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Protein

Cleavage and polyadenylation specificity factor subunit 6

Gene

Cpsf6

Organism
Mus musculus (Mouse)
Status
Reviewed-Annotation score: Annotation score: 3 out of 5-Experimental evidence at protein leveli

Functioni

Component of the cleavage factor Im complex (CFIm) that plays a key role in pre-mRNA 3'-processing. Involved in association with NUDT21/CPSF5 in pre-MRNA 3'-end poly(A) site cleavage and poly(A) addition. CPSF6 binds to cleavage and polyadenylation RNA substrates and promotes RNA looping (By similarity).By similarity

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Biological processi

mRNA processing

Keywords - Ligandi

RNA-binding

Names & Taxonomyi

Protein namesi
Recommended name:
Cleavage and polyadenylation specificity factor subunit 6
Gene namesi
Name:Cpsf6
OrganismiMus musculus (Mouse)
Taxonomic identifieri10090 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeMusMus
Proteomesi
  • UP000000589 Componenti: Chromosome 10

Organism-specific databases

MGIiMGI:1913948. Cpsf6.

Subcellular locationi

  • Nucleus By similarity

  • Note: In punctate subnuclear structures localized adjacent to nuclear speckles, called paraspeckles.By similarity

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 551551Cleavage and polyadenylation specificity factor subunit 6PRO_0000081522Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei404 – 4041PhosphothreonineBy similarity
Modified residuei407 – 4071PhosphothreonineBy similarity

Keywords - PTMi

Phosphoprotein

Proteomic databases

EPDiQ6NVF9.
MaxQBiQ6NVF9.
PaxDbiQ6NVF9.
PRIDEiQ6NVF9.

PTM databases

iPTMnetiQ6NVF9.
PhosphoSiteiQ6NVF9.

Expressioni

Gene expression databases

BgeeiQ6NVF9.
CleanExiMM_CPSF6.
ExpressionAtlasiQ6NVF9. baseline and differential.
GenevisibleiQ6NVF9. MM.

Interactioni

Subunit structurei

Component of the cleavage factor Im (CFIm) complex, composed at least of NUDT21/CPSF5 and CPSF6 or CPSF7. Within the cleavage factor Im complex, the NUDT21/CPSF5 homodimer is at the core of a heterotetramer, and is clasped by two additional subunits (CPSF6 or CPSF7). Interacts with NUDT21/CPSF5, SFRS3, SFRS7, SNRNP70 and TRA2B/SFRS10 (By similarity).By similarity

Protein-protein interaction databases

BioGridi240650. 5 interactions.
DIPiDIP-49394N.
IntActiQ6NVF9. 3 interactions.
MINTiMINT-1563275.
STRINGi10090.ENSMUSP00000068408.

Structurei

3D structure databases

ProteinModelPortaliQ6NVF9.
SMRiQ6NVF9. Positions 80-158.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini81 – 16181RRMPROSITE-ProRule annotationAdd
BLAST

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni81 – 16181Necessary for interaction with NUDT21/CPSF5By similarityAdd
BLAST
Regioni510 – 55142Sufficient for nuclear targetingBy similarityAdd
BLAST

Compositional bias

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Compositional biasi208 – 398191Pro-richAdd
BLAST
Compositional biasi490 – 55162Arg-richAdd
BLAST

Sequence similaritiesi

Belongs to the RRM CPSF6/7 family.Curated
Contains 1 RRM (RNA recognition motif) domain.PROSITE-ProRule annotation

Phylogenomic databases

eggNOGiKOG4849. Eukaryota.
ENOG410Y0H0. LUCA.
GeneTreeiENSGT00730000110905.
HOGENOMiHOG000111137.
InParanoidiQ6NVF9.
KOiK14398.
OrthoDBiEOG74TX09.
PhylomeDBiQ6NVF9.
TreeFamiTF316430.

