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Protein

Putative RNA polymerase II subunit B1 CTD phosphatase RPAP2

Gene

RPAP2

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Protein phosphatase that displays CTD phosphatase activity and regulates transcription of snRNA genes. Recognizes and binds phosphorylated 'Ser-7' of the C-terminal heptapeptide repeat domain (CTD) of the largest RNA polymerase II subunit POLR2A, and mediates dephosphorylation of 'Ser-5' of the CTD, thereby promoting transcription of snRNA genes.2 Publications

Catalytic activityi

[a protein]-serine/threonine phosphate + H2O = [a protein]-serine/threonine + phosphate.

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Zinc fingeri77 – 16084RTR1-typeAdd
BLAST

GO - Molecular functioni

  • CTD phosphatase activity Source: UniProtKB
  • metal ion binding Source: UniProtKB-KW

GO - Biological processi

  • dephosphorylation of RNA polymerase II C-terminal domain Source: UniProtKB
  • snRNA transcription Source: UniProtKB
Complete GO annotation...

Keywords - Molecular functioni

Hydrolase, Protein phosphatase

Keywords - Biological processi

Transcription, Transcription regulation

Keywords - Ligandi

Metal-binding, Zinc

Names & Taxonomyi

Protein namesi
Recommended name:
Putative RNA polymerase II subunit B1 CTD phosphatase RPAP2 (EC:3.1.3.16)
Alternative name(s):
RNA polymerase II-associated protein 2
Gene namesi
Name:RPAP2
Synonyms:C1orf82
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
ProteomesiUP000005640 Componenti: Chromosome 1

Organism-specific databases

HGNCiHGNC:25791. RPAP2.

Subcellular locationi

  • Cytoplasm 1 Publication
  • Nucleus 1 Publication

  • Note: Shuttles between the cytoplasm and the nucleus in a CRM1-dependent manner.

GO - Cellular componenti

  • cytoplasm Source: UniProtKB
  • DNA-directed RNA polymerase II, holoenzyme Source: UniProtKB
  • nucleolus Source: HPA
  • nucleus Source: UniProtKB
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm, Nucleus

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi100 – 1001C → A: Abolishes interaction with RNA polymerase II complex subunits; when associated with A-105. 1 Publication
Mutagenesisi105 – 1051C → A: Abolishes interaction with RNA polymerase II complex subunits; when associated with A-100. 1 Publication
Mutagenesisi136 – 1361C → A: Abolishes interaction with RNA polymerase II complex subunits; when associated with A-140. 1 Publication
Mutagenesisi140 – 1401C → A: Abolishes interaction with RNA polymerase II complex subunits; when associated with A-136. 1 Publication

Organism-specific databases

PharmGKBiPA162401981.

Polymorphism and mutation databases

BioMutaiRPAP2.
DMDMi74750745.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Initiator methioninei1 – 11Removed1 Publication
Chaini2 – 612611Putative RNA polymerase II subunit B1 CTD phosphatase RPAP2PRO_0000250648Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei2 – 21N-acetylalanine1 Publication
Modified residuei433 – 4331Phosphoserine1 Publication
Modified residuei480 – 4801Phosphoserine1 Publication

Keywords - PTMi

Acetylation, Phosphoprotein

Proteomic databases

MaxQBiQ8IXW5.
PaxDbiQ8IXW5.
PRIDEiQ8IXW5.

PTM databases

DEPODiQ8IXW5.
PhosphoSiteiQ8IXW5.

Expressioni

Gene expression databases

BgeeiQ8IXW5.
CleanExiHS_RPAP2.
GenevestigatoriQ8IXW5.

Organism-specific databases

HPAiHPA046443.

Interactioni

Subunit structurei

Associates with the RNA polymerase II complex. Interacts with transcribing RNA polymerase II phosphorylated on 'Ser-7' on CTD.2 Publications

Protein-protein interaction databases

BioGridi122959. 54 interactions.
IntActiQ8IXW5. 4 interactions.
STRINGi9606.ENSP00000359368.

