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Protein

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

Gene

Rprd1b

Organism
Mus musculus (Mouse)
Status
Reviewed-Annotation score: Annotation score: 4 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. Transcriptional regulator which enhances expression of CCND1. Promotes binding of RNA polymerase II to the CCDN1 promoter and to the termination region before the poly-A site but decreases its binding after the poly-A site. Prevents RNA polymerase II from reading through the 3' end termination site and may allow it to be recruited back to the promoter through promotion of the formation of a chromatin loop. Also enhances the transcription of a number of other cell cycle-related genes including CDK2, CDK4, CDK6 and cyclin-E but not CDKN1A, CDKN1B or cyclin-A. Promotes cell proliferation (By similarity).By similarity

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Biological processi

Transcription, Transcription regulation

Enzyme and pathway databases

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

Names & Taxonomyi

Protein namesi
Recommended name:
Regulation of nuclear pre-mRNA domain-containing protein 1B
Alternative name(s):
Cell cycle-related and expression-elevated protein in tumor
Gene namesi
Name:Rprd1b
Synonyms:Crept
OrganismiMus musculus (Mouse)
Taxonomic identifieri10090 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeMusMus
Proteomesi
  • UP000000589 Componenti: Chromosome 2

Organism-specific databases

MGIiMGI:1917720. Rprd1b.

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Initiator methionineiRemovedBy similarity
Chaini2 – 326325Regulation of nuclear pre-mRNA domain-containing protein 1BPRO_0000079442Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei2 – 21N-acetylserineBy similarity
Modified residuei132 – 1321PhosphoserineBy similarity
Modified residuei134 – 1341PhosphoserineCombined sources
Modified residuei161 – 1611PhosphotyrosineBy similarity
Modified residuei166 – 1661PhosphoserineCombined sources

Keywords - PTMi

Acetylation, Phosphoprotein

Proteomic databases

EPDiQ9CSU0.
MaxQBiQ9CSU0.
PaxDbiQ9CSU0.
PRIDEiQ9CSU0.

PTM databases

iPTMnetiQ9CSU0.
PhosphoSiteiQ9CSU0.

Expressioni

Tissue specificityi

Widely expressed in the adult with highest levels in liver, colon, prostate and uterus and lowest levels in heart and kidney. Not detected in rectum.1 Publication

Developmental stagei

Highly expressed during early embryonic development (at protein level). Low levels detected in the adult.1 Publication

Gene expression databases

BgeeiQ9CSU0.
ExpressionAtlasiQ9CSU0. baseline and differential.
GenevisibleiQ9CSU0. MM.

Interactioni

Subunit structurei

Associates with the RNA polymerase II complex.By similarity

GO - Molecular functioni

Protein-protein interaction databases

BioGridi214076. 34 interactions.
IntActiQ9CSU0. 35 interactions.
MINTiMINT-4092403.
STRINGi10090.ENSMUSP00000099412.

Structurei

3D structure databases

ProteinModelPortaliQ9CSU0.
SMRiQ9CSU0. Positions 2-129, 177-305.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini2 – 133132CIDPROSITE-ProRule annotationAdd
BLAST

Sequence similaritiesi

Belongs to the UPF0400 (RTT103) family.Curated
Contains 1 CID domain.PROSITE-ProRule annotation

Phylogenomic databases

eggNOGiKOG2669. Eukaryota.
ENOG410XRAP. LUCA.
GeneTreeiENSGT00400000022016.
HOVERGENiHBG051177.
InParanoidiQ9CSU0.
KOiK15559.
OMAiPFTEEAD.
OrthoDBiEOG7V1FRR.
PhylomeDBiQ9CSU0.
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 (3)i

Sequence statusi: Complete.

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

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

Isoform 1 (identifier: Q9CSU0-1) [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
MSSFSESALE KKLSELSNSQ QSVQTLSLWL IHHRKHAGPI VSVWHRELRK
60 70 80 90 100
AKSNRKLTFL YLANDVIQNS KRKGPEFTRE FESVLVDAFS HVAREADEGC
110 120 130 140 150
KKPLERLLNI WQERSVYGGE FIQQLKLSME DSKSPPPKAA EEKKSLKRTF
160 170 180 190 200
QQIQEEEDDD YPGSYSPQDP SAGPLLTEEL IKALQDLENA ASGDATVRQK
210 220 230 240 250
IASLPQEVQD VSLLEKITDK EAAERLSKTV DEACLLLAEY NGRLAAELED
260 270 280 290 300
RRQLARMLVE YTQNQKEVLS EKEKKLEEYK QKLARVTQVR KELKSHIQSL
310 320
PDLSLLPNVT GGLAPLPSAG DLFSTD
Length:326
Mass (Da):36,884
Last modified:October 10, 2002 - v2
Checksum:i904B9792FBBDFA71
GO
Isoform 2 (identifier: Q9CSU0-2) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     278-294: EYKQKLARVTQVRKELK → RLTQQLQPCSDPQNVSF
     295-326: Missing.

