<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 MDP00579

Description RNA polymerase II transcription mediators isoform 1
SequenceMDGNLEISLDKLPVRALDAIEENGVERYPHELSYDEKRVSLIRRIDFAWALETDEERERKKKQKKKNSKDATATWLVENLQLAHQELSVIIDLINTVEANDAVTVAGMTRPKPLPNEVLSDLAVSAATKLQCYRHLGKYFKQSAKALEQQIAREARFYGALIRLQQNWKVKRQRVAAPSSSNEGFTIDLFDNSLYDSATISRPSSLSVIHIEHDSAGMLAINLPSNSCHSLHFGFLGVHSADIPKESSKIKTHGSVDQTTRDSQKESMSDDESVKETHLLLREVHQSIFNDQVFDMVNREAFNQSAGVNVTGIRENYLQLSIGQGTSLFISLVPSSKGDDQAVDTANAQNLESAIVSLDSFDDVKSGEGKHDITEKKWGFPNRISCEIYLQQIVHEHAFIKGKDRPNSSGTRVSGQSGKVGSGLLGHFSLSLAHRIFSNRVLMKLENVVCRVPYLHLMTHPTWHSRTSSWTIFMKVPQSILHVESQSQKSDFQNMKDAIKSQFRTKVVVNDDRINVEGEGAPNVVGLFKRSSEDICSVNKYDCDLADLPVIILQQVASQVIRWLHEEALMVGIKTNRDFLCLTFELEQGETVSLVAHVDPEDIQGCISWWLVMEDGFAEDWKLQMDMSDGASEYRKFLGHLSLDVLYSTLMDLVSLCGGGGNH
Length663
PositionHead
OrganismTheobroma cacao (Cacao) (Cocoa)
KingdomViridiplantae
LineageEukaryota> Viridiplantae> Streptophyta> Embryophyta> Tracheophyta> Spermatophyta> Magnoliopsida> eudicotyledons> Gunneridae> Pentapetalae> rosids> malvids> Malvales> Malvaceae> Byttnerioideae> Theobroma.
Aromaticity0.07
Grand average of hydropathy-0.352
Instability index40.48
Isoelectric point5.75
Molecular weight74299.06
Publications
PubMed=23731509

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
core mediator complex	GO:0070847	IBA:GO_Central
mediator complex	GO:0016592	IBA:GO_Central

GO - Biological Function
transcription coregulator activity	GO:0003712	IBA:GO_Central

GO - Biological Process
production of miRNAs involved in gene silencing by miRNA	GO:0035196	IEA:EnsemblPlants
regulation of transcription by RNA polymerase II	GO:0006357	IBA:GO_Central









Interaction





Binary Interactions











Repeat regions





Repeats

>MDP00579
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|     338.09|     111|     155|     178|     299|       1
---------------------------------------------------------------------------
  178-  299 (161.92/120.07)	PSSSNEGFTIDLFDNSLYDSATISRPSSLSVIHIE..HDsAGMLAINLPSN.SCHsLHFGFLgVHSADIPKESSKIKTHGSvdQTTRDSQKESmsddeSVKETHLLLREVHQsIFNDQVF....DMVNR
  334-  451 (176.17/99.38)	PSSKGDDQAVDTANAQNLESAIVSLDSFDDVKSGEgkHD.ITEKKWGFPNRiSCE.IYLQQI.VHEHAFIKGKDRPNSSGT..RVSGQSGKVG.....SGLLGHFSLSLAHR.IFSNRVLmkleNVVCR
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|     142.24|      46|     533|       6|      55|       2
---------------------------------------------------------------------------
    6-   55 (68.23/57.54)	EISLDKLPVRALDAIEENGVeRYPHElsyDEKRVSLIRRIDF...AWALETDE
  542-  590 (74.01/49.08)	DCDLADLPVIILQQVASQVI.RWLHE...EALMVGIKTNRDFlclTFELEQGE
---------------------------------------------------------------------------




































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 MDP00579 with Med17 domain of Kingdom Viridiplantae
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