<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 MDP18095

Description Mediator of RNA polymerase II transcription subunit 4
SequenceMLQHQIVQSPARLGLTNPNSPLIPNPTPPKLPPLQTTHHHQDRHTAAPSAALLSLLPPLPRAQALLVQMASLSSKLFEVSPNKSLWVSAFRGSLPTFLSSQGQPHSSASLDSSPSSIKEILSLFSILQIQIFEAVSELQEILDQQDAKQKIDQEICSKDSSLLAFANKLKDAERVLDILVDDYSDYRSNTKRLKLGDGSEDDSLTTSSVSSKLKLSDILSYAHRISYTTFAPPEFGAGQAPLRGALPPAPQDEQMRASQLYNFADLDIGLPKEVDTKEKTIEAIIEPPPLQPVDTNSLANLPGIQGLLPPNFTIPPGWKPGMPVQLPIDIPIKPPAGWKPGDPVALPPMDSLPVQRFDEQQLRPHVPQLKQPEIIQVAPVNLDLGGSDSSDYSSDDASTDDED
Length403
PositionMiddle
OrganismTrifolium pratense (Red clover)
KingdomViridiplantae
LineageEukaryota> Viridiplantae> Streptophyta> Embryophyta> Tracheophyta> Spermatophyta> Magnoliopsida> eudicotyledons> Gunneridae> Pentapetalae> rosids> fabids> Fabales> Fabaceae> Papilionoideae> 50 kb inversion clade> NPAAA clade> Hologalegina> IRL clade> Trifolieae> Trifolium.
Aromaticity0.05
Grand average of hydropathy-0.356
Instability index61.88
Isoelectric point4.85
Molecular weight43819.07
Publications
PubMed=24500806
PubMed=28382043

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
mediator complex	GO:0016592	IEA:InterPro
GO - Biological Function
transcription coregulator activity	GO:0003712	IEA:InterPro
GO - Biological Process
regulation of transcription by RNA polymerase II	GO:0006357	IEA:InterPro

Interaction

Binary Interactions











Repeat regions





Repeats

>MDP18095
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             3|      87.40|      17|      18|     308|     324|       1
---------------------------------------------------------------------------
  291-  306 (22.96/ 8.35)	QPVD.TN.SL.ANLPGIQG
  308-  324 (37.75/18.55)	LPPNFTI.PP.GWKPGMPV
  326-  344 (26.69/10.92)	LPIDIPIkPPaGWKPGDPV
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      60.16|      19|      37|       3|      24|       2
---------------------------------------------------------------------------
    3-   21 (32.80/12.01)	QHQIVQSPARLGLTNPNSP
   66-   84 (27.36/ 7.60)	LVQMASLSSKLFEVSPNKS
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      51.53|      17|      22|     177|     197|       3
---------------------------------------------------------------------------
  177-  197 (24.36/21.96)	DilvdDYSDYRSNTKRLKLGD
  201-  217 (27.18/14.73)	D....DSLTTSSVSSKLKLSD
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      58.62|      19|      37|     232|     250|       4
---------------------------------------------------------------------------
  232-  250 (37.57/20.41)	PPEFGAGQ....APLRGALP...............PAP
  252-  289 (21.05/ 8.16)	DEQMRASQlynfADLDIGLPkevdtkektieaiiePPP
---------------------------------------------------------------------------




































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 MDP18095 with Med4 domain of Kingdom Viridiplantae


     
       
      
        
        
        


      
      
   
   

      

      














Intrinsically Disordered Regions








IDR SequenceStartStop




1) DIPIKPPAGWKPGDPVALPPMDSLPVQRFDEQQLRPHVPQLKQPEIIQVAPVNLDLGGSDSSDYSSDDASTDDED
2) LGLTNPNSPLIPNPTPPKLPPLQTTHHHQDRHTAA
329
13
403
47










Molecular Recognition Features






MoRF SequenceStartStop




NANANA