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Protein

Poly(U)-binding-splicing factor PUF60

Gene

Puf60

Organism
Mus musculus (Mouse)
Status
Reviewed-Annotation score: Annotation score: 4 out of 5-Experimental evidence at protein leveli

Functioni

DNA- and RNA-binding protein, involved in several nuclear processes such as pre-mRNA splicing, apoptosis and transcription regulation. In association with FUBP1 regulates MYC transcription at the P2 promoter through the core-TFIIH basal transcription factor. Acts as a transcriptional repressor through the core-TFIIH basal transcription factor. Represses FUBP1-induced transcriptional activation but not basal transcription. Decreases ERCC3 helicase activity. Is also involved in pre-mRNA splicing. Promotes splicing of an intron with weak 3'-splice site and pyrimidine tract in a cooperative manner with U2AF2. Involved in apoptosis induction when overexpressed in HeLa cells. Modulates alternative splicing of several mRNAs. Binds to relaxed DNA of active promoter regions. Binds to the pyrimidine tract and 3'-splice site regions of pre-mRNA; binding is enhanced in presence of U2AF2. Binds to Y5 RNA in association with TROVE2. Binds to poly(U) RNA (By similarity).By similarity

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Repressor, Ribonucleoprotein

Keywords - Biological processi

Apoptosis, mRNA processing, mRNA splicing, Transcription, Transcription regulation

Keywords - Ligandi

DNA-binding, RNA-binding

Names & Taxonomyi

Protein namesi
Recommended name:
Poly(U)-binding-splicing factor PUF60
Alternative name(s):
60 kDa poly(U)-binding-splicing factor
Gene namesi
Name:Puf60
OrganismiMus musculus (Mouse)
Taxonomic identifieri10090 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeMusMus
Proteomesi
  • UP000000589 Componenti: Chromosome 15

Organism-specific databases

MGIiMGI:1915209. Puf60.

Subcellular locationi

  • Nucleus

  • Note: Colocalizes partially with TROVE2.By similarity

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 564564Poly(U)-binding-splicing factor PUF60PRO_0000299520Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei65 – 651PhosphothreonineBy similarity
Modified residuei117 – 1171PhosphoserineBy similarity
Modified residuei249 – 2491PhosphoserineCombined sources
Modified residuei256 – 2561N6-acetyllysineBy similarity
Modified residuei319 – 3191PhosphothreonineBy similarity
Modified residuei459 – 4591N6-acetyllysineBy similarity
Cross-linki463 – 463Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2)By similarity

Keywords - PTMi

Acetylation, Isopeptide bond, Phosphoprotein, Ubl conjugation

Proteomic databases

EPDiQ3UEB3.
MaxQBiQ3UEB3.
PaxDbiQ3UEB3.
PRIDEiQ3UEB3.

PTM databases

iPTMnetiQ3UEB3.
PhosphoSiteiQ3UEB3.
SwissPalmiQ3UEB3.

Expressioni

Gene expression databases

BgeeiQ3UEB3.
CleanExiMM_PUF60.
GenevisibleiQ3UEB3. MM.

Interactioni

Subunit structurei

Homodimer. Associates with the spliceosome. Found in a complex with TROVE2 and Y5 RNA. Found in a complex with FUBP1 and far upstream element (FUSE) DNA segment. Interacts directly with ERCC3. Interacts with CDK7, GTF2H1 and SFRS11 (By similarity).By similarity

GO - Molecular functioni

Protein-protein interaction databases

BioGridi212566. 1 interaction.
IntActiQ3UEB3. 1 interaction.
MINTiMINT-4121043.
STRINGi10090.ENSMUSP00000098096.

Structurei

3D structure databases

ProteinModelPortaliQ3UEB3.
SMRiQ3UEB3. Positions 123-318, 448-564.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini134 – 21279RRM 1PROSITE-ProRule annotationAdd
BLAST
Domaini231 – 30979RRM 2PROSITE-ProRule annotationAdd
BLAST
Domaini467 – 55488RRM 3; atypicalPROSITE-ProRule annotationAdd
BLAST

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni1 – 521521Inhibits homodimerizationBy similarityAdd
BLAST
Regioni82 – 564483Inhibits transcriptional repression, interaction with ERCC3 and apoptosis inductionBy similarityAdd
BLAST

Compositional bias

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Compositional biasi326 – 38156Ala-richAdd
BLAST

Domaini

The third RNA recognition motif, called PUMP domain, is atypical and may rather mediate homodimerization and/or protein-protein interactions.

