<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 MDP24842

Description Mediator of RNA polymerase II transcription subunit 6
SequenceMAAVDIRDNLLGISWVDSSWIPILNSGSVLDYFSERSNPFYDRTCNNEVVKMQRLTLEHLNQMVGIEYILLHAQEPILFIIRKQQRQSPAQVIPLADYYIIAGVIYQAPDLGSVINSRVLTAVHGIQSAFDEAMSYCRYHPSKGYWWHFKDHEEQDKVKPKAKRKEEPSSIFQRQRVDALLIDLRQKFPPRFVQQKSGEKPVPVDQAKKEAEPLPETVKSEEKESAKSAQQTVSTKGPPEKRMRLQ
Length246
PositionHead
OrganismRattus norvegicus (Rat)
KingdomMetazoa
LineageEukaryota> Metazoa> Chordata> Craniata> Vertebrata> Euteleostomi> Mammalia> Eutheria> Euarchontoglires> Glires> Rodentia> Myomorpha> Muroidea> Muridae> Murinae> Rattus.
Aromaticity0.09
Grand average of hydropathy-0.571
Instability index52.37
Isoelectric point8.71
Molecular weight28320.04
Publications
PubMed=15489334
PubMed=15057822
PubMed=15632090

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	PIRNR:PIRNR023869
GO - Cellular Component
core mediator complex	GO:0070847	IBA:GO_Central
mediator complex	GO:0016592	ISO:RGD
nucleoplasm	GO:0005654	IEA:Ensembl
nucleus	GO:0005634	ISO:RGD
ubiquitin ligase complex	GO:0000151	IDA:RGD
GO - Biological Function
DNA binding	GO:0003677	ISO:RGD
transcription coactivator activity	GO:0003713	ISO:RGD
transcription factor binding	GO:0008134	ISO:RGD
GO - Biological Process
positive regulation of transcription by RNA polymerase II	GO:0045944	ISO:RGD
protein ubiquitination	GO:0016567	IDA:RGD
regulation of transcription by RNA polymerase II	GO:0006357	IBA:GO_Central
stem cell population maintenance	GO:0019827	ISO:RGD

Interaction

Binary Interactions











Repeat regions





Repeats

>MDP24842
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      69.02|      21|      42|     148|     168|       1
---------------------------------------------------------------------------
  148-  168 (37.33/21.99)	HFKDHEEQDKVKP..KAKRKEEP
  191-  213 (31.69/17.76)	RFVQQKSGEKPVPvdQAKKEAEP
---------------------------------------------------------------------------




































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 MDP24842 with Med6 domain of Kingdom Metazoa


     
       
      
        
        
        


      
      
   
   

      

      














Intrinsically Disordered Regions








IDR SequenceStartStop




1) FVQQKSGEKPVPVDQAKKEAEPLPETVKSEEKESAKSAQQTVSTKGPPEKRMRLQ
192
246










Molecular Recognition Features






MoRF SequenceStartStop




1) PVDQAKKEAEPLPETVKSEEKESAKSAQQTVSTKGPPEKRMRLQ
2) RVDALLIDLRQKFPPRFVQ
203
176
246
194