CTR9_CAEEL
ID CTR9_CAEEL Reviewed; 1150 AA.
AC Q03560; C0P268; C0P269; C0P270;
DT 01-FEB-1994, integrated into UniProtKB/Swiss-Prot.
DT 30-MAY-2000, sequence version 3.
DT 03-AUG-2022, entry version 158.
DE RecName: Full=RNA polymerase-associated protein CTR9 {ECO:0000250|UniProtKB:P89105};
GN Name=ctr-9 {ECO:0000312|WormBase:B0464.2a};
GN Synonyms=tpr-3 {ECO:0000312|WormBase:B0464.2a};
GN ORFNames=B0464.2 {ECO:0000312|WormBase:B0464.2a};
OS Caenorhabditis elegans.
OC Eukaryota; Metazoa; Ecdysozoa; Nematoda; Chromadorea; Rhabditida;
OC Rhabditina; Rhabditomorpha; Rhabditoidea; Rhabditidae; Peloderinae;
OC Caenorhabditis.
OX NCBI_TaxID=6239;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=Bristol N2;
RX PubMed=7906398; DOI=10.1038/368032a0;
RA Wilson R., Ainscough R., Anderson K., Baynes C., Berks M., Bonfield J.,
RA Burton J., Connell M., Copsey T., Cooper J., Coulson A., Craxton M.,
RA Dear S., Du Z., Durbin R., Favello A., Fraser A., Fulton L., Gardner A.,
RA Green P., Hawkins T., Hillier L., Jier M., Johnston L., Jones M.,
RA Kershaw J., Kirsten J., Laisster N., Latreille P., Lightning J., Lloyd C.,
RA Mortimore B., O'Callaghan M., Parsons J., Percy C., Rifken L., Roopra A.,
RA Saunders D., Shownkeen R., Sims M., Smaldon N., Smith A., Smith M.,
RA Sonnhammer E., Staden R., Sulston J., Thierry-Mieg J., Thomas K.,
RA Vaudin M., Vaughan K., Waterston R., Watson A., Weinstock L.,
RA Wilkinson-Sproat J., Wohldman P.;
RT "2.2 Mb of contiguous nucleotide sequence from chromosome III of C.
RT elegans.";
RL Nature 368:32-38(1994).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=Bristol N2;
RX PubMed=9851916; DOI=10.1126/science.282.5396.2012;
RG The C. elegans sequencing consortium;
RT "Genome sequence of the nematode C. elegans: a platform for investigating
RT biology.";
RL Science 282:2012-2018(1998).
RN [3]
RP FUNCTION, SUBCELLULAR LOCATION, AND DISRUPTION PHENOTYPE.
RX PubMed=24721716; DOI=10.1016/j.ydbio.2014.04.002;
RA Kubota Y., Tsuyama K., Takabayashi Y., Haruta N., Maruyama R., Iida N.,
RA Sugimoto A.;
RT "The PAF1 complex is involved in embryonic epidermal morphogenesis in
RT Caenorhabditis elegans.";
RL Dev. Biol. 391:43-53(2014).
CC -!- FUNCTION: Component of the PAF1 complex which is a multifunctional
CC complex involved in transcription initiation via genetic interactions
CC with TATA-binding proteins, elongation and transcription-coupled
CC histone modification (By similarity). Ctr-9 is required for epidermal
CC microtubule organization during morphogenesis (PubMed:24721716).
CC {ECO:0000250|UniProtKB:P89105, ECO:0000269|PubMed:24721716}.
CC -!- SUBUNIT: Component of the PAF1 complex which consists of at least cdc-
CC 73, ctr-9, leo-1, pafo-1 and rtfo-1. {ECO:0000250|UniProtKB:P89105}.
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000269|PubMed:24721716}.
CC -!- ALTERNATIVE PRODUCTS:
CC Event=Alternative splicing; Named isoforms=2;
CC Name=a {ECO:0000312|WormBase:B0464.2a};
CC IsoId=Q03560-1; Sequence=Displayed;
CC Name=d {ECO:0000312|WormBase:B0464.2d};
CC IsoId=Q03560-4; Sequence=VSP_057316, VSP_057317;
CC -!- DISRUPTION PHENOTYPE: RNAi-mediated knock-down is mostly embryonic
CC lethal. Embryogenesis proceeds more slowly, with embryos displaying
CC defects in the positioning and shape of epidermal cells. Randomly
CC orientated microtubules are present in epidermal cells during the
CC epidermal elongation process. F-actin accumulation is visible at the
CC leading edge during ventral closure and circumferential actin bundles
CC are present in epidermal cells. Decreased expression of pafo-1,
CC increased cytoplasmic expression of leo-1 and increased nuclear
CC expression of rtfo-1. {ECO:0000269|PubMed:24721716,
CC ECO:0000303|PubMed:24721716}.
