<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 MDP25464

Description Mediator of RNA polymerase II transcription subunit 17
SequenceMEEAVRVDLDKLPIKRLHAIDEAGNEHYPPDTSSEEQRLSAIRRIDFSWVIDKDAKKPKKDTAQQQQQQAWPWQGMMESLQQAQQELSVVIDLISTVEANDAVAVAGMLKPKSLPTETLVDTAVSAATKLQRVRHLSRYFKQSAKTMEQQFQKESRFYGSLIRLQQNWKVKRQRFGGSGPGSEGFMFDLIDTSQLDTAAMPRLSSLPLIPIDQDSSGTLSVQVPQKSCRFLSLNFRGDSANGVENYGHKLKDGISSITSSETDNDDVNKSIKHAHSILRNIHKSIFEEQVFDMVIRETFVQSQGINVTGMREDFLQLAIGQECSLCLSLAHSGDGSDSEMVDHEDHANSEDASNLVLVTMNGKLDPLRKDVTGFPNPRSLEIYLLQLFHENILRKVREKSLNIGRYQSPAQVAGDDYGLLGHFCLTVAHRIFSNKVLVELESVVSRVPYLHLRSLPTWHSRTSSWSLCLKVPQPILAADRIAKPSDNHELKYKSRSQFNTKVIVKDSQISLMGEGSPSIAGSLTGKPSDGYLVNSYNCDLEDLPTMLLQQVASQVIHWLHEEALVLGMNVTRDFLCLYFDLEQGETLGLVANVDPDDTCGCISWYLTIDHPTEDGKMSADSQEFEKRRFLGYVSLEVLYSTLMDLINLCNAGAHH
Length655
PositionHead
OrganismOryza sativa subsp. indica (Rice)
KingdomViridiplantae
LineageEukaryota> Viridiplantae> Streptophyta> Embryophyta> Tracheophyta> Spermatophyta> Magnoliopsida> Liliopsida> Poales> Poaceae> BOP clade> Oryzoideae> Oryzeae> Oryzinae> Oryza> Oryza sativa.
Aromaticity0.07
Grand average of hydropathy-0.364
Instability index46.27
Isoelectric point5.58
Molecular weight73411.23
Publications
PubMed=15685292

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	IEA:EnsemblPlants

GO - Biological Function
transcription coregulator activity	GO:0003712	IEA:InterPro

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	IEA:InterPro









Interaction





Binary Interactions











Repeat regions





Repeats

>MDP25464
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|     244.38|      87|      95|     237|     331|       1
---------------------------------------------------------------------------
  230-  325 (114.40/115.37)	FLSLNFrGDSANG..VENYGHKLKDGISSITSSeTDN...DDVNKSIKhAHSILRNIHksIFEEQVF.DMVIREtfVQSQGINVtGMREDFLQLAiGQECSL
  326-  419 (129.97/94.72)	CLSLAHsGDGSDSemVDHEDHANSEDASNLVLV.TMNgklDPLRKDVT.GFPNPRSLE..IYLLQLFhENILRK..VREKSLNI.GRYQSPAQVA.GDDYGL
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      47.83|      14|      15|     147|     160|       2
---------------------------------------------------------------------------
  147-  160 (26.03/15.17)	MEQQFQ.KESRFYGS
  164-  178 (21.79/11.66)	LQQNWKvKRQRFGGS
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      78.73|      22|     247|     203|     225|       3
---------------------------------------------------------------------------
  203-  225 (34.92/23.33)	LSSLPLIPiDQDSSGTLSVQVPQ
  452-  473 (43.81/25.41)	LRSLPTWH.SRTSSWSLCLKVPQ
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      47.15|      13|      41|     474|     486|       6
---------------------------------------------------------------------------
  474-  486 (23.20/21.94)	PILAADRIAKPSD
  517-  529 (23.94/22.94)	PSIAGSLTGKPSD
---------------------------------------------------------------------------




































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 MDP25464 with Med17 domain of Kingdom Viridiplantae
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