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Protein

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

Gene

RPRD1A

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-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. May act as a negative regulator of cyclin-D1 (CCND1) and cyclin-E (CCNE1) in the cell cycle.1 Publication

GO - Biological processi

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

Enzyme and pathway databases

BioCyciZFISH:ENSG00000141425-MONOMER.
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

HGNCiHGNC:25560. RPRD1A.

Subcellular locationi

GO - Cellular componenti

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

Pathology & Biotechi

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

Associates with the RNA polymerase II complex.1 Publication

Binary interactionsi

WithEntry#Exp.IntActNotes
KPNA3Q8IYQ93EBI-1053506,EBI-742146

Protein-protein interaction databases

BioGridi120494. 47 interactors.
DIPiDIP-50901N.
IntActiQ96P16. 9 interactors.
MINTiMINT-4537177.
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
Contains 1 CID domain.PROSITE-ProRule annotation

Keywords - Domaini

Coiled coil

Phylogenomic databases

eggNOGiKOG2669. Eukaryota.
ENOG410XRAP. LUCA.
GeneTreeiENSGT00400000022016.
HOGENOMiHOG000007456.
HOVERGENiHBG051177.
InParanoidiQ96P16.
OMAiGEDGCKK.
OrthoDBiEOG091G0F8X.
PhylomeDBiQ96P16.
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 (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

Cross-referencesi

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.

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...

Protein-protein interaction databases

BioGridi120494. 47 interactors.
DIPiDIP-50901N.
IntActiQ96P16. 9 interactors.
MINTiMINT-4537177.
STRINGi9606.ENSP00000349955.

PTM databases

iPTMnetiQ96P16.
PhosphoSitePlusiQ96P16.

Polymorphism and mutation databases

BioMutaiRPRD1A.
DMDMi74717048.

Proteomic databases

EPDiQ96P16.
MaxQBiQ96P16.
PaxDbiQ96P16.
PeptideAtlasiQ96P16.
PRIDEiQ96P16.

Protocols and materials databases

DNASUi55197.
Structural Biology KnowledgebaseSearch...

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]

Organism-specific databases

CTDi55197.
DisGeNETi55197.
GeneCardsiRPRD1A.
H-InvDBHIX0014404.
HGNCiHGNC:25560. RPRD1A.
HPAiHPA040602.
MIMi610347. gene.
neXtProtiNX_Q96P16.
OpenTargetsiENSG00000141425.
PharmGKBiPA162402042.
GenAtlasiSearch...

Phylogenomic databases

eggNOGiKOG2669. Eukaryota.
ENOG410XRAP. LUCA.
GeneTreeiENSGT00400000022016.
HOGENOMiHOG000007456.
HOVERGENiHBG051177.
InParanoidiQ96P16.
OMAiGEDGCKK.
OrthoDBiEOG091G0F8X.
PhylomeDBiQ96P16.
TreeFamiTF320926.

Enzyme and pathway databases

BioCyciZFISH:ENSG00000141425-MONOMER.
ReactomeiR-HSA-6807505. RNA polymerase II transcribes snRNA genes.

Miscellaneous databases

ChiTaRSiRPRD1A. human.
GenomeRNAii55197.
PROiQ96P16.
SOURCEiSearch...

Gene expression databases

BgeeiENSG00000141425.
CleanExiHS_RPRD1A.
ExpressionAtlasiQ96P16. baseline and differential.
GenevisibleiQ96P16. 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 nameiRPR1A_HUMAN
AccessioniPrimary (citable) accession number: Q96P16
Secondary accession number(s): A8KA42
, B2RBA3, Q7Z5G8, Q96FY9, Q9NVL4
Entry historyi
Integrated into UniProtKB/Swiss-Prot: November 13, 2007
Last sequence update: December 1, 2001
Last modified: November 2, 2016
This is version 107 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, Direct protein sequencing, Reference proteome

Documents

  1. Human chromosome 18
    Human chromosome 18: 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
  7. Uncharacterized protein families (UPF)
    List of uncharacterized protein family (UPF) entries

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.