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DR EMBL; BX284603; CAA79544.1; -; Genomic_DNA.
DR EMBL; BX284603; CAX51623.1; -; Genomic_DNA.
DR PIR; D88556; D88556.
DR PIR; S28279; S28279.
DR RefSeq; NP_001255000.1; NM_001268071.1. [Q03560-1]
DR RefSeq; NP_001255001.1; NM_001268072.1. [Q03560-4]
DR AlphaFoldDB; Q03560; -.
DR SMR; Q03560; -.
DR BioGRID; 41532; 3.
DR ComplexPortal; CPX-966; PAF1 complex.
DR STRING; 6239.B0464.2c; -.
DR iPTMnet; Q03560; -.
DR EPD; Q03560; -.
DR PaxDb; Q03560; -.
DR PeptideAtlas; Q03560; -.
DR PRIDE; Q03560; -.
DR EnsemblMetazoa; B0464.2a.1; B0464.2a.1; WBGene00007184. [Q03560-1]
DR EnsemblMetazoa; B0464.2a.2; B0464.2a.2; WBGene00007184. [Q03560-1]
DR EnsemblMetazoa; B0464.2d.1; B0464.2d.1; WBGene00007184. [Q03560-4]
DR EnsemblMetazoa; B0464.2d.2; B0464.2d.2; WBGene00007184. [Q03560-4]
DR GeneID; 176335; -.
DR KEGG; cel:CELE_B0464.2; -.
DR UCSC; B0464.2; c. elegans. [Q03560-1]
DR CTD; 176335; -.
DR WormBase; B0464.2a; CE20456; WBGene00007184; ctr-9. [Q03560-1]
DR WormBase; B0464.2d; CE43518; WBGene00007184; ctr-9. [Q03560-4]
DR eggNOG; KOG2002; Eukaryota.
DR GeneTree; ENSGT00390000005097; -.
DR HOGENOM; CLU_006386_0_0_1; -.
DR InParanoid; Q03560; -.
DR OMA; MSNCIEI; -.
DR OrthoDB; 396755at2759; -.
DR PhylomeDB; Q03560; -.
DR Reactome; R-CEL-112382; Formation of RNA Pol II elongation complex.
DR Reactome; R-CEL-674695; RNA Polymerase II Pre-transcription Events.
DR Reactome; R-CEL-75955; RNA Polymerase II Transcription Elongation.
DR PRO; PR:Q03560; -.
DR Proteomes; UP000001940; Chromosome III.
DR Bgee; WBGene00007184; Expressed in embryo and 4 other tissues.
DR GO; GO:0016593; C:Cdc73/Paf1 complex; IBA:GO_Central.
DR GO; GO:0000993; F:RNA polymerase II complex binding; IBA:GO_Central.
DR GO; GO:0016571; P:histone methylation; IC:ComplexPortal.
DR GO; GO:0051569; P:regulation of histone H3-K4 methylation; IBA:GO_Central.
DR GO; GO:0006355; P:regulation of transcription, DNA-templated; IBA:GO_Central.
DR GO; GO:0006368; P:transcription elongation from RNA polymerase II promoter; IC:ComplexPortal.
DR Gene3D; 1.25.40.10; -; 3.
DR InterPro; IPR031101; Ctr9.
DR InterPro; IPR011990; TPR-like_helical_dom_sf.
DR InterPro; IPR019734; TPR_repeat.
DR PANTHER; PTHR14027; PTHR14027; 1.
DR Pfam; PF13181; TPR_8; 2.
DR SMART; SM00028; TPR; 10.
DR SUPFAM; SSF48452; SSF48452; 3.
DR PROSITE; PS50005; TPR; 9.
DR PROSITE; PS50293; TPR_REGION; 1.
PE 3: Inferred from homology;
KW Alternative splicing; Coiled coil; Nucleus; Reference proteome; Repeat;
KW TPR repeat.
