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Protein

Regulation of nuclear pre-mRNA domain-containing protein 1A

Gene

RPRD1A

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

Functioni

Interacts with phosphorylated C-terminal heptapeptide repeat domain (CTD) of the largest RNA polymerase II subunit POLR2A, and participates in dephosphorylation of the CTD by RPAP2. May act as a negative regulator of cyclin-D1 (CCND1) and cyclin-E (CCNE1) in the cell cycle.3 Publications

GO - Molecular functioni

  • identical protein binding Source: IntAct

GO - Biological processi

  • dephosphorylation of RNA polymerase II C-terminal domain Source: UniProtKB
  • snRNA transcription by RNA polymerase II Source: Reactome

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 1A
Alternative name(s):
Cyclin-dependent kinase inhibitor 2B-related protein
p15INK4B-related protein
Gene namesi
Name:RPRD1A
Synonyms:P15RS
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 18

Organism-specific databases

EuPathDBiHostDB:ENSG00000141425.17
HGNCiHGNC:25560 RPRD1A
MIMi610347 gene
neXtProtiNX_Q96P16

Subcellular locationi

Extracellular region or secreted Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi apparatus Nucleus Mitochondrion Manual annotation Automatic computational assertionGraphics by Christian Stolte; Source: COMPARTMENTS

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi65D → A: Partial loss of binding to POLR2A CTD in vitro. 1 Publication1
Mutagenesisi106R → A: Partial loss of binding to POLR2A CTD phosphorylated at 'Ser-2' in the heptad repeats in vitro. 1 Publication1
Mutagenesisi114R → A: Partial loss of binding to POLR2A CTD in vitro. 1 Publication1

Organism-specific databases

DisGeNETi55197
OpenTargetsiENSG00000141425
PharmGKBiPA162402042

Polymorphism and mutation databases

BioMutaiRPRD1A
DMDMi74717048

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Initiator methionineiRemovedCombined sources1 Publication
ChainiPRO_00003113442 – 312Regulation of nuclear pre-mRNA domain-containing protein 1AAdd BLAST311

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei2N-acetylserineCombined sources1 Publication1
Modified residuei153PhosphoserineCombined sources1
Modified residuei156PhosphoserineCombined sources1
Modified residuei285PhosphoserineCombined sources1

Keywords - PTMi

Acetylation, Phosphoprotein

Proteomic databases

EPDiQ96P16
MaxQBiQ96P16
PaxDbiQ96P16
PeptideAtlasiQ96P16
PRIDEiQ96P16

PTM databases

iPTMnetiQ96P16
PhosphoSitePlusiQ96P16

Expressioni

Inductioni

Up-regulated in cells overexpressing CDKN2B.1 Publication

Gene expression databases

BgeeiENSG00000141425
CleanExiHS_RPRD1A
ExpressionAtlasiQ96P16 baseline and differential
GenevisibleiQ96P16 HS

Organism-specific databases

HPAiHPA040602

Interactioni

Subunit structurei

May form a heterodimer with RPRD1B (PubMed:24997600). Associates with the RNA polymerase II subunit POLR2A (via CTD phosphorylated at 'Ser-2' and 'Ser-7' of the heptad repeats) (PubMed:22231121, PubMed:24997600, PubMed:24399136).3 Publications

Binary interactionsi

Show more details

GO - Molecular functioni

  • identical protein binding Source: IntAct

Protein-protein interaction databases

BioGridi120494, 83 interactors
DIPiDIP-50901N
IntActiQ96P16, 16 interactors
MINTiQ96P16
STRINGi9606.ENSP00000349955

Structurei

Secondary structure

1312
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi6 – 15Combined sources10
Helixi20 – 32Combined sources13
Helixi34 – 36Combined sources3
Helixi37 – 50Combined sources14
Helixi53 – 55Combined sources3
Helixi56 – 70Combined sources15
Turni71 – 73Combined sources3
Helixi76 – 95Combined sources20
Helixi98 – 113Combined sources16
Helixi119 – 130Combined sources12

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
4JXTX-ray1.90A1-137[»]
4NACX-ray2.00A/B1-131[»]
ProteinModelPortaliQ96P16
SMRiQ96P16
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini2 – 133CIDPROSITE-ProRule annotationAdd BLAST132

Coiled coil

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Coiled coili244 – 286Sequence analysisAdd BLAST43

Sequence similaritiesi

Belongs to the UPF0400 (RTT103) family.Curated

Keywords - Domaini

Coiled coil

Phylogenomic databases

eggNOGiKOG2669 Eukaryota
ENOG410XRAP LUCA
GeneTreeiENSGT00400000022016
HOGENOMiHOG000007456
HOVERGENiHBG051177
InParanoidiQ96P16
OMAiAQWIMFH
OrthoDBiEOG091G0F8X
PhylomeDBiQ96P16
TreeFamiTF320926

