<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 MDP03747

Description Mediator of RNA polymerase II transcription subunit 13
SequenceMYHGFSFFLLNQIQVQLLREAEQKDALNNIVLSAHLHLQSEGFLSTWTNSFVGPWDPSQGEHNPVISNGLWVAPGNLEEVGAALCQALRNSLERTLRGLSYARFGDVFTKYYPPTRNQNSFRRAQPTIEFVFAATEEAIFVHVVISARYMRNLCSDDIEKVLTHSPRSVGEGLPVIVAPSGMLGRLVGCCPSDLVRQVYSSKLSAATLPGFTQPTICQLRGQSYYVEVALGFPAATTDKVPESENNQIKKELDSAMDPQLSADEHQKLESVDSVLVLERTFIYPPEAVMGCVGNSSWEGWPFWNFSPSSYFRNSISSCLGSSHGLGVNSNFLRLRRQKNSNYSSMASSISSVSSTSNGSEHAVAAEGGDLSADADSMACHQSDLPSNIAGSKMVSKRPRSEIPEVSSRAGKESVDNNQGANGQGRCSWGWDEEGVVMDINLLISEFGDFSDFFQEEELDFGEPPGTAESHSLVIPGSDCGDATFTDSPSTAMDIPEQRFSPVGLSSLEVFNHQTVAPIHDVVSKIQEPQKDIASPSSSQSVVLSSGRSSHLTRAEALLTYAPEYAAIEISAGETPTSLFTNPYQPRSIKPGSSSFNSRVYSYDQSSQMESGEDKPEKSVRLASGNLSRDIGSSNLYTVVQVGKKESDKGLKNTDLQSGKEEASRPISGETSLDSSVVSQRKSDSMFNAGYFLLSMKTALATEIECIRFQAAMCRIRHTLLSLSSKASAELKSALSSLVHTDVSNKLDLVPKYDIKRKENIPARLSIDVDHEVYDRSLENVGVWKPVGTPKGPTHLESFSAKTYTGTSQGLPVKRQPIVDLLSAMALIVQQSTSFVDVALDMDDGDGSFFWLSLDEQKRRGFSCDPSMVHAGCGGILGTCHSKDCAGVDLVDPLSAEVSDSSVISLLQSDVKTALKTAFASMDGPLLVTDWCRGRSNAPESVSMGDAYSFQHPTGDIRESSSSISIGGDSMSPPQSSHVISNDRGTSELEHHRGYHRVRPTVAVLPLPSLLVGYQDDWLKTSANCLSLWEKAPLEPYASPKPVTYYALCPDIEMLTSAATDFFLQLGTIYEVCKLGSHSPQNSGGQMELSPGKYLSSGLVLIECPDQVKIGNGHSSSISSTSEYLQALSKNWTVKSFVTSLTRVIKDIKLNSSILANQKESTSGPCTVIYVVCPFPEPSAVLETLVECSVALGSVMLSPERERKSFLYSQVAKALNCNASVDESSASNVVMLSGFSIPKLVLQIVTIETLLRLHKPNNELAVLKDMAFTVYNKARRIPKAISTSDMFQSPAYMGRSQSTMMHATSPGPTLWKECLVPRMSGSTLSRETEFDASMRSSVTWDNSWPGRAGGFMDPNKIPDVCVQDDRKYAFEPLFILAEPGSVDYSTGMESSKSGVDASGSGIYSSISGGGSDSGASALLEGSDNDNAASLHCCYGWTEDWRWLVCIWTDSKGELLDSLIFPFGGISSRQDTKVLQSLFIQILQHGCQIMSSAPESSNTRPRDVIITRIGGFLELEIQEWQKAIYSFGGNEVKKWPVQLRRSIPEGIPSNSNGPALQQQDMGLMQDRNMPSSPSPLYSPHAKSSFMKGALGQSGNKKQILVEQAGMDSSKGSLHLVRSISLVAISQDHSLHLTCQADLLTRPTPGEGNQSSSGPSSYLEGFTPVKSIGSMSASYLLVPSPSMRYLSPATLQLPTCLTSESPPLAHLLHSKGTAIPLAMGYVISKAVPPVRKDSARLANEDRPSVLSVSIIDHYGGSIAAVQEKMSRGSGKQTRSFTQETAGRDHETEMHNALEAVAAELHSLSWMTVSPVYVERRSALPFHCDMVLRLRRLLHYADRHLSQSTEKGDLA
Length1847
PositionKinase
OrganismOryza punctata (Red rice)
KingdomViridiplantae
LineageEukaryota> Viridiplantae> Streptophyta> Embryophyta> Tracheophyta> Spermatophyta> Magnoliopsida> Liliopsida> Poales> Poaceae> BOP clade> Oryzoideae> Oryzeae> Oryzinae> Oryza.
Aromaticity0.07
Grand average of hydropathy-0.264
Instability index56.15
Isoelectric point5.59
Molecular weight200553.45
Publications









