<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 MDP13030

Description Mediator of RNA polymerase II transcription subunit 4
SequenceMQQQRLKQQHALMQQVYPNPSLMGSPQIEPISSGNLPPGFDASTCRSVYVANIHPQVTEPFLQEVFLSTGPIEGCKLVKKDKATYGFVDYFDRRSAALAIVTLNGRQLFGQPIKVNWAYASSQREDTSGHHNTFVGDLSPRAQSLLLQMASLASKLFEVSPNRAIWVSAFRVSQPSFLSSQMQSMPPPPLESTPTSTKEVISLFASLQTQLFEAVGQLQEILDLQDAKQKIAREIRFKDGAVLAFANKLKEAEQVLDVLVDDYSSYRKPKRLKLEDNGVKDAAAADGDSCTTTVVSRLNLSDILSYAHRISYTTFAPPEFGAGQAPLRGALPPAPQEEQMRASQLYNFADLDVGLPKTAETKEKTVEAIIEPPPAQPADTNPLAKLAALQGLLPPNFTVPAGWKPNMPVELPANLPVPPPGWKPGDPVPLPPLDSLSIPRMEGPNMRPVPPPGLHKQPEPIQVRHVELDILDPDDDSSDYSSDDGSSDDED
Length491
PositionMiddle
OrganismGossypium hirsutum (Upland cotton) (Gossypium mexicanum)
KingdomViridiplantae
LineageEukaryota> Viridiplantae> Streptophyta> Embryophyta> Tracheophyta> Spermatophyta> Magnoliopsida> eudicotyledons> Gunneridae> Pentapetalae> rosids> malvids> Malvales> Malvaceae> Malvoideae> Gossypium.
Aromaticity0.07
Grand average of hydropathy-0.385
Instability index58.82
Isoelectric point5.03
Molecular weight53682.19
Publications
PubMed=25893780

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
mRNA binding	GO:0003729	IBA:GO_Central
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

>MDP13030
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      53.08|      17|      39|     332|     352|       2
---------------------------------------------------------------------------
  332-  352 (26.94/19.16)	PPA.PQEEQmrasQLYNFADLD
  373-  390 (26.15/10.40)	PPAqPADTN....PLAKLAALQ
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             3|     126.36|      31|      31|     131|     161|       3
---------------------------------------------------------------------------
   87-  112 (28.76/13.68)	...FV.DYFDR.RSAA.LAIVTLNGRqLFG.QP
  131-  161 (50.40/29.42)	HNTFVGDLSPRAQSLL.LQMASLASK.LFEVSP
  163-  194 (47.20/27.09)	RAIWVSAFRVSQPSFLsSQMQSMPPP.PLESTP
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      98.19|      32|      37|     210|     242|       4
---------------------------------------------------------------------------
  210-  242 (46.66/37.03)	QLFEAVGQLQEILDLQDAKQKIAReIRFKDGAV
  248-  279 (51.53/36.06)	KLKEAEQVLDVLVDDYSSYRKPKR.LKLEDNGV
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|     116.88|      35|     411|      20|      60|       5
---------------------------------------------------------------------------
   20-   60 (49.81/45.96)	PSLMGsPQIEPISsgnlPPGFDASTcRSVYVANIHPQVTEP
  439-  473 (67.07/39.43)	PRMEG.PNMRPVP....PPGLHKQP.EPIQVRHVELDILDP
---------------------------------------------------------------------------




































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 MDP13030 with Med4 domain of Kingdom Viridiplantae


     
       
      
        
        
        


      
      
   
   

      

      














Intrinsically Disordered Regions








IDR SequenceStartStop




1) FTVPAGWKPNMPVELPANLPVPPPGWKPGDPVPLPPLDSLSIPRMEGPNMRPVPPPGLHKQPEPIQVRHVELDILDPDDDSSDYSSDDGSSDDED
2) PKTAETKEKTVEAIIEPPPAQPADTNPLAKLA
397
356
491
387










Molecular Recognition Features






MoRF SequenceStartStop




1) PGLHKQPEPIQVRHVELDILDPD
452
474