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Protein

Regulation of nuclear pre-mRNA domain-containing protein 2

Gene

RPRD2

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: Annotation score: 4 out of 5-Experimental evidence at protein leveli

Functioni

GO - Biological processi

Complete GO annotation...

Enzyme and pathway databases

ReactomeiR-HSA-6807505. RNA polymerase II transcribes snRNA genes.

Names & Taxonomyi

Protein namesi
Recommended name:
Regulation of nuclear pre-mRNA domain-containing protein 2
Gene namesi
Name:RPRD2
Synonyms:KIAA0460
ORF Names:HSPC099
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 1

Organism-specific databases

HGNCiHGNC:29039. RPRD2.

Subcellular locationi

GO - Cellular componenti

  • DNA-directed RNA polymerase II, holoenzyme Source: UniProtKB
  • nucleoplasm Source: Reactome
Complete GO annotation...

Pathology & Biotechi

Organism-specific databases

OpenTargetsiENSG00000163125.
PharmGKBiPA162402062.

Polymorphism and mutation databases

BioMutaiRPRD2.
DMDMi74746888.

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00002443551 – 1461Regulation of nuclear pre-mRNA domain-containing protein 2Add BLAST1461

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei16PhosphoserineCombined sources1
Modified residuei356PhosphoserineCombined sources1
Modified residuei358PhosphothreonineCombined sources1
Modified residuei374PhosphoserineCombined sources1
Modified residuei473PhosphoserineCombined sources1
Modified residuei476PhosphoserineCombined sources1
Modified residuei479PhosphoserineCombined sources1
Modified residuei482PhosphothreonineCombined sources1
Modified residuei485PhosphoserineCombined sources1
Modified residuei517PhosphothreonineCombined sources1
Modified residuei564PhosphoserineCombined sources1
Modified residuei593PhosphoserineCombined sources1
Modified residuei598PhosphothreonineCombined sources1
Modified residuei614PhosphoserineCombined sources1
Modified residuei663PhosphoserineCombined sources1
Modified residuei665PhosphoserineCombined sources1
Modified residuei716PhosphoserineCombined sources1
Modified residuei723PhosphothreonineCombined sources1
Modified residuei730PhosphoserineBy similarity1
Modified residuei732PhosphothreonineCombined sources1
Modified residuei758PhosphoserineCombined sources1
Modified residuei762PhosphoserineCombined sources1
Modified residuei763PhosphothreonineCombined sources1
Modified residuei769PhosphoserineCombined sources1
Modified residuei817PhosphoserineCombined sources1
Modified residuei826PhosphoserineCombined sources1
Modified residuei900PhosphoserineCombined sources1
Modified residuei909PhosphoserineCombined sources1
Modified residuei928PhosphoserineCombined sources1
Modified residuei965PhosphoserineCombined sources1
Modified residuei976PhosphoserineCombined sources1
Modified residuei1068PhosphoserineBy similarity1
Modified residuei1099PhosphoserineCombined sources1
Modified residuei1366Asymmetric dimethylarginineCombined sources1
Modified residuei1424Asymmetric dimethylarginineCombined sources1
Modified residuei1430Asymmetric dimethylarginineCombined sources1

Keywords - PTMi

Methylation, Phosphoprotein

Proteomic databases

EPDiQ5VT52.
MaxQBiQ5VT52.
PaxDbiQ5VT52.
PeptideAtlasiQ5VT52.
PRIDEiQ5VT52.

PTM databases

iPTMnetiQ5VT52.
PhosphoSitePlusiQ5VT52.

Expressioni

Gene expression databases

BgeeiENSG00000163125.
CleanExiHS_RPRD2.
GenevisibleiQ5VT52. HS.

Organism-specific databases

HPAiHPA045778.
HPA061693.

Interactioni

Subunit structurei

Associates with the RNA polymerase II complex.1 Publication

Protein-protein interaction databases

BioGridi116852. 28 interactors.
DIPiDIP-31155N.
IntActiQ5VT52. 18 interactors.
MINTiMINT-1603162.
STRINGi9606.ENSP00000358064.

