The protein encoded by this gene is a component of the PAF1 complex, which associates with RNA polymerase II and functions in transcriptional regulation and elongation. This complex also plays a role in the modification of histones. [provided by RefSeq, Oct 2016] See more...

Aliases for CTR9 Gene

Aliases for CTR9 Gene

  • CTR9 Homolog, Paf1/RNA Polymerase II Complex Component 2 3 5
  • SH2 Domain Binding Protein 1 (Tetratricopeptide Repeat Containing) 2 3
  • RNA Polymerase-Associated Protein CTR9 Homolog 3 4
  • KIAA0155 2 4
  • P150TSP 2 3
  • SH2BP1 3 4
  • TSBP 2 3
  • Ctr9, Paf1/RNA Polymerase II Complex Component, Homolog (S. Cerevisiae) 2
  • Ctr9, Paf1/RNA Polymerase II Complex Component, Homolog 3
  • TPR-Containing, SH2-Binding Phosphoprotein 3
  • SH2 Domain-Binding Protein 1 4
  • P150 3
  • CTR9 5

External Ids for CTR9 Gene

Previous HGNC Symbols for CTR9 Gene

  • SH2BP1

Previous GeneCards Identifiers for CTR9 Gene

  • GC11P010730
  • GC11P010731
  • GC11P010445

Summaries for CTR9 Gene

Entrez Gene Summary for CTR9 Gene

  • The protein encoded by this gene is a component of the PAF1 complex, which associates with RNA polymerase II and functions in transcriptional regulation and elongation. This complex also plays a role in the modification of histones. [provided by RefSeq, Oct 2016]

GeneCards Summary for CTR9 Gene

CTR9 (CTR9 Homolog, Paf1/RNA Polymerase II Complex Component) is a Protein Coding gene. Diseases associated with CTR9 include Hereditary Wilms' Tumor and Malignant Fibrous Histiocytoma Of Bone. Among its related pathways are Metabolism of proteins and Chromatin Regulation / Acetylation. Gene Ontology (GO) annotations related to this gene include SH2 domain binding and RNA polymerase II complex binding.

UniProtKB/Swiss-Prot Summary for CTR9 Gene

  • Component of the PAF1 complex (PAF1C) which has multiple functions during transcription by RNA polymerase II and is implicated in regulation of development and maintenance of embryonic stem cell pluripotency. PAF1C associates with RNA polymerase II through interaction with POLR2A CTD non-phosphorylated and 'Ser-2'- and 'Ser-5'-phosphorylated forms and is involved in transcriptional elongation, acting both indepentently and synergistically with TCEA1 and in cooperation with the DSIF complex and HTATSF1. PAF1C is required for transcription of Hox and Wnt target genes. PAF1C is involved in hematopoiesis and stimulates transcriptional activity of KMT2A/MLL1; it promotes leukemogenesis through association with KMT2A/MLL1-rearranged oncoproteins, such as KMT2A/MLL1-MLLT3/AF9 and KMT2A/MLL1-MLLT1/ENL. PAF1C is involved in histone modifications such as ubiquitination of histone H2B and methylation on histone H3 'Lys-4' (H3K4me3). PAF1C recruits the RNF20/40 E3 ubiquitin-protein ligase complex and the E2 enzyme UBE2A or UBE2B to chromatin which mediate monoubiquitination of 'Lys-120' of histone H2B (H2BK120ub1); UB2A/B-mediated H2B ubiquitination is proposed to be coupled to transcription. PAF1C is involved in mRNA 3' end formation probably through association with cleavage and poly(A) factors. In case of infection by influenza A strain H3N2, PAF1C associates with viral NS1 protein, thereby regulating gene transcription. Required for mono- and trimethylation on histone H3 'Lys-4' (H3K4me3) and dimethylation on histone H3 'Lys-79' (H3K4me3). Required for Hox gene transcription. Required for the trimethylation of histone H3 'Lys-4' (H3K4me3) on genes involved in stem cell pluripotency; this function is synergistic with CXXC1 indicative for an involvement of the SET1 complex. Involved in transcriptional regulation of IL6-responsive genes and in JAK-STAT pathway; may regulate DNA-association of STAT3 (By similarity).

