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Protein

Pre-mRNA-processing protein 40A

Gene

PRP40A

Organism
Arabidopsis thaliana (Mouse-ear cress)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Component of the Mediator complex, a coactivator involved in the regulated transcription of nearly all RNA polymerase II-dependent genes. Mediator functions as a bridge to convey information from gene-specific regulatory proteins to the basal RNA polymerase II transcription machinery. The Mediator complex, having a compact conformation in its free form, is recruited to promoters by direct interactions with regulatory proteins and serves for the assembly of a functional preinitiation complex with RNA polymerase II and the general transcription factors. Interacts with both the phosphorylated and the dephosphorylated forms of the CTD domain of the RPB1 subunit of the RNA polymerase II.1 Publication

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Biological processi

Transcription, Transcription regulation

Names & Taxonomyi

Protein namesi
Recommended name:
Pre-mRNA-processing protein 40A
Alternative name(s):
Mediator of RNA polymerase II transcription subunit 35a
Gene namesi
Name:PRP40A
Synonyms:MED35_1, MED35A
Ordered Locus Names:At1g44910
ORF Names:F27F5.2, T12C22.20
OrganismiArabidopsis thaliana (Mouse-ear cress)
Taxonomic identifieri3702 [NCBI]
Taxonomic lineageiEukaryotaViridiplantaeStreptophytaEmbryophytaTracheophytaSpermatophytaMagnoliophytaeudicotyledonsGunneridaePentapetalaerosidsmalvidsBrassicalesBrassicaceaeCamelineaeArabidopsis
Proteomesi
  • UP000006548 Componenti: Chromosome 1

Organism-specific databases

TAIRiAT1G44910.

Subcellular locationi

GO - Cellular componenti

  • cytosol Source: TAIR
  • mediator complex Source: UniProtKB
  • U1 snRNP Source: GO_Central
  • U2-type prespliceosome Source: GO_Central
Complete GO annotation...

Keywords - Cellular componenti

Nucleus

Pathology & Biotechi

Disruption phenotypei

No visible phenotype, probably due to the redundancy with PRP40B and PRP40C.1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00004183571 – 958Pre-mRNA-processing protein 40AAdd BLAST958

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei387PhosphoserineCombined sources1

Keywords - PTMi

Phosphoprotein

Proteomic databases

PaxDbiB6EUA9.

PTM databases

iPTMnetiB6EUA9.

Expressioni

Tissue specificityi

Ubiquitous. Highest expression in roots and cauline leaves.1 Publication

Gene expression databases

GenevisibleiB6EUA9. AT.

Interactioni

Subunit structurei

Component of the Mediator complex. Interacts with RPB205 (via CTD domain).2 Publications

Protein-protein interaction databases

BioGridi26282. 1 interactor.
STRINGi3702.AT1G44910.1.

Structurei

3D structure databases

ProteinModelPortaliB6EUA9.
SMRiB6EUA9.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini184 – 217WW 1PROSITE-ProRule annotationAdd BLAST34
Domaini225 – 258WW 2PROSITE-ProRule annotationAdd BLAST34
Domaini404 – 458FF 1Add BLAST55
Domaini471 – 526FF 2Add BLAST56
Domaini532 – 593FF 3Add BLAST62
Domaini611 – 674FF 4Add BLAST64
Domaini679 – 734FF 5Add BLAST56
Domaini736 – 801FF 6Add BLAST66

Compositional bias

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Compositional biasi5 – 153Pro-richAdd BLAST149
Compositional biasi7 – 58Gln-richAdd BLAST52
Compositional biasi270 – 315Ser-richAdd BLAST46
Compositional biasi467 – 470Poly-Arg4
Compositional biasi595 – 600Poly-Glu6
Compositional biasi737 – 861Glu-richAdd BLAST125
Compositional biasi805 – 883Lys-richAdd BLAST79

Sequence similaritiesi

Belongs to the PRPF40 family.Curated
Contains 6 FF domains.Curated
Contains 2 WW domains.PROSITE-ProRule annotation

Keywords - Domaini

Repeat

Phylogenomic databases

eggNOGiKOG0152. Eukaryota.
COG5104. LUCA.
HOGENOMiHOG000030620.
InParanoidiB6EUA9.
KOiK12821.
OMAiDRHNGGD.
OrthoDBiEOG0936040O.
PhylomeDBiB6EUA9.

