<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 MDP00424

Description Mediator of RNA polymerase II transcription subunit 13
SequenceMHFAMINAVLFCSNIMTKSILQNTPPQSLIKYTFLRKLVRLPMIFSLQACRLGQHRPICKTHADGILRVGTAEGRNLAEQPLSDWFLKMASSNGNSEAFSKLKLYAQVCRHDLAPYLAGQSLDSSLLNQRSPTVASPQSSSSQSPCSTTTPSGPQSSTSSSTAQPTNSTPPSSTIGPQAVGGIGGVGMPSAKPSSYTPYGTSGLQGSVSQNGPQSGAQTTGETGPTANQPQATTEPVETTLERDKVGVPTDGESHAVTFPPAIVVYIVDPFSYEDGERDTHSSVWTLGLLRCYVEMLQFLPPHIRNSVSVQIIPCQYLLQPVRIEERHLYGQHLKSLAFSVFTQCRRPLPSNTNIKALTGFGPGLAIDMALRSSERPECLRLYTPPFILAPIKDKQTELGETFGEASQKYNVLFVGYCLSHDQRWLLASCTDQSGELLETCIISIDVPNRARRKKGSARRLGLQKLWEWCLGLVQVTSLPWRVVIGRLGRIGHGELRGMPHRDVCMPHREVCVCVCQVIVEARSSDSALHHSPWSNSPYTAWRCVLGHCPIDKTNDSPTKRKPDGMTYRCRMLL
Length574
PositionMiddle
OrganismOncorhynchus mykiss (Rainbow trout) (Salmo gairdneri)
KingdomMetazoa
LineageEukaryota> Metazoa> Chordata> Craniata> Vertebrata> Euteleostomi> Actinopterygii> Neopterygii> Teleostei> Protacanthopterygii> Salmoniformes> Salmonidae> Salmoninae> Oncorhynchus.
Aromaticity0.07
Grand average of hydropathy-0.270
Instability index57.39
Isoelectric point8.93
Molecular weight62962.33
Publications
PubMed=24755649

Function

Annotated function Component of the Mediator complex, a coactivator involved in 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:RU364134
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

>MDP00424
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      34.59|      15|      21|     145|     165|       1
---------------------------------------------------------------------------
  135-  150 (22.22/ 6.84)	AS.PQSSSSQ...............sPCSTTT
  151-  182 (12.37/11.63)	PSgPQSSTSSstaqptnstppsstigPQAVGG
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      39.18|      15|      21|     218|     236|       2
---------------------------------------------------------------------------
  184-  201 (20.58/ 7.65)	GGVGMPSA.KPSSYT.pygT
  220-  239 (18.60/15.78)	TGETGPTAnQPQATTepveT
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      82.59|      27|      28|     289|     316|       3
---------------------------------------------------------------------------
  289-  316 (44.74/36.05)	LLR.CYVEMLQFLPPHIRN.SVSVqIIPCQ
  318-  346 (37.84/24.87)	LLQpVRIEERHLYGQHLKSlAFSV.FTQCR
---------------------------------------------------------------------------




































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 MDP00424 with Med13 domain of Kingdom Metazoa


     
       
      
        
        
        


      
      
   
   

      

      














Intrinsically Disordered Regions








IDR SequenceStartStop




1) SLLNQRSPTVASPQSSSSQSPCSTTTPSGPQSSTSSSTAQPTNSTPPSSTIGPQAVGGIGGVGMPSAKPSSYTPYGTSGLQGSVSQNGPQSGAQTTGETGPTANQPQATTEPVETTLERDKVGVPTDGE
125
253










Molecular Recognition Features






MoRF SequenceStartStop




1) YRCRMLL
568
574