Family and domain databases

Gene3Di1.25.40.90, 1 hit
InterProiView protein in InterPro
IPR006569 CID_dom
IPR032337 CREPT
IPR008942 ENTH_VHS
IPR006903 RNA_pol_II-bd
PfamiView protein in Pfam
PF16566 CREPT, 1 hit
PF04818 CTD_bind, 1 hit
SMARTiView protein in SMART
SM00582 RPR, 1 hit
SUPFAMiSSF48464 SSF48464, 1 hit
PROSITEiView protein in PROSITE
PS51391 CID, 1 hit

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: Q96P16-1) [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
MSAFSEAALE KKLSELSNSQ QSVQTLSLWL IHHRKHSRPI VTVWERELRK
60 70 80 90 100
AKPNRKLTFL YLANDVIQNS KRKGPEFTKD FAPVIVEAFK HVSSETDESC
110 120 130 140 150
KKHLGRVLSI WEERSVYEND VLEQLKQALY GDKKPRKRTY EQIKVDENEN
160 170 180 190 200
CSSLGSPSEP PQTLDLVRAL QDLENAASGD AAVHQRIASL PVEVQEVSLL
210 220 230 240 250
DKITDKESGE RLSKMVEDAC MLLADYNGRL AAEIDDRKQL TRMLADFLRC
260 270 280 290 300
QKEALAEKEH KLEEYKRKLA RVSLVRKELR SRIQSLPDLS RLPNVTGSHM
310
HLPFAGDIYS ED
Length:312
Mass (Da):35,720
Last modified:December 1, 2001 - v1
Checksum:i61785281F31CB328
GO
Isoform 2 (identifier: Q96P16-3) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     1-51: MSAFSEAALEKKLSELSNSQQSVQTLSLWLIHHRKHSRPIVTVWERELRKA → MRNSNWRFCQTGIYS

Show »
Length:276
Mass (Da):31,625
Checksum:i09748C553C326E55
GO

Sequence cautioni

The sequence AAH10136 differs from that shown. Probable cloning artifact.Curated

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti193E → D in BAA91736 (PubMed:14702039).Curated1
Sequence conflicti234I → V in BAA91736 (PubMed:14702039).Curated1

Natural variant

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_03722921Q → H in a breast cancer sample; somatic mutation. 1 Publication1

Alternative sequence

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Alternative sequenceiVSP_0295311 – 51MSAFS…ELRKA → MRNSNWRFCQTGIYS in isoform 2. 2 PublicationsAdd BLAST51

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF419845 mRNA Translation: AAL15972.1
AK001518 mRNA Translation: BAA91736.1
AK292907 mRNA Translation: BAF85596.1
AK314569 mRNA Translation: BAG37150.1
CH471088 Genomic DNA Translation: EAX01365.1
CH471088 Genomic DNA Translation: EAX01366.1
CH471088 Genomic DNA Translation: EAX01367.1
BC000225 mRNA Translation: AAH00225.2
BC010136 mRNA Translation: AAH10136.1 Sequence problems.
CCDSiCCDS11917.1 [Q96P16-1]
CCDS77178.1 [Q96P16-3]
RefSeqiNP_001290340.1, NM_001303411.1 [Q96P16-3]
NP_001290341.1, NM_001303412.1 [Q96P16-3]
NP_001290342.1, NM_001303413.1
NP_060640.2, NM_018170.4 [Q96P16-1]
XP_011524350.1, XM_011526048.1 [Q96P16-1]
XP_011524351.1, XM_011526049.1 [Q96P16-3]
XP_011524352.1, XM_011526050.1 [Q96P16-3]
UniGeneiHs.464912
Hs.668462

Genome annotation databases

EnsembliENST00000357384; ENSP00000349955; ENSG00000141425 [Q96P16-1]
ENST00000399022; ENSP00000381984; ENSG00000141425 [Q96P16-1]
ENST00000588737; ENSP00000465444; ENSG00000141425 [Q96P16-3]
ENST00000590898; ENSP00000467991; ENSG00000141425 [Q96P16-3]
GeneIDi55197
KEGGihsa:55197
UCSCiuc002kze.2 human [Q96P16-1]

Keywords - Coding sequence diversityi

Alternative splicing, Polymorphism

Similar proteinsi

Entry informationi

Entry nameiRPR1A_HUMAN
AccessioniPrimary (citable) accession number: Q96P16
Secondary accession number(s): A8KA42
, B2RBA3, Q7Z5G8, Q96FY9, Q9NVL4
Entry historyiIntegrated into UniProtKB/Swiss-Prot: November 13, 2007
Last sequence update: December 1, 2001
Last modified: May 23, 2018
This is version 116 of the entry and version 1 of the sequence. See 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, Direct protein sequencing, Reference proteome
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Main funding by: National Institutes of Health