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Protein

RNA polymerase-associated protein CTR9 homolog

Gene

Ctr9

Organism
Mus musculus (Mouse)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

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. 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. Required for mono- and trimethylation on histone H3 'Lys-4' (H3K4me3) and dimethylation on histone H3 'Lys-79' (H3K4me3). Required for Hox gene transcription (By similarity). 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 similarity2 Publications

GO - Molecular functioni

  • RNA polymerase II core binding Source: GO_Central
  • SH2 domain binding Source: MGI

GO - Biological processi

  • blastocyst growth Source: MGI
  • cellular response to lipopolysaccharide Source: UniProtKB
  • endodermal cell fate commitment Source: UniProtKB
  • histone H2B ubiquitination Source: MGI
  • histone H3-K4 trimethylation Source: UniProtKB
  • histone monoubiquitination Source: MGI
  • inner cell mass cell differentiation Source: MGI
  • interleukin-6-mediated signaling pathway Source: UniProtKB
  • JAK-STAT cascade Source: UniProtKB
  • negative regulation of mRNA polyadenylation Source: MGI
  • negative regulation of myeloid cell differentiation Source: UniProtKB
  • negative regulation of transcription from RNA polymerase II promoter Source: UniProtKB
  • positive regulation of histone H2B ubiquitination Source: MGI
  • positive regulation of histone H3-K4 methylation Source: UniProtKB
  • positive regulation of histone H3-K79 methylation Source: UniProtKB
  • positive regulation of transcription elongation from RNA polymerase II promoter Source: UniProtKB
  • positive regulation of transcription from RNA polymerase II promoter Source: UniProtKB
  • regulation of genetic imprinting Source: MGI
  • stem cell population maintenance Source: UniProtKB
  • transcription, DNA-templated Source: UniProtKB-KW
  • trophectodermal cell differentiation Source: MGI
  • Wnt signaling pathway Source: UniProtKB-KW
Complete GO annotation...

Keywords - Biological processi

Transcription, Transcription regulation, Wnt signaling pathway

Names & Taxonomyi

Protein namesi
Recommended name:
RNA polymerase-associated protein CTR9 homolog
Alternative name(s):
SH2 domain-binding protein 1
Tetratricopeptide repeat-containing, SH2-binding phosphoprotein of 150 kDa
Short name:
TPR-containing, SH2-binding phosphoprotein of 150 kDa
Short name:
p150TSP
Gene namesi
Name:Ctr9
Synonyms:Kiaa0155, Sh2bp1
OrganismiMus musculus (Mouse)
Taxonomic identifieri10090 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeMusMus
Proteomesi
  • UP000000589 Componenti: Chromosome 7

Organism-specific databases

MGIiMGI:109345. Ctr9.

Subcellular locationi

GO - Cellular componenti

  • Cdc73/Paf1 complex Source: UniProtKB
  • nuclear speck Source: UniProtKB-SubCell
  • nucleus Source: MGI
  • transcriptionally active chromatin Source: UniProtKB
Complete GO annotation...

Keywords - Cellular componenti

Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 11731173RNA polymerase-associated protein CTR9 homologPRO_0000231589Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei925 – 9251PhosphothreonineCombined sources
Modified residuei932 – 9321PhosphoserineBy similarity
Modified residuei941 – 9411PhosphoserineCombined sources
Modified residuei943 – 9431PhosphoserineBy similarity
Modified residuei970 – 9701PhosphoserineCombined sources
Modified residuei1020 – 10201PhosphoserineBy similarity
Modified residuei1021 – 10211PhosphoserineBy similarity
Modified residuei1037 – 10371PhosphoserineCombined sources
Modified residuei1039 – 10391PhosphoserineCombined sources
Modified residuei1041 – 10411PhosphoserineCombined sources
Modified residuei1079 – 10791PhosphoserineCombined sources
Modified residuei1083 – 10831PhosphoserineCombined sources
Modified residuei1085 – 10851PhosphoserineCombined sources
Modified residuei1095 – 10951PhosphoserineBy similarity
Modified residuei1100 – 11001PhosphoserineBy similarity

Keywords - PTMi

Phosphoprotein

Proteomic databases

EPDiQ62018.
MaxQBiQ62018.
PaxDbiQ62018.
PeptideAtlasiQ62018.
PRIDEiQ62018.

PTM databases

iPTMnetiQ62018.
PhosphoSiteiQ62018.

Expressioni

Tissue specificityi

Widely expressed.1 Publication

Gene expression databases

BgeeiENSMUSG00000005609.
GenevisibleiQ62018. MM.

