This gene encodes a tumor suppressor protein that inhibits DNA synthesis and oncogenic transformation through association with the retinoblastoma 1 protein. The encoded protein also interacts with a complex of other cell cycle regulators to repress cell cycle-dependent gene expression in non-dividing cells. Alternatively spliced transcript variants encoding multiple isoforms ha... See more...

Aliases for LIN9 Gene

Aliases for LIN9 Gene

  • Lin-9 DREAM MuvB Core Complex Component 2 3 5
  • TGS 2 3 4
  • Type I Interferon Receptor Beta Chain-Associated Protein 3 4
  • Beta Subunit-Associated Regulator Of Apoptosis 3 4
  • TUDOR Gene Similar Protein 3 4
  • Rb Related Pathway Actor 2 3
  • PRB-Associated Protein 3 4
  • Protein Lin-9 Homolog 3 4
  • BARA 3 4
  • Lin-9 Homolog (C. Elegans) 2
  • TUDOR Gene Similar 2
  • Lin-9 Homolog 3
  • HuLin-9 4
  • BARPsv 3
  • HLin-9 4
  • Lin-9 3
  • TGS1 3
  • TGS2 3
  • LIN9 5

External Ids for LIN9 Gene

Previous GeneCards Identifiers for LIN9 Gene

  • GC01M222725
  • GC01M224485
  • GC01M226420
  • GC01M196936

Summaries for LIN9 Gene

Entrez Gene Summary for LIN9 Gene

  • This gene encodes a tumor suppressor protein that inhibits DNA synthesis and oncogenic transformation through association with the retinoblastoma 1 protein. The encoded protein also interacts with a complex of other cell cycle regulators to repress cell cycle-dependent gene expression in non-dividing cells. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. [provided by RefSeq, Jul 2012]

GeneCards Summary for LIN9 Gene

LIN9 (Lin-9 DREAM MuvB Core Complex Component) is a Protein Coding gene. Among its related pathways are Cell Cycle, Mitotic and Regulation of PLK1 Activity at G2/M Transition.

UniProtKB/Swiss-Prot Summary for LIN9 Gene

  • Acts as a tumor suppressor. Inhibits DNA synthesis. Its ability to inhibit oncogenic transformation is mediated through its association with RB1. Plays a role in the expression of genes required for the G1/S transition.

Gene Wiki entry for LIN9 Gene

No data available for CIViC Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for LIN9 Gene

Genomics for LIN9 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for LIN9 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
GH01J226307 Promoter/Enhancer 2.2 EPDnew Ensembl ENCODE CraniofacialAtlas 250.7 +0.7 747 3.5 BCLAF1 ZNF600 MYC IKZF1 ZNF580 POLR2A ZNF223 ZNF10 ZSCAN16 NFIC HSALNG0011070 HSALNG0011071 LIN9 ACBD3 H3-3A ACBD3-AS1 ENAH LINC01703 ENSG00000282418 MIXL1
GH01J226311 Enhancer 0.5 Ensembl 250.7 -1.8 -1819 0.2 ZBTB48 ZNF398 YY2 L3MBTL2 ZXDB ZEB2 LIN9 SNODB1629 PARP1
GH01J226121 Promoter/Enhancer 1.9 Ensembl ENCODE CraniofacialAtlas dbSUPER 10.3 +186.7 186724 4.6 ZNF207 MYC ZNF600 ZNF654 ZNF580 ZNF592 ZNF10 ZSCAN16 POLR2A NFIC HSALNG0011056 lnc-ACBD3-3 H3-3A MIXL1 SDE2 LIN9 lnc-H3F3A-2 ACBD3
GH01J226126 Promoter/Enhancer 1.6 FANTOM5 Ensembl ENCODE dbSUPER 11.2 +181.9 181946 2.7 SP1 ZNF600 CEBPA ZNF10 ZIC2 FEZF1 ZNF341 THAP11 POLR2A ELF1 ENSG00000270598 HSALNG0011057 LOC112268255 H3-3A LIN9 MIXL1 ACBD3 PARP1 PYCR2 HSALNG0011056
GH01J226348 Enhancer 1.2 Ensembl ENCODE CraniofacialAtlas 11.8 -40.6 -40556 3.5 IKZF1 ZNF600 ZNF592 NFIC ZIC2 TAL1 EBF1 MYNN ASH2L SMARCA4 HSALNG0011075 ACBD3-AS1 ACBD3 LIN9 PARP1 MIXL1 HSALNG0011077-001
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around LIN9 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for LIN9