Sequence similaritiesi

Belongs to the RRM half pint family.Curated
Contains 3 RRM (RNA recognition motif) domains.PROSITE-ProRule annotation

Keywords - Domaini

Repeat

Phylogenomic databases

eggNOGiKOG0124. Eukaryota.
ENOG410XSGH. LUCA.
GeneTreeiENSGT00760000118913.
HOGENOMiHOG000267001.
HOVERGENiHBG055622.
InParanoidiQ3UEB3.
KOiK12838.
OMAiAFVEYDV.
OrthoDBiEOG70KGPB.
PhylomeDBiQ3UEB3.
TreeFamiTF313987.

Family and domain databases

Gene3Di3.30.70.330. 3 hits.
InterProiIPR012677. Nucleotide-bd_a/b_plait.
IPR006532. PolyU-bd.
IPR000504. RRM_dom.
IPR003954. RRM_dom_euk.
[Graphical view]
PfamiPF00076. RRM_1. 2 hits.
[Graphical view]
SMARTiSM00360. RRM. 3 hits.
SM00361. RRM_1. 2 hits.
[Graphical view]
SUPFAMiSSF54928. SSF54928. 3 hits.
TIGRFAMsiTIGR01645. half-pint. 1 hit.
PROSITEiPS50102. RRM. 3 hits.
[Graphical view]

Sequences (3)i

Sequence statusi: Complete.

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

Isoform 1 (identifier: Q3UEB3-1) [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
MATATIALQV NGQQGGGSEP AAAAAAAAAA VVAAGDKWKP PQGTESIKME
60 70 80 90 100
NGQSTGTKLG LPPLTPEQQE ALQKAKKYAM EQSIKSVLVK QTIAHQQQQL
110 120 130 140 150
TNLQMAAVTM GFGDPLSPLQ SMAAQRQRAL AIMCRVYVGS IYYELGEDTI
160 170 180 190 200
RQAFAPFGPI KSIDMSWDSV TMKHKGFAFV EYEVPEAAQL ALEQMNSVML
210 220 230 240 250
GGRNIKVGRP SNIGQAQPII DQLAEEARAF NRIYVASVHQ DLSDDDIKSV
260 270 280 290 300
FEAFGKIKSC TLARDPTTGK HKGYGFIEYE KAQSSQDAVS SMNLFDLGGQ
310 320 330 340 350
YLRVGKAVTP PMPLLTPATP GGLPPAAAVA AAAATAKITA QEAVAGAAVL
360 370 380 390 400
GTLATPGLVS PALTLAQPLG ALPQAVMAAQ APGVITGVTP ARPPIPVTIP
410 420 430 440 450
SVGVVNPILA SPPTLGLLEP KKEKEEEELF PESERPEMLS EQEHMSISGS
460 470 480 490 500
SARHMVMQKL LRKQESTVMV LRNMVDPKDI DDDLEGEVTE ECGKFGAVNR
510 520 530 540 550
VIIYQEKQGE EEDAEIIVKI FVEFSMASET HKAIQALNGR WFGGRKVVAE
560
VYDQERFDNS DLSA
Length:564
Mass (Da):60,249
Last modified:September 11, 2007 - v2
Checksum:iC30B70E645AB0161
GO
Isoform 2 (identifier: Q3UEB3-2) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     105-121: Missing.

Show »
Length:547
Mass (Da):58,545
Checksum:iE5B938BBF3A60497
GO
Isoform 3 (identifier: Q3UEB3-3) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     1-48: Missing.
     105-121: Missing.

Show »
Length:499
Mass (Da):54,029
Checksum:i099F259F27BCD19F
GO

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti138 – 1381V → A in BAE28998 (PubMed:16141072).Curated

Alternative sequence

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Alternative sequencei1 – 4848Missing in isoform 3. 1 PublicationVSP_027720Add
BLAST
Alternative sequencei105 – 12117Missing in isoform 2 and isoform 3. 2 PublicationsVSP_027721Add
BLAST

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AK149632 mRNA. Translation: BAE28998.1.
AK151526 mRNA. Translation: BAE30474.1.
AK168789 mRNA. Translation: BAE40622.1.
BC010601 mRNA. Translation: AAH10601.1.
CCDSiCCDS37111.1. [Q3UEB3-2]
CCDS37112.1. [Q3UEB3-1]
RefSeqiNP_001158072.1. NM_001164600.1. [Q3UEB3-3]
NP_082640.2. NM_028364.2. [Q3UEB3-1]
NP_598452.2. NM_133691.5. [Q3UEB3-2]
UniGeneiMm.29965.