Interactioni

Subunit structurei

Component of the PAF1 complex, which consists of CDC73, PAF1, LEO1, CTR9, RTF1 and WDR61. Interacts with KMT2A/MLL1 (By similarity). Interacts with STAT3.By similarity1 Publication

GO - Molecular functioni

  • RNA polymerase II core binding Source: GO_Central
  • SH2 domain binding Source: MGI

Protein-protein interaction databases

BioGridi204339. 9 interactions.
IntActiQ62018. 5 interactions.
MINTiMINT-1672610.
STRINGi10090.ENSMUSP00000005749.

Structurei

3D structure databases

ProteinModelPortaliQ62018.
SMRiQ62018. Positions 123-749.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Repeati41 – 7535TPR 1Add
BLAST
Repeati129 – 16234TPR 2Add
BLAST
Repeati163 – 19634TPR 3Add
BLAST
Repeati198 – 23134TPR 4Add
BLAST
Repeati235 – 26834TPR 5Add
BLAST
Repeati306 – 33934TPR 6Add
BLAST
Repeati341 – 37434TPR 7Add
BLAST
Repeati412 – 44433TPR 8Add
BLAST
Repeati451 – 48434TPR 9Add
BLAST
Repeati497 – 53034TPR 10Add
BLAST
Repeati531 – 56434TPR 11Add
BLAST
Repeati566 – 59833TPR 12Add
BLAST
Repeati613 – 64634TPR 13Add
BLAST
Repeati647 – 68034TPR 14Add
BLAST
Repeati681 – 71434TPR 15Add
BLAST
Repeati717 – 75034TPR 16Add
BLAST

Compositional bias

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Compositional biasi904 – 9085Poly-Gly
Compositional biasi933 – 9364Poly-Lys
Compositional biasi944 – 9518Poly-Glu
Compositional biasi959 – 9624Poly-Arg
Compositional biasi971 – 9766Poly-Glu
Compositional biasi1015 – 1172158Ser-richAdd
BLAST

Sequence similaritiesi

Contains 16 TPR repeats.PROSITE-ProRule annotation

Keywords - Domaini

Repeat, TPR repeat

Phylogenomic databases

eggNOGiKOG2002. Eukaryota.
COG0457. LUCA.
GeneTreeiENSGT00390000005097.
HOVERGENiHBG081372.
InParanoidiQ62018.
KOiK15176.
OMAiRNDPKNL.
OrthoDBiEOG091G01GC.
PhylomeDBiQ62018.
TreeFamiTF314342.

Family and domain databases

Gene3Di1.25.40.10. 5 hits.
InterProiIPR031101. Ctr9.
IPR013026. TPR-contain_dom.
IPR011990. TPR-like_helical_dom.
IPR019734. TPR_repeat.
[Graphical view]
PANTHERiPTHR14027:SF2. PTHR14027:SF2. 1 hit.
PfamiPF13181. TPR_8. 3 hits.
[Graphical view]
SMARTiSM00028. TPR. 10 hits.
[Graphical view]
SUPFAMiSSF48452. SSF48452. 3 hits.
PROSITEiPS50005. TPR. 10 hits.
PS50293. TPR_REGION. 1 hit.
[Graphical view]

Sequences (3)i

Sequence statusi: Complete.

This entry describes 3 isoformsi produced by alternative splicing. AlignAdd to basket

Isoform 1 (identifier: Q62018-1) [UniParc]FASTAAdd to basket

This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.

