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

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. Among its related pathways are Formation of HIV elongation complex in the absence of HIV Tat and Protein ubiquitination. GO annotations related to this gene include SH2 domain binding and RNA polymerase II core binding.

UniProtKB/Swiss-Prot 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

Additional gene information for CTR9 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for CTR9 Gene

Genomics for CTR9 Gene

Regulatory Elements for CTR9 Gene

Enhancers for CTR9 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
GH11H009751 2 FANTOM5 Ensembl ENCODE dbSUPER 30.6 -991.2 -991219 15 HDGF MLX ARNT ZFP64 ARID4B SIN3A FEZF1 DMAP1 SLC30A9 ZNF766 CTR9 SBF2 ENSG00000254397 RPL21P97 ST5 SWAP70 TMEM9B-AS1 ZNF143 SBF2-AS1 ENSG00000238387
GH11H010805 1.4 ENCODE dbSUPER 38.6 +56.9 56867 5 HNRNPUL1 HDGF PKNOX1 FOXA2 MLX ARNT ZFP64 ARID4B SIN3A DMAP1 ZBED5 CTR9 EIF4G2 ZBED5-AS1 LOC101928053 ENSG00000255125 SNORD97 GC11M010801
GH11H010366 1.9 FANTOM5 Ensembl ENCODE dbSUPER 21.8 -384.1 -384077 1 HDGF ATF1 ARNT ARID4B SIN3A DMAP1 YY1 ETS1 ZNF143 RUNX3 ZBED5 CTR9 RPL21P97 WEE1 ADM AMPD3 LOC105376544 ENSG00000238387 EIF4G2 RNU6ATAC33P
GH11H010454 1.3 ENCODE dbSUPER 24.7 -293.7 -293718 6 HDGF PKNOX1 FOXA2 ATF1 ARNT SIN3A YY1 TCF12 CBX5 GATA2 CTR9 AMPD3 MTRNR2L8 RPL21P97 LYVE1 MRVI1 GC11M010466 GC11P010430
GH11H010750 1.1 ENCODE 25.1 +0.4 371 2 HDGF PKNOX1 ARNT ARID4B SIN3A DMAP1 ZNF2 YY1 SLC30A9 ZNF143 CTR9 ZBED5 ENSG00000255125 MRVI1
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around CTR9 on UCSC Golden Path with GeneCards custom track

Promoters for CTR9 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000036804 413 2001 HDGF PKNOX1 ARNT ARID4B SIN3A DMAP1 ZNF2 YY1 SLC30A9 ZNF143

Genomic Location for CTR9 Gene

Chromosome:
11
Start:
10,750,987 bp from pter
End:
10,779,755 bp from pter
Size:
28,769 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 mammalian PAF1 complex, which consists of CDC73, PAF1, LEO1, CTR9, RTF1 and WDR61 (PubMed:16024656, PubMed:19952111, PubMed:20178742). Interacts with KMT2A/MLL1. Interacts with STAT3 (By similarity). Interacts with SETD5 (By similarity).
    SequenceCaution:
    • Sequence=BAA09925.2; Type=Erroneous initiation; Evidence={ECO:0000305};

neXtProt entry for CTR9 Gene

Post-translational modifications for CTR9 Gene

  • Ubiquitination at posLast=6262, isoforms=379, posLast=444444, isoforms=472, posLast=645645, isoforms=660, posLast=784784, and isoforms=798
  • Modification sites at PhosphoSitePlus

Other Protein References for CTR9 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for CTR9 Gene

Domains & Families for CTR9 Gene

Protein Domains for CTR9 Gene

Suggested Antigen Peptide Sequences for CTR9 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

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

No data available for 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 core binding IBA --
GO:0005515 protein binding 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 tm1b(EUCOMM)Wtsi

Animal Model Products

CRISPR Products

Inhibitory RNA Products

Clone Products

  • Applied Biological Materials Clones for CTR9
  • Vectors and viruses for ORF, Lenti, Retro, Adenovirus, AAV, and more

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. Note=Found in speckles. {ECO:0000250}.

