<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 MDP27234

Description Mediator of RNA polymerase II transcription subunit 16
SequenceMDPVYEIDWQADVNQITLGHGDIVECAWSASNFFAFTTEKNNQGSVTQYLHILNPNQPWGVFSTKYNDGAITCLQWDHTGTRLVSGDNHGLCCLWTMSNSLCNVWTHQNKHNIFLEGEEILSLGWLHNGARFLFHIDKMESSNLGEKFDRAKFWPTVMQHGGKAMEGFIVVTGSGLAAVRLLLVDGESVESQFRLNVMCHQQIADIAFTSQGKVVVMTTDSEIQHFIQFHEIQLTYNTQDHLISHEVSALPSLQLRCASEEHSPYTYISHAHFVSRENQDHVLICVSGPTGSKFESWLIRKESVQLHRIFQQNTNPVSTTPDVSKCWHYVTNSTHLPQVLNFSIPTLPIDASSSENKVSQESKFFCGFCFAVALADNTIQILHRLFLQVLVTQHLPVTTNSQETTPGKAMKMTQQFGVRHVSFSTLSCAMVCFIAADKHGRLLLYRIPPWLTTPNRTNTMQSLKQLLQLMLYCLVSGKEWWEILLHVHPNLVEPLVKQLSVECGNQTSAVQQVLELRLQALKISIYHITASPVATDLHLKMLFQAISLVFRSLVRPHQQVGGEEIDPATKLQNISRTSTETNIDQLVQNVDTDPQTLQSMQQLIQWVADVALYLLASVPLYKQANRPGYSLYWDRDWLSLLREMLVLIRVWGLLKSACSPVFNVLDSRMDVLSHVFKLVTQLWMASTDDHRMTDLPTSLINECSALPFHIIIPPLEPTPPPNSVLSQMRNFSGTRRFTFGETPQDSYIMLSRQHMMDHVAVAGSSGKVDSLRRIFLGKSPNQELKECVRCGVTTTCNNLLRSTLKVWDQRFVSSCVCGGHWKKLNSHPVPLH
Length832
PositionTail
OrganismCiona intestinalis (Transparent sea squirt) (Ascidia intestinalis)
KingdomMetazoa
LineageEukaryota> Metazoa> Chordata> Tunicata> Ascidiacea> Phlebobranchia> Cionidae> Ciona.
Aromaticity0.09
Grand average of hydropathy-0.111
Instability index41.66
Isoelectric point6.62
Molecular weight94137.88
Publications
PubMed=12481130
PubMed=15114417

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. 
GO - Cellular Component
mediator complex	GO:0016592	IBA:GO_Central

GO - Biological Function
GO - Biological Process
positive regulation of transcription, DNA-templated	GO:0045893	IBA:GO_Central









Interaction





Binary Interactions











Repeat regions





Repeats

>MDP27234
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      68.75|      22|     135|     452|     476|       1
---------------------------------------------------------------------------
  452-  476 (35.42/29.45)	TTPnrtNTMQSLKQLLQ....LMLYCLVS
  592-  617 (33.33/19.04)	TDP...QTLQSMQQLIQwvadVALYLLAS
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|     128.43|      41|     388|     371|     432|       2
---------------------------------------------------------------------------
  307-  353 (59.70/36.93)	HRIFQQ.........NTNPVSTTPdvSKCWHyVTNSTHLPQVlNFSipTLPIDASS
  383-  432 (68.73/47.51)	HRLFLQvlvtqhlpvTTNSQETTP..GKAMK.MTQQFGVRHV.SFS..TLSCAMVC
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      65.17|      21|     123|     494|     554|       4
---------------------------------------------------------------------------
  531-  554 (27.47/70.61)	SPVATDLHLKMlfQAISLVFRsLV
  659-  679 (37.70/ 6.66)	SPVFNVLDSRM..DVLSHVFK.LV
---------------------------------------------------------------------------




































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 MDP27234 with Med16 domain of Kingdom Metazoa
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