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Aliases for LIN54 Gene

Aliases for LIN54 Gene

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

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. 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 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. In G0 phase, the complex binds to more than 800 promoters and is required for repression of E2F target genes. 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. In the complex, acts as a DNA-binding protein that binds the promoter of CDK1 in a sequence-specific manner.

No data available for CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for LIN54 Gene

Genomics for LIN54 Gene

Regulatory Elements for LIN54 Gene

Enhancers for LIN54 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH04G083215 1.8 FANTOM5 Ensembl ENCODE dbSUPER 2.1 -205.2 -205228 4.7 PKNOX1 BMI1 YBX1 RAD21 CBX5 ZNF143 ZNF207 RELB ETV6 IKZF2 PLAC8 LOC391674 THAP9 HPSE COQ2 LIN54 HELQ GC04M083225
GH04G083107 1.7 FANTOM5 ENCODE dbSUPER 2.2 -99.0 -98958 9.3 HDGF FOXA2 PKNOX1 ARID4B SIN3A ZNF2 ZBTB7B YY1 ZNF121 GLIS2 PLAC8 HELQ THAP9 LIN54 COQ2 HPSE GC04P083063
GH04G083315 1.4 FANTOM5 Ensembl ENCODE 1.8 -303.9 -303890 1.8 HDAC1 CTCF RAD21 FOS NFE2 TRIM24 ZNF584 SMARCA5 L3MBTL2 RNF2 HPSE THAP9 PLAC8 COQ2 HELQ LIN54 LOC105377313
GH04G083211 1.6 FANTOM5 Ensembl ENCODE dbSUPER 1.5 -199.6 -199561 2.6 TBP TBL1XR1 ARID3A ELK1 ZSCAN29 RELB ETV6 IKZF2 CHD2 SRF HELQ PLAC8 LIN54 GC04M083225
GH04G083320 1.1 FANTOM5 Ensembl ENCODE 2 -307.8 -307760 1.4 GATA2 HLF MAX FOS HPSE THAP9 PLAC8 COQ2 HELQ LIN54 LOC105377313
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around LIN54 on UCSC Golden Path with GeneCards custom track

Promoters for LIN54 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000170052 1241 4201 MLX AGO1 ZFP64 DMAP1 YY1 SLC30A9 ZNF143 SP3 NFYC TBX21

Genomic Location for LIN54 Gene

Chromosome:
4
Start:
82,909,973 bp from pter
End:
83,012,941 bp from pter
Size:
102,969 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=Translation N-terminally shortened.; 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 isoforms=2, 3357
  • Modification sites at PhosphoSitePlus

No data available for DME Specific Peptides for LIN54 Gene

Domains & Families for LIN54 Gene

Protein Domains for LIN54 Gene

Suggested Antigen Peptide Sequences for LIN54 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

Q6MZP7

UniProtKB/Swiss-Prot:

LIN54_HUMAN :
  • The CXC domains mediate DNA-binding.
  • Belongs to the lin-54 family.
Domain:
  • The CXC domains mediate DNA-binding.
Family:
  • Belongs to the lin-54 family.
genes like me logo Genes that share domains with LIN54: view

No data available for Gene Families for LIN54 Gene

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. In G0 phase, the complex binds to more than 800 promoters and is required for repression of E2F target genes. 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. In the complex, acts as a DNA-binding protein that binds the promoter of CDK1 in a sequence-specific manner.