Structurei

Secondary structure

11461
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi20 – 33Combined sources14
Helixi38 – 50Combined sources13
Helixi52 – 54Combined sources3
Helixi55 – 68Combined sources14
Helixi71 – 87Combined sources17
Turni88 – 92Combined sources5
Helixi95 – 101Combined sources7
Helixi104 – 109Combined sources6
Turni114 – 116Combined sources3
Helixi117 – 130Combined sources14
Helixi135 – 144Combined sources10

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
4FLBX-ray1.80A19-149[»]
ProteinModelPortaliQ5VT52.
SMRiQ5VT52.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini19 – 149CIDPROSITE-ProRule annotationAdd BLAST131

Compositional bias

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Compositional biasi4 – 19Gly/Ser-richAdd BLAST16
Compositional biasi457 – 950Ser-richAdd BLAST494
Compositional biasi1054 – 1057Poly-Gln4
Compositional biasi1152 – 1158Poly-Gly7
Compositional biasi1195 – 1459Pro-richAdd BLAST265

Sequence similaritiesi

Contains 1 CID domain.PROSITE-ProRule annotation

Phylogenomic databases

eggNOGiKOG2669. Eukaryota.
ENOG410XRAP. LUCA.
GeneTreeiENSGT00400000022016.
HOGENOMiHOG000154192.
HOVERGENiHBG104176.
InParanoidiQ5VT52.
OMAiGKGNRGH.
OrthoDBiEOG091G0F8X.
PhylomeDBiQ5VT52.
TreeFamiTF320926.

Family and domain databases

Gene3Di1.25.40.90. 1 hit.
InterProiIPR006569. CID_dom.
IPR032337. CREPT.
IPR008942. ENTH_VHS.
IPR006903. RNA_pol_II-bd.
[Graphical view]
PfamiPF16566. CREPT. 1 hit.
PF04818. CTD_bind. 1 hit.
[Graphical view]
SMARTiSM00582. RPR. 1 hit.
[Graphical view]
SUPFAMiSSF48464. SSF48464. 1 hit.
PROSITEiPS51391. CID. 1 hit.
[Graphical view]

Sequences (5)i

Sequence statusi: Complete.

This entry describes 5 isoformsi produced by alternative splicing. AlignAdd to basket