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

>MDP03747
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No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      88.43|      27|     125|      96|     123|       1
---------------------------------------------------------------------------
   96-  123 (46.46/36.85)	LRGLSY.....ARFGDVFTKYYPPTRNqNSFRR
  219-  250 (41.97/27.64)	LRGQSYyvevaLGFPAATTDKVPESEN.NQIKK
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      59.98|      17|      30|     344|     360|       2
---------------------------------------------------------------------------
  344-  360 (28.19/14.25)	SMASSISSVSSTSNGSE
  376-  392 (31.79/17.09)	SMACHQSDLPSNIAGSK
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|    1168.58|     387|     475|     437|     872|       3
---------------------------------------------------------------------------
  437-  872 (579.53/428.97)	MDINLLISEF..GDfSDffQEEELDFGEppgtaeSHSLVIPGSDCGDATFTDS........PSTAMDIPEQRfspvGLSSLEvfNHQTVAPIHDVVSKIQEPQ.....KDiaspsssqSVVLSSGRSSHLTRAEALLTYA.PE.......YAAIEISAGETPTSLFTNPYQPRSIKPGSSSfnsrvySYDQSSQMESGEDKPEKS..VrLASGNLSRDIGSSNLYTVVqvGKKESDKGL.KNTDLQSGKEEASRPISgETSLDSSVVS.QRKSDSMFNAGYFLL....SMKTALATEIEC.IRFQAAMC...RIRHTLL......SLSSKASAELKSALSSLVHTDVSnkldlVPK..YDIKRKENIpARLSidvdhevydRSLENVGVWKPVG.........TPKGPTHLESFSAKTYTGTSQGLPVKRQPIVDLLSAMALIVQQSTSFVDVALDMDDG.DGSFFWLSLDEQKRRGFsCDPSMVHAGC
  921- 1360 (589.05/335.10)	MDGPLLVTDWcrGR.SN..APESVSMGD......AYSFQHPTGDIRESSSSISiggdsmspPQSSHVISNDR....GTSELE..HHRGYHRVRPTVAVLPLPSllvgyQD........DWLKTSANCLSLWEKAPLEPYAsPKpvtyyalCPDIEMLTSAATDFFLQLGTIYEVCKLGSHS......PQNSGGQMELSPGKYLSSglV.LIECPDQVKIGNGHSSSIS..STSEYLQALsKNWTVKSFVTSLTRVIK.DIKLNSSILAnQKESTSGPCTVIYVVcpfpEPSAVLETLVECsVALGSVMLspeRERKSFLysqvakALNCNASVDESSASNVVMLSGFS.....IPKlvLQIVTIETL.LRLH.........KPNNELAVLKDMAftvynkarrIPKAISTSDMFQSPAYMGRSQSTMMHATSPGPTLWKECLVPRMSGSTLSRETEFDASmRSSVTWDNSWPGRAGGF.MDPNKIPDVC
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|     205.04|      62|     115|     145|     210|       4
---------------------------------------------------------------------------
  145-  210 (99.67/67.10)	ISARYMRNLCSDD....IEKVLTHSPRSVgEGlpvIVAPSGMLG.RLVGCCPSDLVRQVYSSKLSAATLPG
  260-  326 (105.37/59.54)	LSADEHQKLESVDsvlvLERTFIYPPEAV.MG...CVGNSSWEGwPFWNFSPSSYFRNSISSCLGSSHGLG
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|     225.59|      73|     155|    1549|    1626|       5
---------------------------------------------------------------------------
 1549- 1626 (112.27/74.63)	SNGPALQQQdMGLMQDRNMP..SSPSPLYSPHAKSSFMK.GALGQSGNkkQILVEQAGMdsSKGSLHLVRSISLVAISQDH
 1707- 1782 (113.33/61.37)	SKGTAIPLA.MGYVISKAVPpvRKDSARLANEDRPSVLSvSIIDHYGG..SIAAVQEKM..SRGSGKQTRSFTQETAGRDH
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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 MDP03747 with Med13 domain of Kingdom Viridiplantae
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