Gene Ontology (GO) - Molecular Function for LIN54 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003677 DNA binding IEA --
GO:0005515 protein binding IPI 17531812
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

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
peroxisome 1

Gene Ontology (GO) - Cellular Components for LIN54 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IEA --
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

Gene Ontology (GO) - Biological Process for LIN54 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006351 transcription, DNA-templated IEA --
GO:0006355 regulation of transcription, DNA-templated IEA --
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

Unigene Clusters for LIN54 Gene

Lin-54 homolog (C. elegans):
Representative Sequences:

CRISPR Products

Inhibitory RNA 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
ECgene alternative splicing isoforms for
LIN54

Expression for LIN54 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP 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, PaxDb, MaxQB, and MOPED for LIN54 Gene



Protein tissue co-expression partners for LIN54 Gene

NURSA nuclear receptor signaling pathways regulating expression of LIN54 Gene:

LIN54

SOURCE GeneReport for Unigene cluster for LIN54 Gene:

Hs.96952

Evidence on tissue expression from TISSUES for LIN54 Gene

  • Nervous system(4.2)
genes like me logo Genes that share expression patterns with LIN54: view

Primer Products

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 34 35
  • 99.82 (n)
dog
(Canis familiaris)
Mammalia LIN54 34 35
  • 96.53 (n)
cow
(Bos Taurus)
Mammalia LIN54 34 35
  • 95.19 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia -- 35
  • 93 (a)
OneToMany
-- 35
  • 92 (a)
OneToMany
-- 35
  • 83 (a)
OneToMany
-- 35
  • 60 (a)
OneToMany
mouse
(Mus musculus)
Mammalia Lin54 34 16 35
  • 92.52 (n)
rat
(Rattus norvegicus)
Mammalia Lin54 34
  • 90.25 (n)
oppossum
(Monodelphis domestica)
Mammalia LIN54 35
  • 89 (a)
OneToOne
chicken
(Gallus gallus)
Aves LIN54 34 35
  • 81.32 (n)
lizard
(Anolis carolinensis)
Reptilia LIN54 35
  • 79 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia lin54 34
  • 71.35 (n)
Str.16976 34
zebrafish
(Danio rerio)
Actinopterygii lin54 34 35
  • 62.36 (n)
fruit fly
(Drosophila melanogaster)
Insecta mip120 35
  • 15 (a)
OneToMany
worm
(Caenorhabditis elegans)
Secernentea lin-54 35
  • 29 (a)
OneToMany
sea squirt
(Ciona savignyi)
Ascidiacea -- 35
  • 49 (a)
OneToOne
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.8963 34
Species where no ortholog for LIN54 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya 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)

Paralogs for LIN54 Gene

Paralogs for LIN54 Gene

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

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

Variants for LIN54 Gene

Sequence variations from dbSNP and Humsavar for LIN54 Gene

SNP ID Clin Chr 04 pos Sequence Context AA Info Type
rs10000180 -- 82,978,611(+) ACACA(A/G)TGAAC intron-variant
rs1000037570 -- 82,947,715(+) TGTTT(A/C)ACCAA intron-variant
rs1000043824 -- 82,972,986(+) AAAAT(C/T)CGCAA intron-variant
rs1000050755 -- 83,003,833(+) ATTTT(C/T)TTTTA intron-variant
rs1000064431 -- 82,996,882(+) TAGGG(-/A)AAAAA intron-variant

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)

Relevant External Links for LIN54 Gene

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

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for LIN54 Gene

Disorders for LIN54 Gene

Relevant External Links for LIN54

Genetic Association Database (GAD)
LIN54
Human Genome Epidemiology (HuGE) Navigator
LIN54
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
LIN54

No disorders were found for LIN54 Gene.

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

Publications for LIN54 Gene

  1. DYRK1A protein kinase promotes quiescence and senescence through DREAM complex assembly. (PMID: 21498570) Litovchick L. … DeCaprio J.A. (Genes Dev. 2011) 2 3 64
  2. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. (PMID: 20379614) Rose J.E. … Uhl G.R. (Mol. Med. 2010) 3 46 64
  3. 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. (FEBS J. 2009) 3 4 64
  4. Evolutionarily conserved multisubunit RBL2/p130 and E2F4 protein complex represses human cell cycle-dependent genes in quiescence. (PMID: 17531812) Litovchick L. … DeCaprio J.A. (Mol. Cell 2007) 3 4 64
  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 2007) 3 4 64

Products for LIN54 Gene

Sources for LIN54 Gene

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