Genome annotation databases

EnsembliENSMUST00000002599; ENSMUSP00000002599; ENSMUSG00000002524. [Q3UEB3-2]
ENSMUST00000100527; ENSMUSP00000098096; ENSMUSG00000002524. [Q3UEB3-1]
GeneIDi67959.
KEGGimmu:67959.
UCSCiuc007wij.2. mouse. [Q3UEB3-1]
uc007wik.2. mouse. [Q3UEB3-2]
uc011zup.1. mouse. [Q3UEB3-3]

Keywords - Coding sequence diversityi

Alternative splicing

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AK149632 mRNA. Translation: BAE28998.1.
AK151526 mRNA. Translation: BAE30474.1.
AK168789 mRNA. Translation: BAE40622.1.
BC010601 mRNA. Translation: AAH10601.1.
CCDSiCCDS37111.1. [Q3UEB3-2]
CCDS37112.1. [Q3UEB3-1]
RefSeqiNP_001158072.1. NM_001164600.1. [Q3UEB3-3]
NP_082640.2. NM_028364.2. [Q3UEB3-1]
NP_598452.2. NM_133691.5. [Q3UEB3-2]
UniGeneiMm.29965.

3D structure databases

ProteinModelPortaliQ3UEB3.
SMRiQ3UEB3. Positions 123-318, 448-564.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi212566. 1 interaction.
IntActiQ3UEB3. 1 interaction.
MINTiMINT-4121043.
STRINGi10090.ENSMUSP00000098096.

PTM databases

iPTMnetiQ3UEB3.
PhosphoSiteiQ3UEB3.
SwissPalmiQ3UEB3.

Proteomic databases

EPDiQ3UEB3.
MaxQBiQ3UEB3.
PaxDbiQ3UEB3.
PRIDEiQ3UEB3.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENSMUST00000002599; ENSMUSP00000002599; ENSMUSG00000002524. [Q3UEB3-2]
ENSMUST00000100527; ENSMUSP00000098096; ENSMUSG00000002524. [Q3UEB3-1]
GeneIDi67959.
KEGGimmu:67959.
UCSCiuc007wij.2. mouse. [Q3UEB3-1]
uc007wik.2. mouse. [Q3UEB3-2]
uc011zup.1. mouse. [Q3UEB3-3]

Organism-specific databases

CTDi22827.
MGIiMGI:1915209. Puf60.

Phylogenomic databases

eggNOGiKOG0124. Eukaryota.
ENOG410XSGH. LUCA.
GeneTreeiENSGT00760000118913.
HOGENOMiHOG000267001.
HOVERGENiHBG055622.
InParanoidiQ3UEB3.
KOiK12838.
OMAiAFVEYDV.
OrthoDBiEOG70KGPB.
PhylomeDBiQ3UEB3.
TreeFamiTF313987.

Miscellaneous databases

NextBioi326074.
PROiQ3UEB3.
SOURCEiSearch...

Gene expression databases

BgeeiQ3UEB3.
CleanExiMM_PUF60.
GenevisibleiQ3UEB3. MM.

Family and domain databases

Gene3Di3.30.70.330. 3 hits.
InterProiIPR012677. Nucleotide-bd_a/b_plait.
IPR006532. PolyU-bd.
IPR000504. RRM_dom.
IPR003954. RRM_dom_euk.
[Graphical view]
PfamiPF00076. RRM_1. 2 hits.
[Graphical view]
SMARTiSM00360. RRM. 3 hits.
SM00361. RRM_1. 2 hits.
[Graphical view]
SUPFAMiSSF54928. SSF54928. 3 hits.
TIGRFAMsiTIGR01645. half-pint. 1 hit.
PROSITEiPS50102. RRM. 3 hits.
[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] (ISOFORMS 1 AND 2).
    Strain: C57BL/6J.
    Tissue: Bone marrow and Heart.
  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] (ISOFORM 3).
    Strain: NMRI.
    Tissue: Mammary tumor.
  3. Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-249, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    Tissue: Brain, Brown adipose tissue, Kidney, Liver, Lung, Spleen and Testis.

Entry informationi

Entry nameiPUF60_MOUSE
AccessioniPrimary (citable) accession number: Q3UEB3
Secondary accession number(s): Q3TGC6, Q91VR6
Entry historyi
Integrated into UniProtKB/Swiss-Prot: September 11, 2007
Last sequence update: September 11, 2007
Last modified: May 11, 2016
This is version 102 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.