Family and domain databases

Gene3Di1.10.10.440. 5 hits.
InterProiIPR002713. FF_domain.
IPR001202. WW_dom.
[Graphical view]
PfamiPF01846. FF. 4 hits.
PF00397. WW. 2 hits.
[Graphical view]
SMARTiSM00441. FF. 5 hits.
SM00456. WW. 2 hits.
[Graphical view]
SUPFAMiSSF51045. SSF51045. 2 hits.
SSF81698. SSF81698. 5 hits.
PROSITEiPS51676. FF. 6 hits.
PS50020. WW_DOMAIN_2. 2 hits.
[Graphical view]

Sequences (2)i

Sequence statusi: Complete.

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

Isoform 1 (identifier: B6EUA9-1) [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
MANNPPQSSG TQFRPMVPGQ QGQHFVPAAS QPFHPYGHVP PNVQSQPPQY
60 70 80 90 100
SQPIQQQQLF PVRPGQPVHI TSSSQAVSVP YIQTNKILTS GSTQPQPNAP
110 120 130 140 150
PMTGFATSGP PFSSPYTFVP SSYPQQQPTS LVQPNSQMHV AGVPPAANTW
160 170 180 190 200
PVPVNQSTSL VSPVQQTGQQ TPVAVSTDPG NLTPQSASDW QEHTSADGRK
210 220 230 240 250
YYYNKRTKQS NWEKPLELMT PLERADASTV WKEFTTPEGK KYYYNKVTKE
260 270 280 290 300
SKWTIPEDLK LAREQAQLAS EKTSLSEAGS TPLSHHAASS SDLAVSTVTS
310 320 330 340 350
VVPSTSSALT GHSSSPIQAG LAVPVTRPPS VAPVTPTSGA ISDTEATTIK
360 370 380 390 400
GDNLSSRGAD DSNDGATAQN NEAENKEMSV NGKANLSPAG DKANVEEPMV
410 420 430 440 450
YATKQEAKAA FKSLLESVNV HSDWTWEQTL KEIVHDKRYG ALRTLGERKQ
460 470 480 490 500
AFNEYLGQRK KVEAEERRRR QKKAREEFVK MLEECEELSS SLKWSKAMSL
510 520 530 540 550
FENDQRFKAV DRPRDREDLF DNYIVELERK EREKAAEEHR QYMADYRKFL
560 570 580 590 600
ETCDYIKAGT QWRKIQDRLE DDDRCSCLEK IDRLIGFEEY ILDLEKEEEE
610 620 630 640 650
LKRVEKEHVR RAERKNRDAF RTLLEEHVAA GILTAKTYWL DYCIELKDLP
660 670 680 690 700
QYQAVASNTS GSTPKDLFED VTEELEKQYH EDKSYVKDAM KSRKISMVSS
710 720 730 740 750
WLFEDFKSAI SEDLSTQQIS DINLKLIYDD LVGRVKEKEE KEARKLQRLA
760 770 780 790 800
EEFTNLLHTF KEITVASNWE DSKQLVEESQ EYRSIGDESV SQGLFEEYIT
810 820 830 840 850
SLQEKAKEKE RKRDEEKVRK EKERDEKEKR KDKDKERREK EREREKEKGK
860 870 880 890 900
ERSKREESDG ETAMDVSEGH KDEKRKGKDR DRKHRRRHHN NSDEDVSSDR
910 920 930 940 950
DDRDESKKSS RKHGNDRKKS RKHANSPESE SENRHKRQKK ESSRRSGNDE

LEDGEVGE
Length:958
Mass (Da):109,382
Last modified:November 25, 2008 - v1
Checksum:i3A59AB9520C49912
GO
Isoform 2 (identifier: B6EUA9-2) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     923-926: HANS → VGTP
     927-958: Missing.