« Hide

        10         20         30         40         50
MSRGSIEIPL RDTDEVIELD FDQLPEGDEV ISILKQEHTQ LHIWIALALE
60 70 80 90 100
YYKQGKTEEF VKLLEAARID GNLDYRDHEK DQMTCLDTLA AYYVQQARKE
110 120 130 140 150
KNKDNKKDLI TQATLLYTMA DKIIMYDQNH LLGRACFCLL EGDKMDQADA
160 170 180 190 200
QFHFVLNQSP NNIPALLGKA CISFNKKDYR GALAYYKKAL RTNPGCPAEV
210 220 230 240 250
RLGMGHCFVK LNKLEKARLA FSRALELNSK CVGALVGLAV LELNNKEADS
260 270 280 290 300
IKNGVQLLSR AYTIDPSNPM VLNHLANHFF FKKDYSKVQH LALHAFHNTE
310 320 330 340 350
VEAMQAESCY QLARSFHVQE DYDQAFQYYY QATQFASSSF VLPFFGLGQM
360 370 380 390 400
YIYRGDKENA SQCFEKVLKA YPNNYETMKI LGSLYAASED QEKRDIAKGH
410 420 430 440 450
LKKVTEQYPD DVEAWIELAQ ILEQTDIQGA LSAYGTATRI LQEKVQADVP
460 470 480 490 500
PEILNNVGAL HFRLGNLGEA KKYFLASLDR AKAEAEHDEH YYNAISVTTS
510 520 530 540 550
YNLARLYEAM CEFHEAEKLY KNILREHPNY VDCYLRLGAM ARDKGNFYEA
560 570 580 590 600
SDWFKEALQI NQDHPDAWSL IGNLHLAKQE WGPGQKKFER ILKQPATQSD
610 620 630 640 650
TYSMLALGNV WLQTLHQPTR DREKEKRHQD RALAIYKQVL RNDAKNLYAA
660 670 680 690 700
NGIGAVLAHK GYFREARDVF AQVREATADI SDVWLNLAHI YVEQKQYISA
710 720 730 740 750
VQMYENCLRK FYKHQNTEVV LYLARALFKC GKLQECKQTL LKARHVAPSD
760 770 780 790 800
TVLMFNVALV LQRLATSVLK DEKSNLKEVL NAVKELELAH RYFSYLSKVG
810 820 830 840 850
DKMRFDLALA ASEARQCSDL LSQAQYHVAR ARKQDEEERE LRAKQEQEKE
860 870 880 890 900
LLRQKLLKEQ EEKRLREKEE QKKLLEQRAQ YVEKTKNILM FTGETEATKE
910 920 930 940 950
KKRGGGGGRR SKKGGEFDEF VNDDTDDDLP VSKKKKRRKG SGSEQEGEEE
960 970 980 990 1000
EGGERKKKRR RRPPKGEEGS EEEETENGPK PKKRRPPRAE KKKAPKPERL
1010 1020 1030 1040 1050
PPSMKGKIKS KAIISSSDDS SDEDKLKIAD EGHPRNSNSD SDDDERPNRR
1060 1070 1080 1090 1100
ASSESDSDDN QNKSGSEAGS PRRSGRQESD EDSDSDQPSR KRRRSGSEQS
1110 1120 1130 1140 1150
DNESVQSGRS PSGASENEND SRPASPSAES DHESEQGSDN EGSGQGSGNE
1160 1170
SEPEGSNNEA SDRGSEHGSD DSD
Length:1,173
Mass (Da):133,408
Last modified:April 4, 2006 - v2
Checksum:i2FB84564F1BEFD79
GO
Isoform 2 (identifier: Q62018-2) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     704-721: YENCLRKFYKHQNTEVVL → VTSLLLRIVACNVEPWLP
     722-1173: Missing.

Note: No experimental confirmation available.
Show »
Length:721
Mass (Da):82,546
Checksum:i6D0600A36B09374F
GO
Isoform 3 (identifier: Q62018-3) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     816-860: Missing.
     995-1032: Missing.

Note: No experimental confirmation available.
Show »
Length:1,090
Mass (Da):123,864
Checksum:i022D322BACADB17B
GO

Sequence cautioni

The sequence AAH53910 differs from that shown.Contaminating sequence. Potential poly-A sequence starting in position 937.Curated

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti144 – 1441K → Q in AAC42083 (PubMed:8636124).Curated
Sequence conflicti223 – 2231R → S in AAH53910 (PubMed:15489334).Curated
Sequence conflicti242 – 2421E → Q in BAC32223 (PubMed:16141072).Curated
Sequence conflicti390 – 3901D → Y in AAH53910 (PubMed:15489334).Curated
Sequence conflicti719 – 7191V → I in BAE22373 (PubMed:16141072).Curated
Sequence conflicti877 – 8771Q → R in AAH80719 (PubMed:15489334).Curated
Sequence conflicti900 – 9001E → K in AAH80719 (PubMed:15489334).Curated

Alternative sequence

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Alternative sequencei704 – 72118YENCL…TEVVL → VTSLLLRIVACNVEPWLP in isoform 2. 1 PublicationVSP_017846Add
BLAST
Alternative sequencei722 – 1173452Missing in isoform 2. 1 PublicationVSP_017847Add
BLAST
Alternative sequencei816 – 86045Missing in isoform 3. 1 PublicationVSP_017848Add
BLAST
Alternative sequencei995 – 103238Missing in isoform 3. 1 PublicationVSP_017849Add
BLAST

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
L49502 mRNA. Translation: AAC42083.1.
AK040205 mRNA. Translation: BAC30540.1.
AK040331 mRNA. Translation: BAC30566.1.
AK045101 mRNA. Translation: BAC32223.1.
AK083921 mRNA. Translation: BAC39065.2.
AK134990 mRNA. Translation: BAE22373.1.
AK148536 mRNA. Translation: BAE28606.1.
BC053910 mRNA. Translation: AAH53910.1. Sequence problems.
BC080719 mRNA. Translation: AAH80719.1.
AB093211 Transcribed RNA. Translation: BAC41395.1.
CCDSiCCDS21750.1. [Q62018-1]
PIRiT42719.
RefSeqiNP_033457.2. NM_009431.2. [Q62018-1]
UniGeneiMm.255858.