Family and domain databases

Gene3Di3.30.70.330. 1 hit.
InterProiIPR012677. Nucleotide-bd_a/b_plait.
IPR000504. RRM_dom.
[Graphical view]
PfamiPF00076. RRM_1. 1 hit.
[Graphical view]
SMARTiSM00360. RRM. 1 hit.
[Graphical view]
SUPFAMiSSF54928. SSF54928. 1 hit.
PROSITEiPS50102. RRM. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Q6NVF9-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MADGVDHIDI YADVGEEFNQ EAEYGGHDQI DLYDDVISPS ANNGDAPEDR
60 70 80 90 100
DYMDTLPPTV GDDVGKGAAP NVVYTYTGKR IALYIGNLTW WTTDEDLTEA
110 120 130 140 150
VHSLGVNDIL EIKFFENRAN GQSKGFALVG VGSEASSKKL MDLLPKRELH
160 170 180 190 200
GQSPVVTPCN KQFLSQFEMQ SRKTTQSGQM SGEGKAGPPG GGSRAAFPQG
210 220 230 240 250
GRGRGRFPGA VPGGDRFPGP AGPGGPPPPF PAGQTPPRPP LGPPGPPGPP
260 270 280 290 300
GPPPPGQVLP PPLAGPPNRG DRPPPPVLFP GQPFGQPPLG PLPPGPPPPV
310 320 330 340 350
PGYGPPPGPP PPQQGPPPPP GPFPPRPPGP LGPPLTLAPP PHLPGPPPGA
360 370 380 390 400
PPPAPHVNPA FFPPPTNSGM PTSDSRGPPP TDPYGRPPPY DRGDYGPPGR
410 420 430 440 450
EMDTARTPLS EAEFEEIMNR NRAISSSAIS RAVSDASAGD YGSAIETLVT
460 470 480 490 500
AISLIKQSKV SADDRCKVLI SSLQDCLHGI ESKSYGSGSR RERSRERDHS
510 520 530 540 550
RSREKSRRHK SRSRDRHDDY YRERSRERER HRDRDRDRDR ERDREREYRH

R
Length:551
Mass (Da):59,153
Last modified:July 5, 2004 - v1
Checksum:iFCE1420FBE7589C8
GO

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti95 – 951E → K in BAC32898 (PubMed:16141072).Curated
Sequence conflicti266 – 2661P → L in BAC32898 (PubMed:16141072).Curated
Sequence conflicti289 – 2891L → V in BAC33392 (PubMed:16141072).Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AK046856 mRNA. Translation: BAC32898.1.
AK048615 mRNA. Translation: BAC33392.1.
AK168764 mRNA. Translation: BAE40600.1.
BC068133 mRNA. Translation: AAH68133.1.
CCDSiCCDS24193.1.
RefSeqiNP_001013409.1. NM_001013391.2.
XP_006513921.1. XM_006513858.2.
UniGeneiMm.478881.
Mm.478884.
Mm.479892.

Genome annotation databases

EnsembliENSMUST00000069168; ENSMUSP00000068408; ENSMUSG00000055531.
ENSMUST00000177145; ENSMUSP00000135136; ENSMUSG00000055531.
GeneIDi432508.
KEGGimmu:432508.
UCSCiuc007hdd.2. mouse.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AK046856 mRNA. Translation: BAC32898.1.
AK048615 mRNA. Translation: BAC33392.1.
AK168764 mRNA. Translation: BAE40600.1.
BC068133 mRNA. Translation: AAH68133.1.
CCDSiCCDS24193.1.
RefSeqiNP_001013409.1. NM_001013391.2.
XP_006513921.1. XM_006513858.2.
UniGeneiMm.478881.
Mm.478884.
Mm.479892.

3D structure databases

ProteinModelPortaliQ6NVF9.
SMRiQ6NVF9. Positions 80-158.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi240650. 5 interactions.
DIPiDIP-49394N.
IntActiQ6NVF9. 3 interactions.
MINTiMINT-1563275.
STRINGi10090.ENSMUSP00000068408.

PTM databases

iPTMnetiQ6NVF9.
PhosphoSiteiQ6NVF9.

Proteomic databases

EPDiQ6NVF9.
MaxQBiQ6NVF9.
PaxDbiQ6NVF9.
PRIDEiQ6NVF9.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENSMUST00000069168; ENSMUSP00000068408; ENSMUSG00000055531.
ENSMUST00000177145; ENSMUSP00000135136; ENSMUSG00000055531.
GeneIDi432508.
KEGGimmu:432508.
UCSCiuc007hdd.2. mouse.

Organism-specific databases

CTDi11052.
MGIiMGI:1913948. Cpsf6.

Phylogenomic databases

eggNOGiKOG4849. Eukaryota.
ENOG410Y0H0. LUCA.
GeneTreeiENSGT00730000110905.
HOGENOMiHOG000111137.
InParanoidiQ6NVF9.
KOiK14398.
OrthoDBiEOG74TX09.
PhylomeDBiQ6NVF9.
TreeFamiTF316430.

Miscellaneous databases

NextBioi407730.
PROiQ6NVF9.
SOURCEiSearch...

Gene expression databases

BgeeiQ6NVF9.
CleanExiMM_CPSF6.
ExpressionAtlasiQ6NVF9. baseline and differential.
GenevisibleiQ6NVF9. MM.

