<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 MDP03542

Description Mediator of RNA polymerase II transcription subunit 13
SequenceMPQFDFWGELQNVSWFQFLPVEPDPSTASERSSKAEQKDALNNIVLSAHLHLQSEGFLSTWTNSFVGPWDPSQGEHNPVVSNGLWVAPGNLEEVAAALCQALRNSLERRAQPTIEFVFAATEEAIFVHVIISARYMRNLCSDDIEKVLTHSPRSVGEGLPVIVAPSGMLGRLVGCCPSDLVRQVYSSKLSAATLPGFTQPTMCQLRGQSYYVEVALGFPAATTDKVPESENNQIKKELDSAKDPQLSADEHQKLESADSVPVLERTFIYPPEAVMVPMVHQAFVRFSSKRMCSQACVGNSSWEGWPFWNFSPSSYFRNSSCLGSSRGLGVNSNFLRLRRQKNSNYSSMASSISSVSSTSNGSEHAVAAEGGDLSADADSMACHQSDLPSNIAGSKMVSKRPRSEIPEVSSRAGKESVDNNQGVNGQGRCSWGWDEEGVAMDINLLISEFGDFSDFFQEEELDFGEPPGTAESHSLVIPGSDCGDATFTDSPSTAMDIPEQRFSPVGLSSLEVFNHQTVAPIHDVVSKVQEPQKDIVSPTSSQSVVLSSGRSSHLTRAEALLTYAPEYAAIEISTGETPTSLFTNPYQPRSIKPGSSSFNSRVYSYDAAQSSQMESGEDKPEKSVRLASGNLSRDIGSSNLYTVVQVGKKESDKGLKNTDIQSGKEEASRPISGETSLDSSVVSQRKSDSMFNAGYFLLSMKTALATEMECIKFQAAMCRIRHTLLSLSSKASAELKSALSSLVHTDVSNKLDLLPKYDIKRKENIPARLSIDVDHEVYDRSLENVGVWKPVGTPKGPTHLESFSAKTYTGTSQGLPVKRQPIVDLLSAMALIVQQSTSFVDIALDMDDGDGSFFWLSLDEQKRRGFSCDPSMVHAGCGGILGTCHSKDCAGVDLVDPLSAEVSDSSVISLLQSDIKAALKTAFANMDGPLLVTDWCRGRSNASESASMGDAYSFQHPTGDIRESSSSISIGGDSMSPPQSSHVISNDRGTSELEHHRGYHRVRPTVAVLPLPSLLVGYQDDWLKTSANCLSLWEKAPLEPYASPKPVTYYALCPDIEMLTSAATDFFLQLGTIYEVCKLGTHSPQNSGGQMELSPGKYLSSGLVLIECPDQVKIGNGHSSSISSTSEYLQALSRNWTVKSFVTSLTRVIKDIKLNSSILANQKESTSGPCTANSGNMITLIIHAERERKSFLYSQVAKALNCNASVDESSASNVVMLSGFSIPKLVLQIVTVETLLRLHKPNNELAVLKDMAFTVYNKARRIPKAISTSDMFQSPAYMGRSQSTMMHATSPGPTLWKECLVPRMSGSTLSRETEFDASMRSSVTWDNSWPGRAGGFMDPNKIPDVCVQDDRKYAFEPLFILAEPGSVDYSSGMESSKSGVDASGSGIYRSISGGGSDSGASALLEGSDNDNAASLHCCYGWTEDWRWLVCIWTDSKGELLDSLIFPFGGISSRQDTKVLQSLFIQILQHGCQIMSSAPESSNTRPRDVIITRIGGFLELEIQEWQKAIYSFGGNEVKKWPVQLRRSIPEGIPSNSNGPALQQQDMGLMQDRNMPSSPSPLYSPHAKSSFMKGALGQSGNKKQILVEQAGMDSSKGSLHLVRSISLVAISQDHSLHLTCQADLLTRPTPGEGNQTCSGPSSYLEGFTPVKSIGSMSASYLLVPSPSMRYLSPATLQLPTCLTSESPPLAHLLHSKGTAIPLAMGYVVSKAVPPVRKDSARLANEDRPSVLSVSIIDHYGGSIAAVQEKTSRGSGKQTRNFTQEAAGRDHETEMHNVLEAVAAELHSLSWMTVSPVYMERRSALPSHCDMVLRLRRLLHYADRHLSQSTEKGDVA
Length1833
PositionKinase
OrganismOryza meridionalis
KingdomViridiplantae
LineageEukaryota> Viridiplantae> Streptophyta> Embryophyta> Tracheophyta> Spermatophyta> Magnoliopsida> Liliopsida> Poales> Poaceae> BOP clade> Oryzoideae> Oryzeae> Oryzinae> Oryza.
Aromaticity0.07
Grand average of hydropathy-0.297
Instability index55.31
Isoelectric point5.64
Molecular weight199006.55
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