Show »
Length:926
Mass (Da):105,645
Checksum:iBB4C1DD0F7AB4053
GO

Sequence cautioni

The sequence AAF69150 differs from that shown. Reason: Erroneous gene model prediction.Curated
The sequence AAF78276 differs from that shown. Reason: Erroneous gene model prediction.Curated

Alternative sequence

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Alternative sequenceiVSP_044036923 – 926HANS → VGTP in isoform 2. Curated4
Alternative sequenceiVSP_044037927 – 958Missing in isoform 2. CuratedAdd BLAST32

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AC007915 Genomic DNA. Translation: AAF69150.1. Sequence problems.
AC020576 Genomic DNA. Translation: AAF78276.1. Sequence problems.
CP002684 Genomic DNA. Translation: AEE32062.1.
CP002684 Genomic DNA. Translation: AEE32063.1.
AK316856 mRNA. Translation: BAH19565.1.
RefSeqiNP_001117438.1. NM_001123966.1. [B6EUA9-2]
NP_175113.2. NM_103573.4. [B6EUA9-1]
UniGeneiAt.14888.
At.28268.

Genome annotation databases

EnsemblPlantsiAT1G44910.1; AT1G44910.1; AT1G44910. [B6EUA9-1]
GeneIDi841057.
GrameneiAT1G44910.1; AT1G44910.1; AT1G44910.
KEGGiath:AT1G44910.

Keywords - Coding sequence diversityi

Alternative splicing

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AC007915 Genomic DNA. Translation: AAF69150.1. Sequence problems.
AC020576 Genomic DNA. Translation: AAF78276.1. Sequence problems.
CP002684 Genomic DNA. Translation: AEE32062.1.
CP002684 Genomic DNA. Translation: AEE32063.1.
AK316856 mRNA. Translation: BAH19565.1.
RefSeqiNP_001117438.1. NM_001123966.1. [B6EUA9-2]
NP_175113.2. NM_103573.4. [B6EUA9-1]
UniGeneiAt.14888.
At.28268.

3D structure databases

ProteinModelPortaliB6EUA9.
SMRiB6EUA9.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi26282. 1 interactor.
STRINGi3702.AT1G44910.1.

PTM databases

iPTMnetiB6EUA9.

Proteomic databases

PaxDbiB6EUA9.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblPlantsiAT1G44910.1; AT1G44910.1; AT1G44910. [B6EUA9-1]
GeneIDi841057.
GrameneiAT1G44910.1; AT1G44910.1; AT1G44910.
KEGGiath:AT1G44910.

Organism-specific databases

TAIRiAT1G44910.

Phylogenomic databases

eggNOGiKOG0152. Eukaryota.
COG5104. LUCA.
HOGENOMiHOG000030620.
InParanoidiB6EUA9.
KOiK12821.
OMAiDRHNGGD.
OrthoDBiEOG0936040O.
PhylomeDBiB6EUA9.

Miscellaneous databases

PROiB6EUA9.

Gene expression databases

GenevisibleiB6EUA9. AT.

Family and domain databases

Gene3Di1.10.10.440. 5 hits.
InterProiIPR002713. FF_domain.
IPR001202. WW_dom.
[Graphical view]
PfamiPF01846. FF. 4 hits.
PF00397. WW. 2 hits.
[Graphical view]
SMARTiSM00441. FF. 5 hits.
SM00456. WW. 2 hits.
[Graphical view]
SUPFAMiSSF51045. SSF51045. 2 hits.
SSF81698. SSF81698. 5 hits.
PROSITEiPS51676. FF. 6 hits.
PS50020. WW_DOMAIN_2. 2 hits.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiPR40A_ARATH
AccessioniPrimary (citable) accession number: B6EUA9
Secondary accession number(s): B3H7M9
, B9DFP8, Q9LPD8, Q9MAL4
Entry historyi
Integrated into UniProtKB/Swiss-Prot: July 11, 2012
Last sequence update: November 25, 2008
Last modified: November 2, 2016
This is version 63 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programPlant Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. Arabidopsis thaliana
    Arabidopsis thaliana: entries and gene names
  2. 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.