Structurei

3D structure databases

ProteinModelPortaliQ8IXW5.
SMRiQ8IXW5. Positions 53-172.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Coiled coil

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Coiled coili33 – 6836Sequence AnalysisAdd
BLAST

Domaini

The RTR1-type zinc finger mediates interactions with RNA polymerase II complex subunits.1 Publication

Sequence similaritiesi

Belongs to the RPAP2 family.Curated
Contains 1 RTR1-type zinc finger.Curated

Zinc finger

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Zinc fingeri77 – 16084RTR1-typeAdd
BLAST

Keywords - Domaini

Coiled coil, Zinc-finger

Phylogenomic databases

eggNOGiNOG241465.
GeneTreeiENSGT00390000017965.
HOGENOMiHOG000253960.
HOVERGENiHBG080953.
InParanoidiQ8IXW5.
OMAiIIFRTSC.
OrthoDBiEOG7XWPQD.
PhylomeDBiQ8IXW5.
TreeFamiTF331431.

Family and domain databases

InterProiIPR007308. DUF408.
[Graphical view]
PfamiPF04181. RPAP2_Rtr1. 1 hit.
[Graphical view]
PROSITEiPS51479. ZF_RTR1. 1 hit.
[Graphical view]

Sequences (2)i

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

This entry describes 2 isoformsi produced by alternative splicing. AlignAdd to basket

Isoform 1 (identifier: Q8IXW5-1) [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
MADFAGPSSA GRKAGAPRCS RKAAGTKQTS TLKQEDASKR KAELEAAVRK
60 70 80 90 100
KIEFERKALH IVEQLLEENI TEEFLMECGR FITPAHYSDV VDERSIVKLC
110 120 130 140 150
GYPLCQKKLG IVPKQKYKIS TKTNKVYDIT ERKSFCSNFC YQASKFFEAQ
160 170 180 190 200
IPKTPVWVRE EERHPDFQLL KEEQSGHSGE EVQLCSKAIK TSDIDNPSHF
210 220 230 240 250
EKQYESSSSS THSDSSSDNE QDFVSSILPG NRPNSTNIRP QLHQKSIMKK
260 270 280 290 300
KAGHKANSKH KDKEQTVVDV TEQLGDCKLD SQEKDATCEL PLQKVNTQSS
310 320 330 340 350
SNSTLPERLK ASENSESEYS RSEITLVGIS KKSAEHFKRK FAKSNQVSRS
360 370 380 390 400
VSSSVQVCPE VGKRNLLKVL KETLIEWKTE ETLRFLYGQN YASVCLKPEA
410 420 430 440 450
SLVKEELDED DIISDPDSHF PAWRESQNSL DESLPFRGSG TAIKPLPSYE
460 470 480 490 500
NLKKETEKLN LRIREFYRGR YVLGEETTKS QDSEEHDSTF PLIDSSSQNQ
510 520 530 540 550
IRKRIVLEKL SKVLPGLLVP LQITLGDIYT QLKNLVRTFR LTNRNIIHKP
560 570 580 590 600
AEWTLIAMVL LSLLTPILGI QKHSQEGMVF TRFLDTLLEE LHLKNEDLES
610
LTIIFRTSCL PE
Length:612
Mass (Da):69,509
Last modified:March 1, 2003 - v1
Checksum:i43D6DE7C30BB5C96
GO
Isoform 2 (identifier: Q8IXW5-2) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     563-596: LLTPILGIQKHSQEGMVFTRFLDTLLEELHLKNE → FLLNVKTRIKTFMMIYFHLMNS
     597-612: Missing.

Show »
Length:584
Mass (Da):66,473
Checksum:iC01259C16617931A
GO

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti421 – 4211P → R in AAH31070 (PubMed:15489334).Curated
Sequence conflicti467 – 4671Y → C in BAB14465 (PubMed:14702039).Curated
Isoform 2 (identifier: Q8IXW5-2)
Sequence conflicti584 – 5841S → N in AAH31070 (PubMed:15489334).Curated

Alternative sequence

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Alternative sequencei563 – 59634LLTPI…HLKNE → FLLNVKTRIKTFMMIYFHLM NS in isoform 2. 1 PublicationVSP_020680Add
BLAST
Alternative sequencei597 – 61216Missing in isoform 2. 1 PublicationVSP_020681Add
BLAST

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AK023212 mRNA. Translation: BAB14465.1.
AL451010 Genomic DNA. Translation: CAH70763.1.
BC031070 mRNA. Translation: AAH31070.1.
BC039014 mRNA. Translation: AAH39014.1.
CCDSiCCDS740.1. [Q8IXW5-1]
RefSeqiNP_079089.2. NM_024813.2. [Q8IXW5-1]
UniGeneiHs.444421.

