<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 MDP32103

Description Mediator of RNA polymerase II transcription subunit 4
SequenceMMQSHHPSPARLGLTASSPSLPPNPAAGNPTSSPPQGNPSAAAAVGAAAAAAPTLTTSPSLLPLLPPLPRAQALLQLISALASNLFELSPSRAAWISAYRGSLPTFLPSPSSAPPPPLPAPISSTKEALSLLNTLQTQLFEAVAELQETLDLQDARARLAREARAKDASILAFAKKLREAHHVLDRLVDDYADYRRDPKRPRGAAAADDPEPVSDGDFGASLHSKLNLDDVLTYAHRISYTTFAPPEHGAGLPLRGALPPAPQENEMRMSQLYQFADLDVGVPKSQEAKERTAAEGDATPLFQPSPTQEAAVLPITVPHPHGWRNGALPLEIPLPPPGWKPGDPITLPPDGILAGVKGEEPRASVQQMPVVVPAMVPKAQEPIQVRHVDLDINNSSSSDEYSSDVGSSEEDDED
Length414
PositionMiddle
OrganismOryza sativa subsp. japonica (Rice)
KingdomViridiplantae
LineageEukaryota> Viridiplantae> Streptophyta> Embryophyta> Tracheophyta> Spermatophyta> Magnoliopsida> Liliopsida> Poales> Poaceae> BOP clade> Oryzoideae> Oryzeae> Oryzinae> Oryza> Oryza sativa.
Aromaticity0.04
Grand average of hydropathy-0.348
Instability index58.75
Isoelectric point5.00
Molecular weight43785.69
Publications
PubMed=16100779
PubMed=23299411
PubMed=24280374

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

>MDP32103
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             3|     291.97|      86|      88|      51|     136|       1
---------------------------------------------------------------------------
    8-   81 (86.52/29.25)	.......SPARLG.LTASSPSLPPN.PaagNPTSSPPQGNPSAAAA...........VgaaaaAAPTLTTSPSLLPLLPPLPR.A.QALLQLISAL
   82-  173 (129.31/47.39)	ASNLFELSPSRAAWISAYRGSLPTFLP...SPSSAPPPPLPAPISSTKEALSLLNTLQtqlfeAVAELQETLDLQDARARLAReA.RAKDASILAF
  174-  234 (76.15/24.85)	AKKLREAHHVLDRLVDDY.ADYRRDPK...RPRGAAAADDPEPVSDGDFGASLHSKLN...........................lDDVLTY....
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      49.27|      13|      73|     245|     262|       2
---------------------------------------------------------------------------
  245-  259 (21.29/ 7.32)	PPEHGAGLPLrgALP
  336-  348 (27.98/ 6.47)	PPGWKPGDPI..TLP
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|     102.93|      33|      71|     281|     319|       3
---------------------------------------------------------------------------
  281-  319 (43.66/38.73)	GVpKSQEAKERTAAEGDATPLFQPSpTQEaavlPITVPH
  355-  387 (59.28/32.03)	GV.KGEEPRASVQQMPVVVPAMVPK.AQE....PIQVRH
---------------------------------------------------------------------------




































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 MDP32103 with Med4 domain of Kingdom Viridiplantae


     
       
      
        
        
        


      
      
   
   

      

      














Intrinsically Disordered Regions








IDR SequenceStartStop




1) DVGVPKSQEAKERTAAEGDATPLFQPSPTQEAAVLPITVP
2) MMQSHHPSPARLGLTASSPSLPPNPAAGNPTSSPPQGNPSAAAAVGAAA
3) RNGALPLEIPLPPPGWKPGDPITLPPDGILAGVKGEEPRASVQQMPVVVPAMVPKAQEPIQVRHVDLDINNSSSSDEYSSDVGSSEEDDED
279
1
324
318
49
414










Molecular Recognition Features






MoRF SequenceStartStop




1) IQVRHVDLDI
2) YADYRR
383
191
392
196