Gene Wiki entry for CTR9 Gene

No data available for CIViC Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for CTR9 Gene

Genomics for CTR9 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for CTR9 Gene
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around CTR9 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for CTR9

Top Transcription factor binding sites by QIAGEN in the CTR9 gene promoter:
  • AP-2alpha
  • AP-2alphaA
  • AP-2beta
  • AP-2gamma
  • CUTL1
  • Elk-1
  • NF-kappaB
  • NF-kappaB1
  • NF-kappaB2
  • p53

Genomic Locations for CTR9 Gene

Genomic Locations for CTR9 Gene
chr11:10,751,246-10,801,625
(GRCh38/hg38)
Size:
50,380 bases
Orientation:
Plus strand
chr11:10,772,534-10,801,290
(GRCh37/hg19)
Size:
28,757 bases
Orientation:
Plus strand

Genomic View for CTR9 Gene

Genes around CTR9 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
CTR9 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for CTR9 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for CTR9 Gene

Proteins for CTR9 Gene

  • Protein details for CTR9 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q6PD62-CTR9_HUMAN
    Recommended name:
    RNA polymerase-associated protein CTR9 homolog
    Protein Accession:
    Q6PD62
    Secondary Accessions:
    • D3DQV8
    • Q15015

    Protein attributes for CTR9 Gene

    Size:
    1173 amino acids
    Molecular mass:
    133502 Da
    Quaternary structure:
    • Component of the PAF1 complex, which consists of CDC73, PAF1, LEO1, CTR9, RTF1 and WDR61 (PubMed:16024656, PubMed:19952111, PubMed:20178742). The PAF1 complex interacts with PHF5A (By similarity). Interacts with KMT2A/MLL1 (PubMed:20541477). Interacts with STAT3 (By similarity). Interacts with SETD5 (By similarity). Interacts with ERCC6 (PubMed:26030138).
    SequenceCaution:
    • Sequence=BAA09925.2; Type=Erroneous initiation; Evidence={ECO:0000305};

    Three dimensional structures from OCA and Proteopedia for CTR9 Gene

neXtProt entry for CTR9 Gene

Post-translational modifications for CTR9 Gene

  • Ubiquitination at Lys62, Lys379, Lys444, Lys472, Lys645, Lys660, Lys784, and Lys798
  • Modification sites at PhosphoSitePlus

Other Protein References for CTR9 Gene

No data available for DME Specific Peptides for CTR9 Gene

Domains & Families for CTR9 Gene

Gene Families for CTR9 Gene

Protein Domains for CTR9 Gene

Suggested Antigen Peptide Sequences for CTR9 Gene

GenScript: Design optimal peptide antigens:
  • SH2 domain-binding protein 1 (CTR9_HUMAN)
genes like me logo Genes that share domains with CTR9: view

No data available for Graphical View of Domain Structure and UniProtKB/Swiss-Prot for CTR9 Gene

Function for CTR9 Gene

Molecular function for CTR9 Gene

UniProtKB/Swiss-Prot Function:
Component of the PAF1 complex (PAF1C) which has multiple functions during transcription by RNA polymerase II and is implicated in regulation of development and maintenance of embryonic stem cell pluripotency. PAF1C associates with RNA polymerase II through interaction with POLR2A CTD non-phosphorylated and 'Ser-2'- and 'Ser-5'-phosphorylated forms and is involved in transcriptional elongation, acting both indepentently and synergistically with TCEA1 and in cooperation with the DSIF complex and HTATSF1. PAF1C is required for transcription of Hox and Wnt target genes. PAF1C is involved in hematopoiesis and stimulates transcriptional activity of KMT2A/MLL1; it promotes leukemogenesis through association with KMT2A/MLL1-rearranged oncoproteins, such as KMT2A/MLL1-MLLT3/AF9 and KMT2A/MLL1-MLLT1/ENL. PAF1C is involved in histone modifications such as ubiquitination of histone H2B and methylation on histone H3 'Lys-4' (H3K4me3). PAF1C recruits the RNF20/40 E3 ubiquitin-protein ligase complex and the E2 enzyme UBE2A or UBE2B to chromatin which mediate monoubiquitination of 'Lys-120' of histone H2B (H2BK120ub1); UB2A/B-mediated H2B ubiquitination is proposed to be coupled to transcription. PAF1C is involved in mRNA 3' end formation probably through association with cleavage and poly(A) factors. In case of infection by influenza A strain H3N2, PAF1C associates with viral NS1 protein, thereby regulating gene transcription. Required for mono- and trimethylation on histone H3 'Lys-4' (H3K4me3) and dimethylation on histone H3 'Lys-79' (H3K4me3). Required for Hox gene transcription. Required for the trimethylation of histone H3 'Lys-4' (H3K4me3) on genes involved in stem cell pluripotency; this function is synergistic with CXXC1 indicative for an involvement of the SET1 complex. Involved in transcriptional regulation of IL6-responsive genes and in JAK-STAT pathway; may regulate DNA-association of STAT3 (By similarity).