Genome annotation databases

EnsembliENST00000610020; ENSP00000476948; ENSG00000122484. [Q8IXW5-1]
GeneIDi79871.
KEGGihsa:79871.
UCSCiuc001dot.2. human. [Q8IXW5-1]

Keywords - Coding sequence diversityi

Alternative splicing

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AK023212 mRNA. Translation: BAB14465.1.
AL451010 Genomic DNA. Translation: CAH70763.1.
BC031070 mRNA. Translation: AAH31070.1.
BC039014 mRNA. Translation: AAH39014.1.
CCDSiCCDS740.1. [Q8IXW5-1]
RefSeqiNP_079089.2. NM_024813.2. [Q8IXW5-1]
UniGeneiHs.444421.

3D structure databases

ProteinModelPortaliQ8IXW5.
SMRiQ8IXW5. Positions 53-172.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi122959. 54 interactions.
IntActiQ8IXW5. 4 interactions.
STRINGi9606.ENSP00000359368.

PTM databases

DEPODiQ8IXW5.
PhosphoSiteiQ8IXW5.

Polymorphism and mutation databases

BioMutaiRPAP2.
DMDMi74750745.

Proteomic databases

MaxQBiQ8IXW5.
PaxDbiQ8IXW5.
PRIDEiQ8IXW5.

Protocols and materials databases

DNASUi79871.
Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000610020; ENSP00000476948; ENSG00000122484. [Q8IXW5-1]
GeneIDi79871.
KEGGihsa:79871.
UCSCiuc001dot.2. human. [Q8IXW5-1]

Organism-specific databases

CTDi79871.
GeneCardsiGC01P092764.
HGNCiHGNC:25791. RPAP2.
HPAiHPA046443.
MIMi611476. gene.
neXtProtiNX_Q8IXW5.
PharmGKBiPA162401981.
GenAtlasiSearch...

Phylogenomic databases

eggNOGiNOG241465.
GeneTreeiENSGT00390000017965.
HOGENOMiHOG000253960.
HOVERGENiHBG080953.
InParanoidiQ8IXW5.
OMAiIIFRTSC.
OrthoDBiEOG7XWPQD.
PhylomeDBiQ8IXW5.
TreeFamiTF331431.

Miscellaneous databases

ChiTaRSiRPAP2. human.
GeneWikiiRPAP2.
GenomeRNAii79871.
NextBioi69637.
PROiQ8IXW5.
SOURCEiSearch...

Gene expression databases

BgeeiQ8IXW5.
CleanExiHS_RPAP2.
GenevestigatoriQ8IXW5.