Isoform 1 (identifier: Q5VT52-1) [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
MAAGGGGGSS KASSSSASSA GALESSLDRK FQSVTNTMES IQGLSSWCIE
60 70 80 90 100
NKKHHSTIVY HWMKWLRRSA YPHRLNLFYL ANDVIQNCKR KNAIIFRESF
110 120 130 140 150
ADVLPEAAAL VKDPSVSKSV ERIFKIWEDR NVYPEEMIVA LREALSTTFK
160 170 180 190 200
TQKQLKENLN KQPNKQWKKS QTSTNPKAAL KSKIVAEFRS QALIEELLLY
210 220 230 240 250
KRSEDQIELK EKQLSTMRVD VCSTETLKCL KDKTGGKKFS KEFEEASSKL
260 270 280 290 300
EEFVNGLDKQ VKNGPSLTEA LENAGIFYEA QYKEVKVVAN AYKTFANRVN
310 320 330 340 350
NLKKKLDQLK STLPDPEESP VPSPSMDAPS PTGSESPFQG MGGEESQSPT
360 370 380 390 400
MESEKSATPE PVTDNRDVED MELSDVEDDG SKIIVEDRKE KPAEKSAVST
410 420 430 440 450
SVPTKPTENI SKASSCTPVP VTMTATPPLP KPVNTSLSPS PALALPNLAN
460 470 480 490 500
VDLAKISSIL SSLTSVMKNT GVSPASRPSP GTPTSPSNLT SGLKTPAPAT
510 520 530 540 550
TTSHNPLANI LSKVEITPES ILSALSKTQT QSAPALQGLS SLLQSVTGNP
560 570 580 590 600
VPASEAASQS TSASPANTTV STIKGRNLPS SAQPFIPKSF NYSPNSSTSE
610 620 630 640 650
VSSTSASKAS IGQSPGLPST TFKLPSNSLG FTATHNTSPA APPTEVTICQ
660 670 680 690 700
SSEVSKPKLE SESTSPSLEM KIHNFLKGNP GFSGLNLNIP ILSSLGSSAP
710 720 730 740 750
SESHPSDFQR GPTSTSIDNI DGTPVRDERS GTPTQDEMMD KPTSSSVDTM
760 770 780 790 800
SLLSKIISPG SSTPSSTRSP PPGRDESYPR ELSNSVSTYR PFGLGSESPY
810 820 830 840 850
KQPSDGMERP SSLMDSSQEK FYPDTSFQED EDYRDFEYSG PPPSAMMNLE
860 870 880 890 900
KKPAKSILKS SKLSDTTEYQ PILSSYSHRA QEFGVKSAFP PSVRALLDSS
910 920 930 940 950
ENCDRLSSSP GLFGAFSVRG NEPGSDRSPS PSKNDSFFTP DSNHNSLSQS
960 970 980 990 1000
TTGHLSLPQK QYPDSPHPVP HRSLFSPQNT LAAPTGHPPT SGVEKVLAST
1010 1020 1030 1040 1050
ISTTSTIEFK NMLKNASRKP SDDKHFGQAP SKGTPSDGVS LSNLTQPSLT
1060 1070 1080 1090 1100
ATDQQQQEEH YRIETRVSSS CLDLPDSTEE KGAPIETLGY HSASNRRMSG
1110 1120 1130 1140 1150
EPIQTVESIR VPGKGNRGHG REASRVGWFD LSTSGSSFDN GPSSASELAS
1160 1170 1180 1190 1200
LGGGGSGGLT GFKTAPYKER APQFQESVGS FRSNSFNSTF EHHLPPSPLE
1210 1220 1230 1240 1250
HGTPFQREPV GPSSAPPVPP KDHGGIFSRD APTHLPSVDL SNPFTKEAAL
1260 1270 1280 1290 1300
AHAAPPPPPG EHSGIPFPTP PPPPPPGEHS SSGGSGVPFS TPPPPPPPVD
1310 1320 1330 1340 1350
HSGVVPFPAP PLAEHGVAGA VAVFPKDHSS LLQGTLAEHF GVLPGPRDHG
1360 1370 1380 1390 1400
GPTQRDLNGP GLSRVRESLT LPSHSLEHLG PPHGGGGGGG SNSSSGPPLG
1410 1420 1430 1440 1450
PSHRDTISRS GIILRSPRPD FRPREPFLSR DPFHSLKRPR PPFARGPPFF
1460
APKRPFFPPR Y
Length:1,461
Mass (Da):156,020
Last modified:December 7, 2004 - v1
Checksum:iE08CAF3148F89F67
GO
Isoform 2 (identifier: Q5VT52-2) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     1-37: Missing.

Note: No experimental confirmation available.
Show »
Length:1,424
Mass (Da):152,588
Checksum:iEFB18C42C73F5B93
GO
Isoform 3 (identifier: Q5VT52-3) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     146-171: Missing.

Show »
Length:1,435
Mass (Da):152,876
Checksum:i3425769AF329312E
GO
Isoform 4 (identifier: Q5VT52-4) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     147-152: TTFKTQ → KCLFLS
     153-1461: Missing.

Note: Gene prediction based on EST data.
Show »
Length:152
Mass (Da):17,001
Checksum:i4FFBE10E974AC878
GO
Isoform 5 (identifier: Q5VT52-5) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     146-171: Missing.
     932-960: SKNDSFFTPDSNHNSLSQSTTGHLSLPQK → KHPCRSHGSPTHVRRGESPGLHHFHHVDD
     961-1461: Missing.

Note: No experimental confirmation available.
Show »
Length:934
Mass (Da):100,272
Checksum:iA3D3BB446939BB42
GO

Sequence cautioni

The sequence AAF28922 differs from that shown. Reason: Erroneous initiation.Curated
The sequence AAH45623 differs from that shown. Reason: Erroneous initiation.Curated

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti167W → C in AAF28922 (Ref. 6) Curated1
Sequence conflicti174T → A in BAG51793 (PubMed:14702039).Curated1
Sequence conflicti1297P → L in BAG51793 (PubMed:14702039).Curated1
Sequence conflicti1385G → R in BAG51793 (PubMed:14702039).Curated1

