<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 MDP12856

Description Mediator of RNA polymerase II transcription subunit 4
SequenceMQQQRLKQQHALVQQVYPNPSLMGSPQIEPISSGNLPPGFDASNCRSVYVANIHPQVTEPFLQEVFLSTGPIEGCKLVKKDKATYGFVDYVDRRSAALAIVTLNGRQLFGQPIKVNWAYASSQREDTSGHHNTFVGDLSPRAQSLLLQMASLASKLFEVSPNRAIWVSAFRGSLPSFLSSQMQSMPPPPLESTPTSTKEVISLFASLQTQLFEAVGQLQEILDLQDAKQKIAKEIRFKDGAVVAFANKLKEAEQVLDVLVDDYSSYRKPKRLKLEDNGVKDAAAADGDSCTTTVASRLNLSDILSYAHRISYTTFAPPEFGAGQAPLRGALPPAPQEEQMRASQLYNFADLDVGLPKTAETKEKTVEAIIEPPPAQPADTNPLANLAALQGLLPPNFTVPAGWKPNMPVELPANLPVPPPGWKPGDPVPLPPLDSLSIPRMEGPNMRPVPPPGLHKPPEPIQVRHVELDILDPDDDSSDYSSDDGSSDDED
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-0.376
Instability index57.33
Isoelectric point4.98
Molecular weight53442.85
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

>MDP12856
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      57.88|      18|      31|     410|     428|       1
---------------------------------------------------------------------------
  376-  403 (23.83/ 6.90)	QPADTNplanlaalqgLLPPNFTV.PAGW
  404-  422 (34.05/17.10)	KPNMPV..........ELPANLPVpPPGW
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|     101.60|      35|      46|      87|     129|       2
---------------------------------------------------------------------------
   87-  122 (57.66/42.92)	FV.DYVDR.RSAALAIVTLNGRqLFG.QPIKVNW..AYASS
  134-  173 (43.93/17.77)	FVgDLSPRaQSLLLQMASLASK.LFEvSPNRAIWvsAFRGS
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      97.94|      32|      37|     210|     242|       3
---------------------------------------------------------------------------
  210-  242 (46.44/49.93)	QLFEAVGQLQEILDLQDAKQKiAKEIRFKDGAV
  248-  279 (51.50/48.83)	KLKEAEQVLDVLVDDYSSYRK.PKRLKLEDNGV
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      71.55|      21|      23|     427|     448|       7
---------------------------------------------------------------------------
  427-  448 (36.73/21.09)	PVPL..PPlDSLSIPRMEGPNMRP
  451-  473 (34.83/15.87)	PPGLhkPP.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 MDP12856 with Med4 domain of Kingdom Viridiplantae


     
       
      
        
        
        


      
      
   
   

      

      














Intrinsically Disordered Regions








IDR SequenceStartStop




1) FTVPAGWKPNMPVELPANLPVPPPGWKPGDPVPLPPLDSLSIPRMEGPNMRPVPPPGLHKPPEPIQVRHVELDILDPDDDSSDYSSDDGSSDDED
2) PKTAETKEKTVEAIIEPPPAQPADTNPLANLAALQG
397
356
491
391










Molecular Recognition Features






MoRF SequenceStartStop




1) PGLHKPPEPIQVRHVELDILDPDDDSSDYSSDDG
452
485