Genome annotation databases

EnsembliENSMUST00000005749; ENSMUSP00000005749; ENSMUSG00000005609. [Q62018-1]
GeneIDi22083.
KEGGimmu:22083.
UCSCiuc009jfw.1. mouse. [Q62018-2]
uc009jfx.1. mouse. [Q62018-1]

Keywords - Coding sequence diversityi

Alternative splicing

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
L49502 mRNA. Translation: AAC42083.1.
AK040205 mRNA. Translation: BAC30540.1.
AK040331 mRNA. Translation: BAC30566.1.
AK045101 mRNA. Translation: BAC32223.1.
AK083921 mRNA. Translation: BAC39065.2.
AK134990 mRNA. Translation: BAE22373.1.
AK148536 mRNA. Translation: BAE28606.1.
BC053910 mRNA. Translation: AAH53910.1. Sequence problems.
BC080719 mRNA. Translation: AAH80719.1.
AB093211 Transcribed RNA. Translation: BAC41395.1.
CCDSiCCDS21750.1. [Q62018-1]
PIRiT42719.
RefSeqiNP_033457.2. NM_009431.2. [Q62018-1]
UniGeneiMm.255858.

3D structure databases

ProteinModelPortaliQ62018.
SMRiQ62018. Positions 123-749.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi204339. 9 interactions.
IntActiQ62018. 5 interactions.
MINTiMINT-1672610.
STRINGi10090.ENSMUSP00000005749.

PTM databases

iPTMnetiQ62018.
PhosphoSiteiQ62018.

Proteomic databases

EPDiQ62018.
MaxQBiQ62018.
PaxDbiQ62018.
PeptideAtlasiQ62018.
PRIDEiQ62018.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENSMUST00000005749; ENSMUSP00000005749; ENSMUSG00000005609. [Q62018-1]
GeneIDi22083.
KEGGimmu:22083.
UCSCiuc009jfw.1. mouse. [Q62018-2]
uc009jfx.1. mouse. [Q62018-1]

Organism-specific databases

CTDi9646.
MGIiMGI:109345. Ctr9.
RougeiSearch...

Phylogenomic databases

eggNOGiKOG2002. Eukaryota.
COG0457. LUCA.
GeneTreeiENSGT00390000005097.
HOVERGENiHBG081372.
InParanoidiQ62018.
KOiK15176.
OMAiRNDPKNL.
OrthoDBiEOG091G01GC.
PhylomeDBiQ62018.
TreeFamiTF314342.

Miscellaneous databases

ChiTaRSiCtr9. mouse.
PROiQ62018.
SOURCEiSearch...

Gene expression databases

BgeeiENSMUSG00000005609.
GenevisibleiQ62018. MM.

Family and domain databases

Gene3Di1.25.40.10. 5 hits.
InterProiIPR031101. Ctr9.
IPR013026. TPR-contain_dom.
IPR011990. TPR-like_helical_dom.
IPR019734. TPR_repeat.
[Graphical view]
PANTHERiPTHR14027:SF2. PTHR14027:SF2. 1 hit.
PfamiPF13181. TPR_8. 3 hits.
[Graphical view]
SMARTiSM00028. TPR. 10 hits.
[Graphical view]
SUPFAMiSSF48452. SSF48452. 3 hits.
PROSITEiPS50005. TPR. 10 hits.
PS50293. TPR_REGION. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiCTR9_MOUSE
AccessioniPrimary (citable) accession number: Q62018
Secondary accession number(s): Q3UFF5
, Q3UY40, Q66JX4, Q7TPS6, Q8BND9, Q8BRD1, Q8C9W7, Q8C9Y3, Q8CHI1
Entry historyi
Integrated into UniProtKB/Swiss-Prot: April 4, 2006
Last sequence update: April 4, 2006
Last modified: September 7, 2016
This is version 136 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. MGD cross-references
    Mouse Genome Database (MGD) cross-references in UniProtKB/Swiss-Prot
  2. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.