Natural variant

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_061700351M → V.Corresponds to variant rs41273537dbSNPEnsembl.1

Alternative sequence

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Alternative sequenceiVSP_0195461 – 37Missing in isoform 2. 1 PublicationAdd BLAST37
Alternative sequenceiVSP_019547146 – 171Missing in isoform 3 and isoform 5. 2 PublicationsAdd BLAST26
Alternative sequenceiVSP_035574147 – 152TTFKTQ → KCLFLS in isoform 4. Curated6
Alternative sequenceiVSP_035575153 – 1461Missing in isoform 4. CuratedAdd BLAST1309
Alternative sequenceiVSP_053733932 – 960SKNDS…SLPQK → KHPCRSHGSPTHVRRGESPG LHHFHHVDD in isoform 5. 1 PublicationAdd BLAST29
Alternative sequenceiVSP_053734961 – 1461Missing in isoform 5. 1 PublicationAdd BLAST501

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AK056707 mRNA. Translation: BAG51793.1.
AK291703 mRNA. Translation: BAF84392.1.
AK304380 mRNA. Translation: BAG65218.1.
BX641025 mRNA. Translation: CAE46016.1.
AL356356, AL611942, BX284695 Genomic DNA. Translation: CAI15496.1.
AL356356, AL611942, BX284695 Genomic DNA. Translation: CAI15497.1.
AL611942, AL356356, BX284695 Genomic DNA. Translation: CAH70313.1.
AL611942, AL356356, BX284695 Genomic DNA. Translation: CAH70314.1.
AL611942 Genomic DNA. Translation: CAH70315.1.
BX284695, AL356356, AL611942 Genomic DNA. Translation: CAI17373.1.
BX284695, AL356356, AL611942 Genomic DNA. Translation: CAI17374.1.
CH471121 Genomic DNA. Translation: EAW53552.1.
BC045623 mRNA. Translation: AAH45623.2. Different initiation.
AF161362 mRNA. Translation: AAF28922.1. Different initiation.
AB007929 mRNA. Translation: BAA32305.2.
CCDSiCCDS44216.1. [Q5VT52-1]
CCDS72907.1. [Q5VT52-3]
PIRiT00074.
RefSeqiNP_001284602.1. NM_001297673.1. [Q5VT52-5]
NP_001284603.1. NM_001297674.1. [Q5VT52-3]
NP_056018.2. NM_015203.4. [Q5VT52-1]
UniGeneiHs.213666.

Genome annotation databases

EnsembliENST00000369067; ENSP00000358063; ENSG00000163125. [Q5VT52-4]
ENST00000369068; ENSP00000358064; ENSG00000163125. [Q5VT52-1]
ENST00000401000; ENSP00000383785; ENSG00000163125. [Q5VT52-3]
GeneIDi23248.
KEGGihsa:23248.
UCSCiuc001eup.5. human. [Q5VT52-1]

Keywords - Coding sequence diversityi

Alternative splicing, Polymorphism

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AK056707 mRNA. Translation: BAG51793.1.
AK291703 mRNA. Translation: BAF84392.1.
AK304380 mRNA. Translation: BAG65218.1.
BX641025 mRNA. Translation: CAE46016.1.
AL356356, AL611942, BX284695 Genomic DNA. Translation: CAI15496.1.
AL356356, AL611942, BX284695 Genomic DNA. Translation: CAI15497.1.
AL611942, AL356356, BX284695 Genomic DNA. Translation: CAH70313.1.
AL611942, AL356356, BX284695 Genomic DNA. Translation: CAH70314.1.
AL611942 Genomic DNA. Translation: CAH70315.1.
BX284695, AL356356, AL611942 Genomic DNA. Translation: CAI17373.1.
BX284695, AL356356, AL611942 Genomic DNA. Translation: CAI17374.1.
CH471121 Genomic DNA. Translation: EAW53552.1.
BC045623 mRNA. Translation: AAH45623.2. Different initiation.
AF161362 mRNA. Translation: AAF28922.1. Different initiation.
AB007929 mRNA. Translation: BAA32305.2.
CCDSiCCDS44216.1. [Q5VT52-1]
CCDS72907.1. [Q5VT52-3]
PIRiT00074.
RefSeqiNP_001284602.1. NM_001297673.1. [Q5VT52-5]
NP_001284603.1. NM_001297674.1. [Q5VT52-3]
NP_056018.2. NM_015203.4. [Q5VT52-1]
UniGeneiHs.213666.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
4FLBX-ray1.80A19-149[»]
ProteinModelPortaliQ5VT52.
SMRiQ5VT52.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi116852. 28 interactors.
DIPiDIP-31155N.
IntActiQ5VT52. 18 interactors.
MINTiMINT-1603162.
STRINGi9606.ENSP00000358064.