Top Transcription factor binding sites by QIAGEN in the LIN9 gene promoter:
  • AML1a
  • c-Myb
  • C/EBPalpha
  • Elk-1
  • En-1
  • MIF-1
  • MyoD
  • POU2F1
  • POU2F1a
  • RFX1

Genomic Locations for LIN9 Gene

Latest Assembly
chr1:226,231,149-226,310,082
(GRCh38/hg38)
Size:
78,934 bases
Orientation:
Minus strand

Previous Assembly
chr1:226,418,850-226,497,468
(GRCh37/hg19 by Entrez Gene)
Size:
78,619 bases
Orientation:
Minus strand

chr1:226,418,850-226,497,570
(GRCh37/hg19 by Ensembl)
Size:
78,721 bases
Orientation:
Minus strand

Genomic View for LIN9 Gene

Genes around LIN9 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
LIN9 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for LIN9 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for LIN9 Gene

Proteins for LIN9 Gene

  • Protein details for LIN9 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q5TKA1-LIN9_HUMAN
    Recommended name:
    Protein lin-9 homolog
    Protein Accession:
    Q5TKA1
    Secondary Accessions:
    • Q5U5L8
    • Q5U7E1
    • Q6PI55
    • Q6ZTV4
    • Q7Z3J1

    Protein attributes for LIN9 Gene

    Size:
    542 amino acids
    Molecular mass:
    61946 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. Interacts with RB1.
    SequenceCaution:
    • Sequence=AAH43444.1; Type=Erroneous initiation; Evidence={ECO:0000305}; Sequence=CAD97871.1; Type=Erroneous initiation; Evidence={ECO:0000305};

    Three dimensional structures from OCA and Proteopedia for LIN9 Gene

    Alternative splice isoforms for LIN9 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for LIN9 Gene

Post-translational modifications for LIN9 Gene

  • Ubiquitination at Lys32
  • Modification sites at PhosphoSitePlus

No data available for DME Specific Peptides for LIN9 Gene

Domains & Families for LIN9 Gene

Gene Families for LIN9 Gene

Human Protein Atlas (HPA):
  • Predicted intracellular proteins

Protein Domains for LIN9 Gene

InterPro:

Suggested Antigen Peptide Sequences for LIN9 Gene

GenScript: Design optimal peptide antigens:
  • Lin-9 homolog (C. elegans) (B1ANK3_HUMAN)
  • Lin-9 homolog (C. elegans) (B1B046_HUMAN)
  • pRB-associated protein (LIN9_HUMAN)
  • LIN9 protein (Q6P142_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q5TKA1

UniProtKB/Swiss-Prot:

LIN9_HUMAN :
  • Belongs to the lin-9 family.
Family:
  • Belongs to the lin-9 family.
genes like me logo Genes that share domains with LIN9: view

Function for LIN9 Gene

Molecular function for LIN9 Gene

UniProtKB/Swiss-Prot Function:
Acts as a tumor suppressor. Inhibits DNA synthesis. Its ability to inhibit oncogenic transformation is mediated through its association with RB1. Plays a role in the expression of genes required for the G1/S transition.

