<p>This section provides information about the protein and gene name(s) and synonym(s) and about the organism that is the source of the protein sequence.<p><a href='/help/names_and_taxonomy_section' target='_top'>More...</a></p>Detailed information on MDP29386

Description Mediator of RNA polymerase II transcription subunit 4
SequenceMMQSHMPSPARLGMTASSPSLPPNPAPVNPTSSPPQASSSSSAAAPGAGVPTATLTTSPSLLPLLPPLPRAQSLLHIMSSLAANLFELSPNRTAWISSYRGSLPTFLPSSSTSGMPPPLPTPVSNTKEAMSLLTSVQTQLFETVTELQETLDLQDARARLVREARAKDAALLAFAKKLREAHHVLDRLVDDYADYRRDPKRPRGAPVVDEPEPVSHGDFGASLHSKLKLDDILTYAHRISYTTFAPPEHGAGMPLRGALPPAPQDNELRMSQLYQFADLDVGVPKKPLETKDGAAVETEATPLFEPPQEEPPRPSMLPITVPPGWPKGLPKDLPVDIPLPPPGWKPGDPIELGGIMASVKAEEPRPSMPMPVGVQPIVPRAQEPIQVAAVELDINISSSSDEYSSDVGSSEEDDED
Length416
PositionMiddle
OrganismBrachypodium distachyon (Purple false brome) (Trachynia distachya)
KingdomViridiplantae
LineageEukaryota> Viridiplantae> Streptophyta> Embryophyta> Tracheophyta> Spermatophyta> Magnoliopsida> Liliopsida> Poales> Poaceae> BOP clade> Pooideae> Brachypodieae> Brachypodium.
Aromaticity0.04
Grand average of hydropathy-0.370
Instability index70.12
Isoelectric point4.93
Molecular weight44489.95
Publications
PubMed=20148030

Function

Annotated function 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. Mediator is recruited to promoters by direct interactions with regulatory proteins and serves as a scaffold for the assembly of a functional preinitiation complex with RNA polymerase II and the general transcription factors. 
ECO:0000256	RuleBase:RU364141
GO - Cellular Component
core mediator complex	GO:0070847	IBA:GO_Central
mediator complex	GO:0016592	IEA:EnsemblPlants
GO - Biological Function
transcription coregulator activity	GO:0003712	IBA:GO_Central
GO - Biological Process
regulation of transcription by RNA polymerase II	GO:0006357	IBA:GO_Central

Interaction

Binary Interactions











Repeat regions





Repeats

>MDP29386
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             3|     119.27|      27|      50|     310|     337|       1
---------------------------------------------------------------------------
    7-   30 (30.93/ 7.31)	..PSPAR.LGMTAsSPSLP...PNPAPVNP
  310-  337 (50.92/18.95)	EPPRPSM.LPITV.PPGWPKGlPKDLPVDI
  362-  387 (37.42/10.29)	EEPRPSMpMPVGV.QPIVPRA...QEPIQV
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             3|     150.32|      37|      52|      51|      87|       2
---------------------------------------------------------------------------
   52-  104 (54.56/17.25)	TATLTTSPSLLPL...LPPLP....RAQSLLHIMSSL..........................AANLFElspnrtawissyrgslP
  105-  142 (48.59/14.68)	TFLPSSSTSGMP.....PPLPtpvsNTKEAMSLLTSV..........................QTQLFE.................
  243-  306 (47.18/14.07)	TFAPPEHGAGMPLrgaLPPAP....QDNELR..MSQLyqfadldvgvpkkpletkdgaaveteATPLFE................P
---------------------------------------------------------------------------




































Explaination for Stockholm format
  The  "Stockholm" format is a system for marking up features in a multiple alignment. These mark-up annotations are preceded by a 'magic' label, of which there are four types. The Stockholm format is used by HMMER, Pfam, and Belvu. Mark-up lines include any characters except whitespace. Underscore ("_") is used instead of space. 

 #=GR (seqname) PP (Generic per-Sequence AND per-Column markup, exactly 1 char per column) where PP is Posterior Probability  [0-9*], (0=0.00-0.05; 1=0.05-0.15; *=0.95-1.00) 
 
 #=GC PP_cons line is Stockholm-format consensus posterior probability annotation for the entire column.  It’s calculated simply as the arithmetic mean of the per-residue posterior probabilities in that column.  This should prove useful in phylogenetic inference applications, for example, where it’s common to mask away non confidently aligned columns of a multiple alignment. The PP_cons line provides an objective measure of the confidence assigned to each column.
 
 #=GC RF line is Stockholm-format reference coordinate annotation, with an x marking each column that the profile considered to be consensus.





Alignment of MDP29386 with Med4 domain of Kingdom Viridiplantae


     
       
      
        
        
        


      
      
   
   

      

      














Intrinsically Disordered Regions








IDR SequenceStartStop




1) KGLPKDLPVDIPLPPPGWKPGDPIELGGIMASVKAEEPRPSMPMPVGVQPIVPRAQEPIQVAAVELDINISSSSDEYSSDVGSSEEDDED
2) MMQSHMPSPARLGMTASSPSLPPNPAPVNPTSSPPQASSSSSAAAPGAGVPTATLTTSPSLLPLL
3) VGVPKKPLETKDGAAVETEATPLFEPPQEEPPRPSMLPITVPPGW
327
1
281
416
65
325










Molecular Recognition Features






MoRF SequenceStartStop




1) IVPRAQE
377
383