Family and domain databases

InterProiIPR007308. DUF408.
[Graphical view]
PfamiPF04181. RPAP2_Rtr1. 1 hit.
[Graphical view]
PROSITEiPS51479. ZF_RTR1. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "Complete sequencing and characterization of 21,243 full-length human cDNAs."
    Ota T., Suzuki Y., Nishikawa T., Otsuki T., Sugiyama T., Irie R., Wakamatsu A., Hayashi K., Sato H., Nagai K., Kimura K., Makita H., Sekine M., Obayashi M., Nishi T., Shibahara T., Tanaka T., Ishii S.
    , Yamamoto J., Saito K., Kawai Y., Isono Y., Nakamura Y., Nagahari K., Murakami K., Yasuda T., Iwayanagi T., Wagatsuma M., Shiratori A., Sudo H., Hosoiri T., Kaku Y., Kodaira H., Kondo H., Sugawara M., Takahashi M., Kanda K., Yokoi T., Furuya T., Kikkawa E., Omura Y., Abe K., Kamihara K., Katsuta N., Sato K., Tanikawa M., Yamazaki M., Ninomiya K., Ishibashi T., Yamashita H., Murakawa K., Fujimori K., Tanai H., Kimata M., Watanabe M., Hiraoka S., Chiba Y., Ishida S., Ono Y., Takiguchi S., Watanabe S., Yosida M., Hotuta T., Kusano J., Kanehori K., Takahashi-Fujii A., Hara H., Tanase T.-O., Nomura Y., Togiya S., Komai F., Hara R., Takeuchi K., Arita M., Imose N., Musashino K., Yuuki H., Oshima A., Sasaki N., Aotsuka S., Yoshikawa Y., Matsunawa H., Ichihara T., Shiohata N., Sano S., Moriya S., Momiyama H., Satoh N., Takami S., Terashima Y., Suzuki O., Nakagawa S., Senoh A., Mizoguchi H., Goto Y., Shimizu F., Wakebe H., Hishigaki H., Watanabe T., Sugiyama A., Takemoto M., Kawakami B., Yamazaki M., Watanabe K., Kumagai A., Itakura S., Fukuzumi Y., Fujimori Y., Komiyama M., Tashiro H., Tanigami A., Fujiwara T., Ono T., Yamada K., Fujii Y., Ozaki K., Hirao M., Ohmori Y., Kawabata A., Hikiji T., Kobatake N., Inagaki H., Ikema Y., Okamoto S., Okitani R., Kawakami T., Noguchi S., Itoh T., Shigeta K., Senba T., Matsumura K., Nakajima Y., Mizuno T., Morinaga M., Sasaki M., Togashi T., Oyama M., Hata H., Watanabe M., Komatsu T., Mizushima-Sugano J., Satoh T., Shirai Y., Takahashi Y., Nakagawa K., Okumura K., Nagase T., Nomura N., Kikuchi H., Masuho Y., Yamashita R., Nakai K., Yada T., Nakamura Y., Ohara O., Isogai T., Sugano S.
    Nat. Genet. 36:40-45(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1).
  2. "The DNA sequence and biological annotation of human chromosome 1."
    Gregory S.G., Barlow K.F., McLay K.E., Kaul R., Swarbreck D., Dunham A., Scott C.E., Howe K.L., Woodfine K., Spencer C.C.A., Jones M.C., Gillson C., Searle S., Zhou Y., Kokocinski F., McDonald L., Evans R., Phillips K.
    , Atkinson A., Cooper R., Jones C., Hall R.E., Andrews T.D., Lloyd C., Ainscough R., Almeida J.P., Ambrose K.D., Anderson F., Andrew R.W., Ashwell R.I.S., Aubin K., Babbage A.K., Bagguley C.L., Bailey J., Beasley H., Bethel G., Bird C.P., Bray-Allen S., Brown J.Y., Brown A.J., Buckley D., Burton J., Bye J., Carder C., Chapman J.C., Clark S.Y., Clarke G., Clee C., Cobley V., Collier R.E., Corby N., Coville G.J., Davies J., Deadman R., Dunn M., Earthrowl M., Ellington A.G., Errington H., Frankish A., Frankland J., French L., Garner P., Garnett J., Gay L., Ghori M.R.J., Gibson R., Gilby L.M., Gillett W., Glithero R.J., Grafham D.V., Griffiths C., Griffiths-Jones S., Grocock R., Hammond S., Harrison E.S.I., Hart E., Haugen E., Heath P.D., Holmes S., Holt K., Howden P.J., Hunt A.R., Hunt S.E., Hunter G., Isherwood J., James R., Johnson C., Johnson D., Joy A., Kay M., Kershaw J.K., Kibukawa M., Kimberley A.M., King A., Knights A.J., Lad H., Laird G., Lawlor S., Leongamornlert D.A., Lloyd D.M., Loveland J., Lovell J., Lush M.J., Lyne R., Martin S., Mashreghi-Mohammadi M., Matthews L., Matthews N.S.W., McLaren S., Milne S., Mistry S., Moore M.J.F., Nickerson T., O'Dell C.N., Oliver K., Palmeiri A., Palmer S.A., Parker A., Patel D., Pearce A.V., Peck A.I., Pelan S., Phelps K., Phillimore B.J., Plumb R., Rajan J., Raymond C., Rouse G., Saenphimmachak C., Sehra H.K., Sheridan E., Shownkeen R., Sims S., Skuce C.D., Smith M., Steward C., Subramanian S., Sycamore N., Tracey A., Tromans A., Van Helmond Z., Wall M., Wallis J.M., White S., Whitehead S.L., Wilkinson J.E., Willey D.L., Williams H., Wilming L., Wray P.W., Wu Z., Coulson A., Vaudin M., Sulston J.E., Durbin R.M., Hubbard T., Wooster R., Dunham I., Carter N.P., McVean G., Ross M.T., Harrow J., Olson M.V., Beck S., Rogers J., Bentley D.R.