PTM databases

iPTMnetiQ5VT52.
PhosphoSitePlusiQ5VT52.

Polymorphism and mutation databases

BioMutaiRPRD2.
DMDMi74746888.

Proteomic databases

EPDiQ5VT52.
MaxQBiQ5VT52.
PaxDbiQ5VT52.
PeptideAtlasiQ5VT52.
PRIDEiQ5VT52.

Protocols and materials databases

DNASUi23248.
Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000369067; ENSP00000358063; ENSG00000163125. [Q5VT52-4]
ENST00000369068; ENSP00000358064; ENSG00000163125. [Q5VT52-1]
ENST00000401000; ENSP00000383785; ENSG00000163125. [Q5VT52-3]
GeneIDi23248.
KEGGihsa:23248.
UCSCiuc001eup.5. human. [Q5VT52-1]

Organism-specific databases

CTDi23248.
GeneCardsiRPRD2.
H-InvDBHIX0019981.
HGNCiHGNC:29039. RPRD2.
HPAiHPA045778.
HPA061693.
MIMi614695. gene.
neXtProtiNX_Q5VT52.
OpenTargetsiENSG00000163125.
PharmGKBiPA162402062.
HUGEiSearch...
GenAtlasiSearch...

Phylogenomic databases

eggNOGiKOG2669. Eukaryota.
ENOG410XRAP. LUCA.
GeneTreeiENSGT00400000022016.
HOGENOMiHOG000154192.
HOVERGENiHBG104176.
InParanoidiQ5VT52.
OMAiGKGNRGH.
OrthoDBiEOG091G0F8X.
PhylomeDBiQ5VT52.
TreeFamiTF320926.

Enzyme and pathway databases

ReactomeiR-HSA-6807505. RNA polymerase II transcribes snRNA genes.

Miscellaneous databases

ChiTaRSiRPRD2. human.
GeneWikiiKIAA0460.
GenomeRNAii23248.
PROiQ5VT52.
SOURCEiSearch...

Gene expression databases

BgeeiENSG00000163125.
CleanExiHS_RPRD2.
GenevisibleiQ5VT52. HS.

Family and domain databases

Gene3Di1.25.40.90. 1 hit.
InterProiIPR006569. CID_dom.
IPR032337. CREPT.
IPR008942. ENTH_VHS.
IPR006903. RNA_pol_II-bd.
[Graphical view]
PfamiPF16566. CREPT. 1 hit.
PF04818. CTD_bind. 1 hit.
[Graphical view]
SMARTiSM00582. RPR. 1 hit.
[Graphical view]
SUPFAMiSSF48464. SSF48464. 1 hit.
PROSITEiPS51391. CID. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiRPRD2_HUMAN
AccessioniPrimary (citable) accession number: Q5VT52
Secondary accession number(s): A8K6N8
, B3KPT1, B4E2Q6, O75048, Q5VT51, Q5VT53, Q6MZL4, Q86XD2, Q9P0D7
Entry historyi
Integrated into UniProtKB/Swiss-Prot: June 27, 2006
Last sequence update: December 7, 2004
Last modified: November 30, 2016
This is version 114 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

3D-structure, Complete proteome, Reference proteome

Documents

  1. Human chromosome 1
    Human chromosome 1: entries, gene names and cross-references to MIM
  2. Human entries with polymorphisms or disease mutations
    List of human entries with polymorphisms or disease mutations
  3. Human polymorphisms and disease mutations
    Index of human polymorphisms and disease mutations
  4. MIM cross-references
    Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
  5. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  6. 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.