FT CHAIN 1..1150
FT /note="RNA polymerase-associated protein CTR9"
FT /id="PRO_0000106421"
FT REPEAT 143..176
FT /note="TPR 1"
FT /evidence="ECO:0000255"
FT REPEAT 177..210
FT /note="TPR 2"
FT /evidence="ECO:0000255"
FT REPEAT 212..245
FT /note="TPR 3"
FT /evidence="ECO:0000255"
FT REPEAT 247..282
FT /note="TPR 4"
FT /evidence="ECO:0000255"
FT REPEAT 320..353
FT /note="TPR 5"
FT /evidence="ECO:0000255"
FT REPEAT 355..388
FT /note="TPR 6"
FT /evidence="ECO:0000255"
FT REPEAT 432..464
FT /note="TPR 7"
FT /evidence="ECO:0000255"
FT REPEAT 471..504
FT /note="TPR 8"
FT /evidence="ECO:0000255"
FT REPEAT 594..627
FT /note="TPR 9"
FT /evidence="ECO:0000255"
FT REPEAT 643..677
FT /note="TPR 10"
FT /evidence="ECO:0000255"
FT REPEAT 679..711
FT /note="TPR 11"
FT /evidence="ECO:0000255"
FT REPEAT 712..745
FT /note="TPR 12"
FT /evidence="ECO:0000255"
FT REPEAT 748..781
FT /note="TPR 13"
FT /evidence="ECO:0000255"
FT REGION 935..1150
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COILED 848..916
FT /evidence="ECO:0000255"
FT COILED 972..1028
FT /evidence="ECO:0000255"
FT COMPBIAS 935..952
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 992..1028
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 1039..1095
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 1118..1150
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT VAR_SEQ 25..206
FT /note="EVIEINCSELPDGEEVLQILEAEEAKLSYWIEVALEYYRQDRVDLFMMILES
FT AGSRAGLEYEGVKQDQMRALDILAAYWMTQGYREKAKDKKSDFFSKATVLFNTADKIAM
FT YEWSHLTVRAWFYLFERDKSTNKYELADQQFNYVVKTNPKNVLPLIGKAVIAFNKKDYK
FT TAIYYFRKAIRQ -> GTHLKRLRRFSIEVWNLMQNWATASEKSVQYLESLVNSRLKLL
FT YSREVDVEESAKLTKDQSDRVLNEIVVMNSKLNQTMSDFEKVIGKFEVAQGRMSAWKQL
FT TEKSQNIEEKYIVETLDENLPLIITMLKKELKVKQDVLFDFAQNDSRDVFTLVLLTFKH
FT EPFVDVALLSKLFALVASEAQ (in isoform d)"
FT /id="VSP_057316"
FT VAR_SEQ 207..1150
FT /note="Missing (in isoform d)"
FT /id="VSP_057317"
SQ SEQUENCE 1150 AA; 132345 MW; 1A7054727FBC96B7 CRC64;
MDESIDDVQE TRTIAIPLKD SHEDEVIEIN CSELPDGEEV LQILEAEEAK LSYWIEVALE
YYRQDRVDLF MMILESAGSR AGLEYEGVKQ DQMRALDILA AYWMTQGYRE KAKDKKSDFF
SKATVLFNTA DKIAMYEWSH LTVRAWFYLF ERDKSTNKYE LADQQFNYVV KTNPKNVLPL
IGKAVIAFNK KDYKTAIYYF RKAIRQCRHT IADLRVGIGH CFAKMGMMDK AKTAFERAME
IEPYNVSAMC GLGIILLNTY DHDSLKHAVS LFGRSYNLQT DHPVALIHLA NHFFFKKEIE
RAWTLAWHAA TYNDCDSIKA EAFYQMGRCR HAQGQFDGAY KYYYQARQAN NGEHTLAHYG
LGQMYIHRNE IEEAIKCFDT VHKRLPNNTD TMKILGSLYA HVQLNDPAQT AEARQKGRDV
LGKYLAVEND DYEACIDLAQ LLEATDPKRS LELYENAIDL LVTNESIQPQ PEMLNNVGAL
YMSMKQYEKA EHHFKRAKER LEEQLNTDEG SLLLERRSAP EKSHLLTIRY NLALCLEHLC
RTVEAEQMYK DIVKECPGYI DGYLRLGCIT RDRHQVYESS LWLKQGVQFD QASPIVWTLI
GNLHFAKNEW MPAQKKFEFI LSKIFNNKIP DPYSLVALGN VWFEQLLNPS RKKEDEKKYI
DRALQMYQKA LKLQPKNMYA ANGIGCVLAY KRNWNDARDV FSQVRESTSE FYDVWLNIAH
VCMEREQWMA AVQMYSSAMK KFRKENDSTL QHYLAKAYYR ANMLNEAKEA LECAMLDQLD
NTQLKFNYAI VLKKSAKEVL RGHKMTSEQV TAAIDDLKFA DKIFQYISKN DDRQSSHTGM
RISRTICAEE AKNCKDLLTQ AKHKLAAAQT QDEEERRLME KQEKEKIALQ NKMIEEARAK
EEAEKQKLED MKNLRLSFIE MTKDVLRLPE IVEEKRRGGG GRKRRNDDGD EFVNDSSDAG
NYDGEEGGED GERRERRKKD KAAKKASRKK RERRDSGGPD SNRRDEKKRK RKEERDRKLQ
EKLSAKQSAK IKSRAFLSSS ESSDDDKPKP AADSSDDEVD PRPPVDEFDS PTRTDSDSDR
ETTTKKKKKK AVVDSDEGSV SGSGSGSDND DKPIIGGSDD DDDDKPAGGN SRDSDGSDAP
KKKVIESDSD