    Nature 441:315-321(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
  3. "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] (ISOFORMS 1 AND 2).
    Tissue: Brain.
  4. "Systematic analysis of the protein interaction network for the human transcription machinery reveals the identity of the 7SK capping enzyme."
    Jeronimo C., Forget D., Bouchard A., Li Q., Chua G., Poitras C., Therien C., Bergeron D., Bourassa S., Greenblatt J., Chabot B., Poirier G.G., Hughes T.R., Blanchette M., Price D.H., Coulombe B.
    Mol. Cell 27:262-274(2007) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, IDENTIFICATION BY MASS SPECTROMETRY, IDENTIFICATION IN THE RNA POLYMERASE II COMPLEX.
  5. Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-433, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    Tissue: Cervix carcinoma.
  6. "System-wide temporal characterization of the proteome and phosphoproteome of human embryonic stem cell differentiation."
    Rigbolt K.T., Prokhorova T.A., Akimov V., Henningsen J., Johansen P.T., Kratchmarova I., Kassem M., Mann M., Olsen J.V., Blagoev B.
    Sci. Signal. 4:RS3-RS3(2011) [PubMed] [Europe PMC] [Abstract]
    Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-480, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
  7. "Control of the RNA polymerase II phosphorylation state in promoter regions by CTD interaction domain-containing proteins RPRD1A and RPRD1B."
    Ni Z., Olsen J.B., Guo X., Zhong G., Ruan E.D., Marcon E., Young P., Guo H., Li J., Moffat J., Emili A., Greenblatt J.F.
    Transcription 2:237-242(2011) [PubMed] [Europe PMC] [Abstract]
    Cited for: IDENTIFICATION IN THE RNA POLYMERASE II COMPLEX.
  8. "Ser7 phosphorylation of the CTD recruits the RPAP2 Ser5 phosphatase to snRNA genes."
    Egloff S., Zaborowska J., Laitem C., Kiss T., Murphy S.
    Mol. Cell 45:111-122(2012) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, SUBCELLULAR LOCATION, MUTAGENESIS OF CYS-100; CYS-105; CYS-136 AND CYS-140.
  9. Cited for: ACETYLATION [LARGE SCALE ANALYSIS] AT ALA-2, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS], CLEAVAGE OF INITIATOR METHIONINE [LARGE SCALE ANALYSIS].

Entry informationi

Entry nameiRPAP2_HUMAN
AccessioniPrimary (citable) accession number: Q8IXW5
Secondary accession number(s): C9JKB5, Q49AS7, Q9H8Y2
Entry historyi
Integrated into UniProtKB/Swiss-Prot: October 3, 2006
Last sequence update: March 1, 2003
Last modified: April 29, 2015
This is version 99 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program
DisclaimerAny medical or genetic information present in this entry is provided for research, educational and informational purposes only. It is not in any way intended to be used as a substitute for professional medical advice, diagnosis, treatment or care.

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. Human chromosome 1
    Human chromosome 1: entries, gene names and cross-references to MIM
  2. MIM cross-references
    Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
  3. SIMILARITY comments
    Index of protein domains and families
  4. Uncharacterized protein families (UPF)
    List of uncharacterized protein family (UPF) entries

External Data

Dasty 3

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 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.