Note: No experimental confirmation available.
Show »
Length:294
Mass (Da):33,512
Checksum:i51BDAC942555DCE2
GO
Isoform 3 (identifier: Q9CSU0-3) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     220-224: KEAAE → AETEA
     225-326: Missing.

Note: No experimental confirmation available.
Show »
Length:224
Mass (Da):25,336
Checksum:i654C9B2E23620CC1
GO

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti17 – 171S → G in BAE30966 (PubMed:15489334).Curated
Sequence conflicti17 – 171S → G in BAE31047 (PubMed:15489334).Curated
Sequence conflicti139 – 1391Missing in BAB27954 (PubMed:16141072).Curated
Sequence conflicti139 – 1391Missing in BAE28092 (PubMed:16141072).Curated
Sequence conflicti139 – 1391Missing in BAE28237 (PubMed:16141072).Curated
Sequence conflicti139 – 1391Missing in CAM23183 (PubMed:19468303).Curated
Sequence conflicti139 – 1391Missing in CAM23185 (PubMed:19468303).Curated
Sequence conflicti139 – 1391Missing in AAH42447 (PubMed:15489334).Curated
Sequence conflicti139 – 1391Missing in AAH54350 (PubMed:15489334).Curated
Sequence conflicti206 – 22217QEVQD…TDKEA → SGSARRVAARENYRCRN in BAE24207 (PubMed:16141072).CuratedAdd
BLAST
Sequence conflicti223 – 326104Missing in BAE24207 (PubMed:16141072).CuratedAdd
BLAST
Sequence conflicti270 – 2701S → P in BAB27954 (PubMed:16141072).Curated
Sequence conflicti317 – 3171P → S in BAE28092 (PubMed:16141072).Curated
Sequence conflicti317 – 3171P → S in BAE28237 (PubMed:16141072).Curated

Alternative sequence

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Alternative sequencei220 – 2245KEAAE → AETEA in isoform 3. CuratedVSP_035576
Alternative sequencei225 – 326102Missing in isoform 3. CuratedVSP_035577Add
BLAST
Alternative sequencei278 – 29417EYKQK…RKELK → RLTQQLQPCSDPQNVSF in isoform 2. 1 PublicationVSP_018618Add
BLAST
Alternative sequencei295 – 32632Missing in isoform 2. 1 PublicationVSP_018619Add
BLAST

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
DQ372939 mRNA. Translation: ABD34792.1.
AK011979 mRNA. Translation: BAB27954.3.
AK139995 mRNA. Translation: BAE24207.1.
AK147718 mRNA. Translation: BAE28092.1.
AK147930 mRNA. Translation: BAE28237.1.
AK152125 mRNA. Translation: BAE30966.1.
AK152220 mRNA. Translation: BAE31047.1.
AL669824 Genomic DNA. Translation: CAM23181.1.
AL669824 Genomic DNA. Translation: CAM23182.1.
AL669824 Genomic DNA. Translation: CAM23183.1.
AL669824 Genomic DNA. Translation: CAM23184.1.
AL669824 Genomic DNA. Translation: CAM23185.1.
BC028819 mRNA. Translation: AAH28819.3.
BC042447 mRNA. Translation: AAH42447.1.
BC054350 mRNA. Translation: AAH54350.1.
CCDSiCCDS71176.1. [Q9CSU0-2]
CCDS71177.1. [Q9CSU0-1]
RefSeqiNP_001278063.1. NM_001291134.1. [Q9CSU0-1]
NP_001278064.1. NM_001291135.1. [Q9CSU0-2]
NP_001278065.1. NM_001291136.1.
NP_081710.1. NM_027434.3.
UniGeneiMm.290810.

Genome annotation databases

EnsembliENSMUST00000029180; ENSMUSP00000029180; ENSMUSG00000027651. [Q9CSU0-1]
ENSMUST00000109518; ENSMUSP00000105144; ENSMUSG00000027651. [Q9CSU0-2]
ENSMUST00000152452; ENSMUSP00000118434; ENSMUSG00000027651. [Q9CSU0-3]
GeneIDi70470.
KEGGimmu:70470.
UCSCiuc008npl.2. mouse. [Q9CSU0-1]
uc008npn.2. mouse. [Q9CSU0-2]