Family and domain databases

Gene3Di3.30.70.330. 1 hit.
InterProiIPR012677. Nucleotide-bd_a/b_plait.
IPR000504. RRM_dom.
[Graphical view]
PfamiPF00076. RRM_1. 1 hit.
[Graphical view]
SMARTiSM00360. RRM. 1 hit.
[Graphical view]
SUPFAMiSSF54928. SSF54928. 1 hit.
PROSITEiPS50102. RRM. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

  1. "The transcriptional landscape of the mammalian genome."
    Carninci P., Kasukawa T., Katayama S., Gough J., Frith M.C., Maeda N., Oyama R., Ravasi T., Lenhard B., Wells C., Kodzius R., Shimokawa K., Bajic V.B., Brenner S.E., Batalov S., Forrest A.R., Zavolan M., Davis M.J.
    , Wilming L.G., Aidinis V., Allen J.E., Ambesi-Impiombato A., Apweiler R., Aturaliya R.N., Bailey T.L., Bansal M., Baxter L., Beisel K.W., Bersano T., Bono H., Chalk A.M., Chiu K.P., Choudhary V., Christoffels A., Clutterbuck D.R., Crowe M.L., Dalla E., Dalrymple B.P., de Bono B., Della Gatta G., di Bernardo D., Down T., Engstrom P., Fagiolini M., Faulkner G., Fletcher C.F., Fukushima T., Furuno M., Futaki S., Gariboldi M., Georgii-Hemming P., Gingeras T.R., Gojobori T., Green R.E., Gustincich S., Harbers M., Hayashi Y., Hensch T.K., Hirokawa N., Hill D., Huminiecki L., Iacono M., Ikeo K., Iwama A., Ishikawa T., Jakt M., Kanapin A., Katoh M., Kawasawa Y., Kelso J., Kitamura H., Kitano H., Kollias G., Krishnan S.P., Kruger A., Kummerfeld S.K., Kurochkin I.V., Lareau L.F., Lazarevic D., Lipovich L., Liu J., Liuni S., McWilliam S., Madan Babu M., Madera M., Marchionni L., Matsuda H., Matsuzawa S., Miki H., Mignone F., Miyake S., Morris K., Mottagui-Tabar S., Mulder N., Nakano N., Nakauchi H., Ng P., Nilsson R., Nishiguchi S., Nishikawa S., Nori F., Ohara O., Okazaki Y., Orlando V., Pang K.C., Pavan W.J., Pavesi G., Pesole G., Petrovsky N., Piazza S., Reed J., Reid J.F., Ring B.Z., Ringwald M., Rost B., Ruan Y., Salzberg S.L., Sandelin A., Schneider C., Schoenbach C., Sekiguchi K., Semple C.A., Seno S., Sessa L., Sheng Y., Shibata Y., Shimada H., Shimada K., Silva D., Sinclair B., Sperling S., Stupka E., Sugiura K., Sultana R., Takenaka Y., Taki K., Tammoja K., Tan S.L., Tang S., Taylor M.S., Tegner J., Teichmann S.A., Ueda H.R., van Nimwegen E., Verardo R., Wei C.L., Yagi K., Yamanishi H., Zabarovsky E., Zhu S., Zimmer A., Hide W., Bult C., Grimmond S.M., Teasdale R.D., Liu E.T., Brusic V., Quackenbush J., Wahlestedt C., Mattick J.S., Hume D.A., Kai C., Sasaki D., Tomaru Y., Fukuda S., Kanamori-Katayama M., Suzuki M., Aoki J., Arakawa T., Iida J., Imamura K., Itoh M., Kato T., Kawaji H., Kawagashira N., Kawashima T., Kojima M., Kondo S., Konno H., Nakano K., Ninomiya N., Nishio T., Okada M., Plessy C., Shibata K., Shiraki T., Suzuki S., Tagami M., Waki K., Watahiki A., Okamura-Oho Y., Suzuki H., Kawai J., Hayashizaki Y.
    Science 309:1559-1563(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
    Strain: C57BL/6J.
    Tissue: Head, Kidney and Medulla oblongata.
  2. "The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)."
    The MGC Project Team
    Genome Res. 14:2121-2127(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
    Strain: C57BL/6J.
    Tissue: Brain.
  3. Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    Tissue: Brain, Kidney, Liver, Lung and Spleen.

Entry informationi

Entry nameiCPSF6_MOUSE
AccessioniPrimary (citable) accession number: Q6NVF9
Secondary accession number(s): Q8BX86, Q8BXI8
Entry historyi
Integrated into UniProtKB/Swiss-Prot: February 7, 2006
Last sequence update: July 5, 2004
Last modified: April 13, 2016
This is version 112 of the entry and version 1 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.