 Gene

Disorders for LIN54 Gene

MalaCards: The human disease database

(4) MalaCards diseases for LIN54 Gene - From: LncRNADisease and DISEASES

- elite association - COSMIC cancer census association via MalaCards
Search LIN54 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for LIN54

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
Open Targets Platform
genes like me logo Genes that share disorders with LIN54: view

No data available for UniProtKB/Swiss-Prot and Genatlas for LIN54 Gene

Publications for LIN54 Gene

  1. Structural basis for LIN54 recognition of CHR elements in cell cycle-regulated promoters. (PMID: 27465258) Marceau AH … Rubin SM (Nature communications 2016) 3 4
  2. DYRK1A protein kinase promotes quiescence and senescence through DREAM complex assembly. (PMID: 21498570) Litovchick L … DeCaprio JA (Genes & development 2011) 2 3
  3. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. (PMID: 20379614) Rose JE … Uhl GR (Molecular medicine (Cambridge, Mass.) 2010) 3 41
  4. LIN54 is an essential core subunit of the DREAM/LINC complex that binds to the cdc2 promoter in a sequence-specific manner. (PMID: 19725879) Schmit F … Gaubatz S (The FEBS journal 2009) 3 4
  5. LINC, a human complex that is related to pRB-containing complexes in invertebrates regulates the expression of G2/M genes. (PMID: 17671431) Schmit F … Gaubatz S (Cell cycle (Georgetown, Tex.) 2007) 3 4

Products for LIN54 Gene

Sources for LIN54 Gene