<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 MDP25596

Description Mediator of RNA polymerase II transcription subunit 4
SequenceMLQHQIVQSPARLGLTNPNSPSLQNPTPPKFPAASSQQQQHPSSALLSLLPPLRRAQSLLLQMASLASKFFEVSPNRALWVSAFRGSLPTFLSSQTQSISPLESTPFSSKDILSLFTSLQTQLFEAVAELQEILDLQDAKQRLARDIKSHDSALLNFANKLKEAETLLDILVDDYSDYRKPKIAKSSLTEDDDVSNTTTSATTTTVASQLNLSDILSYAHRISYTTFAPPEFGAGTAPLRGAFPPAPQEEQMRVSQLYAFADLDVGLPKTETRERIIEPIIEPPPPPQSADTNPLGNLAGLFPPSLTVPSGWKPGMPVVLPTDLPPPPPGWKPGDPLPLPPLDSLPLPRTNEQQLQPAVAPQGLHKPPETIQVRHVQIDILDQDDDSSDYSSDDGSSDDED
Length401
PositionMiddle
OrganismRicinus communis (Castor bean)
KingdomViridiplantae
LineageEukaryota> Viridiplantae> Streptophyta> Embryophyta> Tracheophyta> Spermatophyta> Magnoliopsida> eudicotyledons> Gunneridae> Pentapetalae> rosids> fabids> Malpighiales> Euphorbiaceae> Acalyphoideae> Acalypheae> Ricinus.
Aromaticity0.06
Grand average of hydropathy-0.404
Instability index69.23
Isoelectric point4.66
Molecular weight43645.51
Publications
PubMed=20729833

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:InterPro
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

>MDP25596
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             4|     190.56|      39|      39|     283|     321|       1
---------------------------------------------------------------------------
  229-  264 (42.12/14.87)	......PPEFGAG..TAP...LRGAFPPA...PQ..EEQMRVSqlyafadLD
  283-  321 (82.41/35.56)	PP....PPPQSAD..TNPLGNLAGLFPPSLTVPSGWKPGMPVV.......LP
  325-  338 (37.29/12.39)	PP....PPP.........................GWKPGDP.........LP
  340-  371 (28.74/ 8.01)	PPldslPLPRTNEqqLQPAVAPQGLHKPPETI....................
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      89.98|      33|      37|     110|     145|       2
---------------------------------------------------------------------------
  110-  145 (44.39/38.81)	KDilSLFTSLQTQLFEAvAELQEIL..DLQD.AKQRLAR
  150-  185 (45.59/28.91)	HD..SALLNFANKLKEA.ETLLDILvdDYSDyRKPKIAK
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      97.72|      31|      37|       3|      38|       3
---------------------------------------------------------------------------
    8-   38 (57.74/31.45)	QSP..ARLGLTNP....NSPSLQNPT.PPKFPAASSQQ
   40-   77 (39.98/12.42)	QHPssALLSLLPPlrraQSLLLQMASlASKFFEVSPNR
---------------------------------------------------------------------------




































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 MDP25596 with Med4 domain of Kingdom Viridiplantae


     
       
      
        
        
        


      
      
   
   

      

      














Intrinsically Disordered Regions








IDR SequenceStartStop




1) ETRERIIEPIIEPPPPPQSADTNPLGNLAGLFPP
2) QSPARLGLTNPNSPSLQNPTPPKFPAASSQQ
3) WKPGMPVVLPTDLPPPPPGWKPGDPLPLPPLDSLPLPRTNEQQLQPAVAPQGLHKPPETIQVRHVQIDILDQDDDSSDYSSDDGSSDDED
271
8
312
304
38
401










Molecular Recognition Features






MoRF SequenceStartStop




1) LHKPPETIQVRHVQIDILDQDDDSSDYSSDDGSSDDED
364
401