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

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 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 from RNA polymerase II promoter ISS --
GO:0001711 endodermal cell fate commitment ISS,IEA --
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

Unigene Clusters for CTR9 Gene

Ctr9, Paf1/RNA polymerase II complex component, homolog (S. cerevisiae):
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

Clone Products

  • Applied Biological Materials Clones for CTR9
  • Vectors and viruses for ORF, Lenti, Retro, Adenovirus, AAV, and more

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
ECgene alternative splicing isoforms for
CTR9

Expression for CTR9 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP 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, PaxDb, MaxQB, and MOPED for CTR9 Gene



Protein tissue co-expression partners for CTR9 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of CTR9 Gene:

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(4.3)
  • Blood(4.2)
  • Bone marrow(4.2)
  • Nervous system(3.4)
genes like me logo Genes that share expression patterns with CTR9: view

Primer Products

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 33 34
  • 99.7 (n)
oppossum
(Monodelphis domestica)
Mammalia CTR9 34
  • 95 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia -- 34
  • 94 (a)
OneToMany
-- 34
  • 81 (a)
OneToMany
dog
(Canis familiaris)
Mammalia CTR9 33 34
  • 93.38 (n)
cow
(Bos Taurus)
Mammalia CTR9 33 34
  • 91.33 (n)
mouse
(Mus musculus)
Mammalia Ctr9 33 16 34
  • 90.01 (n)
rat
(Rattus norvegicus)
Mammalia Ctr9 33
  • 89.78 (n)
chicken
(Gallus gallus)
Aves CTR9 33 34
  • 83.02 (n)
lizard
(Anolis carolinensis)
Reptilia CTR9 34
  • 92 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia ctr9 33
  • 74.5 (n)
African clawed frog
(Xenopus laevis)
Amphibia Xl.1944 33
zebrafish
(Danio rerio)
Actinopterygii ctr9 33 34
  • 74.22 (n)
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.8444 33
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP001559 33
  • 63.62 (n)
fruit fly
(Drosophila melanogaster)
Insecta CG2469 33 34
  • 63.54 (n)
worm
(Caenorhabditis elegans)
Secernentea B0464.2 33 34
  • 52.27 (n)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes CTR9 34
  • 23 (a)
OneToOne
thale cress
(Arabidopsis thaliana)
eudicotyledons ELF8 33
  • 33.8 (n)
rice
(Oryza sativa)
Liliopsida Os07g0476200 33
  • 48.35 (n)
sea squirt
(Ciona savignyi)
Ascidiacea CSA.5656 34
  • 71 (a)
OneToOne
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.9648 33
Species where no ortholog for CTR9 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya 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)

Paralogs for CTR9 Gene

No data available for Paralogs for CTR9 Gene

Variants for CTR9 Gene

Sequence variations from dbSNP and Humsavar for CTR9 Gene

SNP ID Clin Chr 11 pos Sequence Context AA Info Type
rs869312709 Uncertain significance 10,763,811(+) ATTAC(A/G)AAACT reference, missense
rs1000085934 -- 10,752,882(+) TACCA(C/T)GTGTA intron-variant
rs1000154224 -- 10,760,381(+) TCTTA(C/T)CTAAA intron-variant
rs1000181715 -- 10,751,440(+) TTCCC(C/T)TCCGG reference, missense
rs1000218360 -- 10,769,752(+) TATTG(G/T)TTTTA intron-variant

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)

Relevant External Links for CTR9 Gene

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

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

Disorders for CTR9 Gene

Relevant External Links for CTR9

Genetic Association Database (GAD)
CTR9
Human Genome Epidemiology (HuGE) Navigator
CTR9
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
CTR9

No disorders were found for CTR9 Gene.

No data available for MalaCards , 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 60
  2. 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 60
  3. 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 60
  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 60
  5. A genome-scale RNAi screen for Oct4 modulators defines a role of the Paf1 complex for embryonic stem cell identity. (PMID: 19345177) Ding L … Buchholz F (Cell stem cell 2009) 3 4 60

Products for CTR9 Gene

Sources for CTR9 Gene

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