<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 MDP05376

Description Mediator of RNA polymerase II transcription subunit 13 (Fragment)
SequenceLFFPTVYEVCKLGTHSPQNSGGQMELSPGKYLSSGLVLTECPDQVKIGNGHSSSISSTSEYLQALSRNWTVKSFVTSLTRVIKDIKLNSSILANQKESTSGPCTVIYVVCPFPEPSAVLETLVECSVALGSVMLSPERERKSFLYSQVAKALNCNASVDESSASNVVMLSGFSIPKLVLQIVTVETLLRLHKPNNELAVLKDMAFTVYNKARRIPKAISTSDMFQSPAYMGRSQSTMMHATSPGPTLWKECLVPRMSGSTLSRETEFDASMRSSVTWDNSWPGRAGGFMDPNKIPDVCVQDDRKYAFEPLFILAEPGSVDYSSGMESSKSGVDASGSGIYSSISGGGSDSGASASALLEGSDNDNAASLHCCYGWTEDWRWLVCIWTDSKGELLDSLIFPFGGISSRQDTKVLQSLFIQILQHGCQIMSSAPESSNTRPRDVIITRIGGFLELEIQEWQKAIYSFGGNEVKKWPVQLRRSIPEGIPSNSNGPALQQQDMGLMQDRNMPSSPSPLYSPHAKSSFMKGALGQSGNKKQILVEQAGMDSSKGSLHLVRSISLVAISQDHSLHLTCQADLLTRPTPGK
Length584
PositionKinase
OrganismOryza sativa subsp. japonica (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-0.209
Instability index55.45
Isoelectric point6.41
Molecular weight63405.31
Publications
PubMed=16100779
PubMed=24280374

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. 
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

>MDP05376
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No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|     128.70|      37|     285|     226|     262|       2
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  226-  262 (69.27/43.27)	SPAYMGRSQSTMMHATSPGPTLWKECLVPR..MSGSTLS
  512-  550 (59.43/36.08)	SPLYSPHAKSSFMKGALGQSGNKKQILVEQagMDSSKGS
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      95.58|      27|     286|      30|      56|       3
---------------------------------------------------------------------------
   30-   56 (48.09/29.16)	KYLSSGLVLTECPDQVKIGNGHSSSIS
  304-  330 (47.49/28.71)	KYAFEPLFILAEPGSVDYSSGMESSKS
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|     218.82|      80|     271|      87|     181|       4
---------------------------------------------------------------------------
   87-  181 (107.50/133.40)	LNSSilaNQKESTSGPCTviY........VVCPFPEPSA.VLETLVecsVALGSVmlSPERERKSF..LYSQVAKAlNCN..ASVDESSAS...NVVM..LSGFsipkLVLQI
  358-  455 (111.31/87.28)	LEGS...DNDNAASLHCC..YgwtedwrwLVCIWTDSKGeLLDSLI...FPFGGI..SSRQDTKVLqsLFIQILQH.GCQimSSAPESSNTrprDVIItrIGGF....LELEI
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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 MDP05376 with Med13 domain of Kingdom Viridiplantae
Unable to open file!