Phenotypes From GWAS Catalog for LIN9 Gene

Gene Ontology (GO) - Molecular Function for LIN9 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003677 DNA binding IBA 21873635
GO:0005515 protein binding IPI 17159899
genes like me logo Genes that share ontologies with LIN9: view
genes like me logo Genes that share phenotypes with LIN9: view

Animal Models for LIN9 Gene

MGI Knock Outs for LIN9:

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for LIN9

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for LIN9 Gene

Localization for LIN9 Gene

Subcellular locations from UniProtKB/Swiss-Prot for LIN9 Gene

Nucleus, nucleoplasm. Note=Found in perinucleolar structures. Associated with chromatin.

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 LIN9 gene
Compartment Confidence
nucleus 5
cytoskeleton 2
plasma membrane 1
extracellular 1
mitochondrion 1
endoplasmic reticulum 1
endosome 1
cytosol 1
lysosome 1
golgi apparatus 1

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for LIN9 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IEA --
GO:0005654 nucleoplasm IDA,TAS --
GO:0017053 transcriptional repressor complex IEA --
genes like me logo Genes that share ontologies with LIN9: view

Pathways & Interactions for LIN9 Gene

genes like me logo Genes that share pathways with LIN9: view

Pathways by source for LIN9 Gene

1 BioSystems pathway for LIN9 Gene
1 KEGG pathway for LIN9 Gene

SIGNOR curated interactions for LIN9 Gene

Is activated by:

Gene Ontology (GO) - Biological Process for LIN9 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000003 reproduction IBA 21873635
GO:0006351 transcription, DNA-templated IEA --
GO:0006357 regulation of transcription by RNA polymerase II IBA 21873635
GO:0007049 cell cycle IEA --
GO:0051726 regulation of cell cycle TAS --
genes like me logo Genes that share ontologies with LIN9: view

Drugs & Compounds for LIN9 Gene

No Compound Related Data Available

Transcripts for LIN9 Gene

mRNA/cDNA for LIN9 Gene

9 REFSEQ mRNAs :
12 NCBI additional mRNA sequence :
6 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for LIN9

Alternative Splicing Database (ASD) splice patterns (SP) for LIN9 Gene

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

Relevant External Links for LIN9 Gene

GeneLoc Exon Structure for
LIN9

Expression for LIN9 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for LIN9 Gene

mRNA differential expression in normal tissues according to GTEx for LIN9 Gene

This gene is overexpressed in Heart - Left Ventricle (x5.4).

Protein differential expression in normal tissues from HIPED for LIN9 Gene

This gene is overexpressed in Heart (46.8), CD8 Tcells (9.9), and Testis (9.8).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for LIN9 Gene



Protein tissue co-expression partners for LIN9 Gene

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for LIN9

SOURCE GeneReport for Unigene cluster for LIN9 Gene:

Hs.120817

mRNA Expression by UniProt/SwissProt for LIN9 Gene:

Q5TKA1-LIN9_HUMAN
Tissue specificity: Expressed in thymus and testis.

Evidence on tissue expression from TISSUES for LIN9 Gene

  • Heart(4.4)
  • Intestine(2.9)
  • Muscle(2.7)
  • Nervous system(2.4)
  • Kidney(2.3)
  • Liver(2.3)
  • Stomach(2.3)
genes like me logo Genes that share expression patterns with LIN9: view

Primer products for research

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery and Phenotype-based relationships between genes and organs from Gene ORGANizer for LIN9 Gene

Orthologs for LIN9 Gene

This gene was present in the common ancestor of animals.