Phenotypes From GWAS Catalog for CTR9 Gene

Gene Ontology (GO) - Molecular Function for CTR9 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000993 RNA polymerase II complex binding IBA 21873635
GO:0005515 protein binding IEA,IPI 15923622
GO:0042169 SH2 domain binding IEA --
genes like me logo Genes that share ontologies with CTR9: view
genes like me logo Genes that share phenotypes with CTR9: view

Animal Models for CTR9 Gene

MGI Knock Outs for CTR9:
  • Ctr9 Ctr9<tm1b(EUCOMM)Wtsi>

Animal Model Products

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for CTR9

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for CTR9 Gene

Localization for CTR9 Gene

Subcellular locations from UniProtKB/Swiss-Prot for CTR9 Gene

Nucleus speckle.

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 CTR9 gene
Compartment Confidence
nucleus 5
cytosol 2
plasma membrane 1
extracellular 1
cytoskeleton 1
mitochondrion 1

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for CTR9 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IEA --
GO:0005654 nucleoplasm TAS --
GO:0016593 Cdc73/Paf1 complex IEA,IDA 16307923
GO:0016607 nuclear speck IEA --
GO:0035327 transcriptionally active chromatin IEA,ISS --
genes like me logo Genes that share ontologies with CTR9: view

Pathways & Interactions for CTR9 Gene

genes like me logo Genes that share pathways with CTR9: view

Pathways by source for CTR9 Gene

Gene Ontology (GO) - Biological Process for CTR9 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000122 negative regulation of transcription by RNA polymerase II IEA,ISS --
GO:0001711 endodermal cell fate commitment IEA,ISS --
GO:0001826 inner cell mass cell differentiation IEA --
GO:0001829 trophectodermal cell differentiation IEA --
GO:0001832 blastocyst growth IEA --
genes like me logo Genes that share ontologies with CTR9: view

No data available for SIGNOR curated interactions for CTR9 Gene

Drugs & Compounds for CTR9 Gene

No Compound Related Data Available

Transcripts for CTR9 Gene

mRNA/cDNA for CTR9 Gene

2 REFSEQ mRNAs :
6 NCBI additional mRNA sequence :
6 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 CTR9

Alternative Splicing Database (ASD) splice patterns (SP) for CTR9 Gene

ExUns: 1 ^ 2 ^ 3 ^ 4 ^ 5 ^ 6 ^ 7 ^ 8 ^ 9 ^ 10 ^ 11 ^ 12a · 12b ^ 13a · 13b ^ 14a · 14b · 14c ^ 15 ^ 16a · 16b · 16c · 16d ^ 17 ^ 18 ^ 19 ^
SP1: - -
SP2: -
SP3: - - -
SP4: -
SP5:
SP6:

ExUns: 20a · 20b ^ 21 ^ 22a · 22b ^ 23 ^ 24 ^ 25
SP1: - -
SP2:
SP3:
SP4:
SP5:
SP6:

Relevant External Links for CTR9 Gene

GeneLoc Exon Structure for
CTR9

Expression for CTR9 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for CTR9 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for CTR9 Gene

This gene is overexpressed in Lung (22.1), Lymph node (7.2), and Peripheral blood mononuclear cells (6.2).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for CTR9 Gene



Protein tissue co-expression partners for CTR9 Gene

- Elite partner

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for CTR9

SOURCE GeneReport for Unigene cluster for CTR9 Gene:

Hs.725151

mRNA Expression by UniProt/SwissProt for CTR9 Gene:

Q6PD62-CTR9_HUMAN
Tissue specificity: Widely expressed.

Evidence on tissue expression from TISSUES for CTR9 Gene

  • Liver(4.5)
  • Blood(4.4)
  • Bone marrow(4.3)
  • Nervous system(3.7)
  • Kidney(2.5)
  • Heart(2.3)
  • Spleen(2.2)
  • Skin(2.2)
  • Thyroid gland(2.1)
  • Muscle(2.1)
genes like me logo Genes that share expression patterns with CTR9: view

No data available for mRNA differential expression in normal tissues and Phenotype-based relationships between genes and organs from Gene ORGANizer for CTR9 Gene