>MDP03542
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             4|     250.93|      54|     762|     586|     640|       1
---------------------------------------------------------------------------
  530-  585 (54.40/31.31)	.EPQKdiV..SPTSS..QSVVLS..SGRSSHLTRAEAlltyAPEyAAI.EISTG..ETPTSL..FTNP
  586-  640 (88.35/61.80)	YQPRS..I..KPGSSSFNSRVYSyDAAQSSQMESGED....KPE.KSV.RLASG..NLSRDI.GSSNL
  641-  677 (42.53/22.47)	Y.......................TVVQVGKKES..D....KGL.KNT.DIQSGkeEASRPIsGETSL
 1355- 1403 (65.64/39.68)	FEPLF..IlaEPGSVDYSS......GMESSK..SGVD....ASG.SGIyRSISG..GGS.DS.GASAL
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|     284.46|      88|     765|     756|     845|       2
---------------------------------------------------------------------------
  756-  845 (143.82/93.52)	KYDIKRKENIPARLSIDVDHEVYDRslENVGVWKPVGTPKGPTHLESFSAKT..YTGTSQGLPVKRQPIVDLL....SAMALIVQQSTSFVDIALD
 1518- 1611 (140.64/86.04)	KWPVQLRRSIPEGIPSNSNGPALQQ..QDMGLMQDRNMPSSPSPLYSPHAKSsfMKGALGQSGNKKQILVEQAgmdsSKGSLHLVRSISLVAISQD
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      66.64|      20|      30|     431|     451|       4
---------------------------------------------------------------------------
  431-  451 (33.02/27.85)	WGwDEEGVAMDINLLI..SEFGD
  463-  484 (33.62/21.14)	FG.EPPGTAESHSLVIpgSDCGD
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|     320.08|     103|     605|    1010|    1126|       6
---------------------------------------------------------------------------
 1010- 1126 (154.31/125.56)	PLPSllVGYQddwlkTSANCLSLWEK.APLEPYASPKpvTYYALCPDIEM.LTSAATdffLQLGT..IYEVCKLgTHSPQNSGGQMELSPGKYLSSGLVLIEcPDQVKIGNGHSSSISSTS
 1626- 1732 (165.77/95.14)	PTPG..EGNQ.....TCSGPSSYLEGfTPVKSIGSMS..ASYLLVPSPSMrYLSPAT...LQLPTclTSESPPL.AHLLHSKGTAIPLAMGYVVSKAVPPVR.KDSARLANEDRPSVLSVS
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      81.86|      22|      23|     283|     304|       9
---------------------------------------------------------------------------
  283-  304 (43.32/22.25)	FVRFS.SKRMCSQACVGNSSWEG
  307-  329 (38.54/19.00)	FWNFSpSSYFRNSSCLGSSRGLG
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|     115.27|      36|     216|     678|     721|      11
---------------------------------------------------------------------------
  678-  721 (50.06/64.35)	DSSVVSQRKSDsmFNAgyfllSMKTALAtEMECIKFQAAMCRIR
  904-  939 (65.21/50.01)	DSSVISLLQSD..IKA.....ALKTAFA.NMDGPLLVTDWCRGR
---------------------------------------------------------------------------




































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 MDP03542 with Med13 domain of Kingdom Viridiplantae
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