Keywords - Coding sequence diversityi

Alternative splicing

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
DQ372939 mRNA. Translation: ABD34792.1.
AK011979 mRNA. Translation: BAB27954.3.
AK139995 mRNA. Translation: BAE24207.1.
AK147718 mRNA. Translation: BAE28092.1.
AK147930 mRNA. Translation: BAE28237.1.
AK152125 mRNA. Translation: BAE30966.1.
AK152220 mRNA. Translation: BAE31047.1.
AL669824 Genomic DNA. Translation: CAM23181.1.
AL669824 Genomic DNA. Translation: CAM23182.1.
AL669824 Genomic DNA. Translation: CAM23183.1.
AL669824 Genomic DNA. Translation: CAM23184.1.
AL669824 Genomic DNA. Translation: CAM23185.1.
BC028819 mRNA. Translation: AAH28819.3.
BC042447 mRNA. Translation: AAH42447.1.
BC054350 mRNA. Translation: AAH54350.1.
CCDSiCCDS71176.1. [Q9CSU0-2]
CCDS71177.1. [Q9CSU0-1]
RefSeqiNP_001278063.1. NM_001291134.1. [Q9CSU0-1]
NP_001278064.1. NM_001291135.1. [Q9CSU0-2]
NP_001278065.1. NM_001291136.1.
NP_081710.1. NM_027434.3.
UniGeneiMm.290810.

3D structure databases

ProteinModelPortaliQ9CSU0.
SMRiQ9CSU0. Positions 2-129, 177-305.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi214076. 34 interactions.
IntActiQ9CSU0. 35 interactions.
MINTiMINT-4092403.
STRINGi10090.ENSMUSP00000099412.

PTM databases

iPTMnetiQ9CSU0.
PhosphoSiteiQ9CSU0.

Proteomic databases

EPDiQ9CSU0.
MaxQBiQ9CSU0.
PaxDbiQ9CSU0.
PRIDEiQ9CSU0.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENSMUST00000029180; ENSMUSP00000029180; ENSMUSG00000027651. [Q9CSU0-1]
ENSMUST00000109518; ENSMUSP00000105144; ENSMUSG00000027651. [Q9CSU0-2]
ENSMUST00000152452; ENSMUSP00000118434; ENSMUSG00000027651. [Q9CSU0-3]
GeneIDi70470.
KEGGimmu:70470.
UCSCiuc008npl.2. mouse. [Q9CSU0-1]
uc008npn.2. mouse. [Q9CSU0-2]

Organism-specific databases

CTDi58490.
MGIiMGI:1917720. Rprd1b.

Phylogenomic databases

eggNOGiKOG2669. Eukaryota.
ENOG410XRAP. LUCA.
GeneTreeiENSGT00400000022016.
HOVERGENiHBG051177.
InParanoidiQ9CSU0.
KOiK15559.
OMAiPFTEEAD.
OrthoDBiEOG7V1FRR.
PhylomeDBiQ9CSU0.
TreeFamiTF320926.

Enzyme and pathway databases

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

Miscellaneous databases

PROiQ9CSU0.
SOURCEiSearch...

Gene expression databases

BgeeiQ9CSU0.
ExpressionAtlasiQ9CSU0. baseline and differential.
GenevisibleiQ9CSU0. MM.

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...

Publicationsi

« Hide 'large scale' publications
  1. "CREPT accelerates tumorigenesis by regulating the transcription of cell-cycle-related genes."
    Lu D., Wu Y., Wang Y., Ren F., Wang D., Su F., Zhang Y., Yang X., Jin G., Hao X., He D., Zhai Y., Irwin D.M., Hu J., Sung J.J., Yu J., Jia B., Chang Z.
    Cancer Cell 21:92-104(2012) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1), TISSUE SPECIFICITY, DEVELOPMENTAL STAGE.
    Strain: BALB/cJ.
  2. "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 macrophage, Corpora quadrigemina, Embryo and Melanocyte.
  3. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: C57BL/6J.
  4. "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 1).
    Strain: C57BL/6J and FVB/N.
    Tissue: Liver, Mammary gland and Retina.
  5. Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    Tissue: Embryonic brain.
  6. "The phagosomal proteome in interferon-gamma-activated macrophages."
    Trost M., English L., Lemieux S., Courcelles M., Desjardins M., Thibault P.
    Immunity 30:143-154(2009) [PubMed] [Europe PMC] [Abstract]
    Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-134, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
  7. Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-134 AND SER-166, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    Tissue: Brain, Heart, Kidney, Liver, Lung, Pancreas, Spleen and Testis.

Entry informationi

Entry nameiRPR1B_MOUSE
AccessioniPrimary (citable) accession number: Q9CSU0
Secondary accession number(s): A2ACF2
, A2ACF4, A2ACF5, A2ACF6, Q1WDE6, Q3U8H1, Q3UGH1, Q3USX3, Q6GTJ6
Entry historyi
Integrated into UniProtKB/Swiss-Prot: October 10, 2002
Last sequence update: October 10, 2002
Last modified: June 8, 2016
This is version 109 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
  3. 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.