Orthologs for CTR9 Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for CTR9 Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
Mammalia CTR9 30 31
  • 99.7 (n)
OneToOne
Oppossum
(Monodelphis domestica)
Mammalia CTR9 31
  • 95 (a)
OneToOne
Platypus
(Ornithorhynchus anatinus)
Mammalia -- 31
  • 94 (a)
OneToMany
-- 31
  • 81 (a)
OneToMany
Dog
(Canis familiaris)
Mammalia CTR9 30 31
  • 93.38 (n)
OneToOne
Cow
(Bos Taurus)
Mammalia CTR9 30 31
  • 91.33 (n)
OneToOne
Mouse
(Mus musculus)
Mammalia Ctr9 30 17 31
  • 90.01 (n)
OneToOne
Rat
(Rattus norvegicus)
Mammalia Ctr9 30
  • 89.78 (n)
Chicken
(Gallus gallus)
Aves CTR9 30 31
  • 83.02 (n)
OneToOne
Lizard
(Anolis carolinensis)
Reptilia CTR9 31
  • 92 (a)
OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia ctr9 30
  • 74.5 (n)
African clawed frog
(Xenopus laevis)
Amphibia Xl.1944 30
Zebrafish
(Danio rerio)
Actinopterygii ctr9 30 31
  • 74.22 (n)
OneToOne
Rainbow Trout
(Oncorhynchus mykiss)
Actinopterygii Omy.8444 30
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP001559 30
  • 63.62 (n)
Fruit Fly
(Drosophila melanogaster)
Insecta CG2469 30 31
  • 63.54 (n)
OneToOne
Worm
(Caenorhabditis elegans)
Secernentea B0464.2 30 31
  • 52.27 (n)
OneToOne
Baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes CTR9 31
  • 23 (a)
OneToOne
Thale Cress
(Arabidopsis thaliana)
eudicotyledons ELF8 30
  • 33.8 (n)
Rice
(Oryza sativa)
Liliopsida Os07g0476200 30
  • 48.35 (n)
Sea Squirt
(Ciona savignyi)
Ascidiacea CSA.5656 31
  • 71 (a)
OneToOne
Sea Vase
(Ciona intestinalis)
Ascidiacea Cin.9648 30
Species where no ortholog for CTR9 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)
  • 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)
  • 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)
  • Tomato (Lycopersicon esculentum)
  • Toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • Wheat (Triticum aestivum)

Evolution for CTR9 Gene

ENSEMBL:
Gene Tree for CTR9 (if available)
TreeFam:
Gene Tree for CTR9 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for CTR9: view image

Paralogs for CTR9 Gene

No data available for Paralogs for CTR9 Gene

Variants for CTR9 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for CTR9 Gene

SNP ID Clinical significance and condition Chr 11 pos Variation AA Info Type
731780 Benign: not provided 10,768,070(+) A/G INTRON_VARIANT
749267 Benign: not provided 10,768,467(+) G/A SYNONYMOUS_VARIANT
793003 Likely Benign: not provided 10,764,631(+) G/A SYNONYMOUS_VARIANT
850332 Uncertain Significance: not provided 10,770,636(+) A/C INTRON_VARIANT
855730 Uncertain Significance: not provided 10,778,821(+) C/T MISSENSE_VARIANT

Additional dbSNP identifiers (rs#s) for CTR9 Gene

Structural Variations from Database of Genomic Variants (DGV) for CTR9 Gene

Variant ID Type Subtype PubMed ID
nsv483000 CNV loss 15286789
nsv832063 CNV loss 17160897

Variation tolerance for CTR9 Gene

Residual Variation Intolerance Score: 6.05% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 1.85; 34.71% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for CTR9 Gene

Human Gene Mutation Database (HGMD)
CTR9
SNPedia medical, phenotypic, and genealogical associations of SNPs for
CTR9

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for CTR9 Gene

Disorders for CTR9 Gene

MalaCards: The human disease database

(3) MalaCards diseases for CTR9 Gene - From: DISEASES

Disorder Aliases PubMed IDs
hereditary wilms' tumor
  • wt1
malignant fibrous histiocytoma of bone
  • malignant fibrous histiocytoma of the bone
wilms tumor 1
  • wt1
- elite association - COSMIC cancer census association via MalaCards
Search CTR9 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for CTR9

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 CTR9: view

No data available for UniProtKB/Swiss-Prot and Genatlas for CTR9 Gene

Publications for CTR9 Gene

  1. Prediction of the coding sequences of unidentified human genes. IV. The coding sequences of 40 new genes (KIAA0121-KIAA0160) deduced by analysis of cDNA clones from human cell line KG-1. (PMID: 8590280) Nagase T … Nomura N (DNA research : an international journal for rapid publication of reports on genes and genomes 1995) 2 3 4
  2. Identification of Novel Proteins Co-Purifying with Cockayne Syndrome Group B (CSB) Reveals Potential Roles for CSB in RNA Metabolism and Chromatin Dynamics. (PMID: 26030138) Nicolai S … Proietti-De-Santis L (PloS one 2015) 3 4
  3. System-wide temporal characterization of the proteome and phosphoproteome of human embryonic stem cell differentiation. (PMID: 21406692) Rigbolt KT … Blagoev B (Science signaling 2011) 3 4
  4. The human PAF1 complex acts in chromatin transcription elongation both independently and cooperatively with SII/TFIIS. (PMID: 20178742) Kim J … Roeder RG (Cell 2010) 3 4
  5. The PAF complex synergizes with MLL fusion proteins at HOX loci to promote leukemogenesis. (PMID: 20541477) Muntean AG … Hess JL (Cancer cell 2010) 3 4

Products for CTR9 Gene

Sources for CTR9 Gene