Orthologs for LIN9 Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
Mammalia LIN9 29 30
  • 99.86 (n)
OneToOne
Oppossum
(Monodelphis domestica)
Mammalia -- 30
  • 97 (a)
OneToMany
-- 30
  • 97 (a)
OneToMany
Cow
(Bos Taurus)
Mammalia LIN9 29 30
  • 95.04 (n)
OneToOne
Platypus
(Ornithorhynchus anatinus)
Mammalia LIN9 30
  • 94 (a)
OneToOne
Dog
(Canis familiaris)
Mammalia LIN9 29 30
  • 92.79 (n)
OneToOne
Mouse
(Mus musculus)
Mammalia Lin9 29 16 30
  • 89.98 (n)
OneToOne
Rat
(Rattus norvegicus)
Mammalia Lin9 29
  • 89.9 (n)
Chicken
(Gallus gallus)
Aves LIN9 29 30
  • 84.48 (n)
OneToOne
Lizard
(Anolis carolinensis)
Reptilia LIN9 30
  • 90 (a)
OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia lin9 29
  • 76.13 (n)
African clawed frog
(Xenopus laevis)
Amphibia Xl.3885 29
Zebrafish
(Danio rerio)
Actinopterygii LIN9 (2 of 2) 30
  • 79 (a)
OneToMany
lin9 30
  • 78 (a)
OneToMany
LOC100330674 29
  • 72.28 (n)
wufb79c09 29
Fruit Fly
(Drosophila melanogaster)
Insecta mip130 29 30
  • 45.98 (n)
OneToMany
aly 30
  • 20 (a)
OneToMany
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP004624 29
  • 45.81 (n)
Worm
(Caenorhabditis elegans)
Secernentea lin-9 29 30
  • 49.13 (n)
OneToOne
Sea Vase
(Ciona intestinalis)
Ascidiacea Cin.27 29
Species where no ortholog for LIN9 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • 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 Squirt (Ciona savignyi)
  • 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 LIN9 Gene

ENSEMBL:
Gene Tree for LIN9 (if available)
TreeFam:
Gene Tree for LIN9 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for LIN9: view image
Alliance of Genome Resources:
Additional Orthologs for LIN9

Paralogs for LIN9 Gene

No data available for Paralogs for LIN9 Gene

Variants for LIN9 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for LIN9 Gene

SNP ID Clinical significance and condition Chr 01 pos Variation AA Info Type
rs144086241 Benign: not provided 226,233,494(-) T/C
NM_173083.3(LIN9):c.1323A>G (p.Ala441=)
SYNONYMOUS

dbSNP identifiers (rs#s) for variants without ClinVar clinical significance for LIN9 Gene

All consequence types are included: molecular consequences (e.g. missense, synonymous), and location-based (e.g. intron, upstream).

Structural Variations from Database of Genomic Variants (DGV) for LIN9 Gene

Variant ID Type Subtype PubMed ID
esv3589011 CNV gain 21293372
esv3891148 CNV loss 25118596
nsv517107 CNV gain+loss 19592680
nsv832759 CNV loss 17160897
nsv832770 CNV loss 17160897

Variation tolerance for LIN9 Gene

Residual Variation Intolerance Score: 9.86% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 4.45; 64.07% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for LIN9 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
LIN9
Leiden Open Variation Database (LOVD)
LIN9

SNP Genotyping and Copy Number Assays for research

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for LIN9 Gene

Disorders for LIN9 Gene

Additional Disease Information for LIN9

Human Genome Epidemiology Navigator
(HuGE)
Atlas
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
Open Targets Platform
Open Targets Platform

No disorders were found for LIN9 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for LIN9 Gene

Publications for LIN9 Gene

  1. Inhibition of oncogenic transformation by mammalian Lin-9, a pRB-associated protein. (PMID: 15538385) Gagrica S … Gaubatz S (The EMBO journal 2004) 2 3 4 22
  2. LIN9, a subunit of the DREAM complex, regulates mitotic gene expression and proliferation of embryonic stem cells. (PMID: 23667535) Esterlechner J … Gaubatz S (PloS one 2013) 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 40
  4. Genome-wide association study identifies GPC5 as a novel genetic locus protective against sudden cardiac arrest. (PMID: 20360844) Arking DE … Chugh SS (PloS one 2010) 3 40
  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 LIN9 Gene

Sources for LIN9 Gene