<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 MDP29506

Description Mediator of RNA polymerase II transcription subunit 13
SequenceMPEFPSPSSPAGGGRRRTLNNADNKPDLHGTMNDPYYYDCRILVDATPEKSSRKKSTFVRHFSCTSSHALVKIAAAIVDPRAVVLHGREPHGEQGGGGATGERGHSRSRAERTDPTTTAPFFSGSNRRQVADLFRRPPSSFSDVFGMLIRDPRCYVYSCIGYLKVDIFDRSHFCLFLIEKANNVTAKCNNSLKKSLIVHAIGLACVKKGELQNVSWFQFLPVEPDPSTASERSSKAEQKDALNNIVLSAHLHLQSEGFLSTWTNSFVGPWDPSQGEHNPVVSNGLWVAPGNLEEVAAALCQALRNSLERRAQPTIEFVFAATEEAIFVHVIISARYMRNLCSDDIEKVLTHSPRSVGEGLPVIVAPSGMLGRLVGCCPSDLVRQVYSSKLSAATLPGFTQPTMCQLRGQSYYVEVALGFPAATTDKVPESENNQIKKELDSAKDPQLSADEHQKLESADSVPVLERTFIYPPEAVMVPMVHQAFVRFSSKRMCSQACVGNSSWEGWPFWNFSPSSYFRNSSCLGSSRGLGVNSNFLRLRRQKNSNYSSMASSISSVSSTSNGSEHAVAAEGGDLSADADSMACHQSDLPSNIAGSKMVSKRPRSEIPEVSSRAGKESVDNNQGVNGQGRCSWGWDEEGVAMDINLLISEFGDFSDFFQEEELDFGEPPGTAESHSLVIPGPDCGDATFTDSPSTAMDIPEQRFSPVGLSSLEVFNHQTVAPIHDVVSKVQEPQKDIASPTSSQSVVLSSGRSSHLTRAEALLTYAPEYAAIEISTGETPTSLFTNPYQPRSIKPGSSSFNSRVYSYDAAQSSQMESGEDKPEKSVRLASGNLSRDIGSSNLYTVVQVGKKESDKGLKNTDIQSGKEEASRPISGETSLDSSVVSQRKSDSMFNAGYFLLSMKTALATEMECIKFQAAMCRIRHTLLSLSSKASAELKSALSSLVHTDVSNKLDLVPKYDIKRKENIPARLSIDVDHEVYDRSLENVGVWKPVGTPKGPTHLESFSAKTYTGTSQGLPVKRQPIVDLLSAMALIVQQSTSFVDIALDMDDGDGSFFWLSLDEQKRRGFSCDPSMVHAGCGGILGMCHSKDCAGVDLVDPLSAEVSDSSVISLLQSDIKAALKTAFANMDGPLLVTDWCRGRSNAAEYASMGDAYSFQHPTGDIRESSSSISIGGDSMSPPQSSHVISNDRGTSELEHHRGYHRVRPTVAVLPLPSLLVGYQDDWLKTSANCLSLWEKAPLEPYASPKPVTYYALCPDIEMLTSAATDFFLQLGTIYEVCKLGTHSPQNSGGQMELSPGKYLSSGLVLTECPDQVKIGNGHSSSISSTSEYLQALSRNWTVKSFVTSLTRVIKDIKLNSSILANQKESTSGPCTVIYVVCPFPEPSAVLETLVECSVALGSVMLSPERERKSFLYSQVAKALNCNASVDESSASNVVMLSGFSIPKLVLQIVTVETLLRLHKPNNELAVLKDMAFTVYNKARRIPKAISTSDMFQSPAYMGRSQSTMMHATSPGPTLWKECLVPRMSGSTLSRETEFDASMRSSVTWDNSWPGRAGGFMDPNKIPDVCVQDDRKYAFEPLFILAEPGSVDYSSGMESSKSGVDASGSGIYSSISGGGSDSGASASALLEGSDNDNAASLHCCYGWTEDWRWLVCIWTDSKGELLDSLIFPFGGISSRQDTKVLQSLFIQILQHGCQIMSSAPESSNTRPRDVIITRIGGFLELEIQEWQKAIYSFGGNEVKKWPVQLRRSIPEGIPSNSNGPALQQQDMGLMQDRNMPSSPSPLYSPHAKSSFMKGALGQSGNKKQILVEQAGMDSSKGSLHLVRSISLVAISQDHSLHLTCQADLLTRPTPGEGNQTSSGPSSYLEGFTPVKSIGSMSASYLLVPSPSMRYLSPATLQLPTCLTSESPPLAHLLHSKGTAIPLAMGYVVSKAVPPVRKDSARLANEDRPSVLSVSIIDHYGGSIAAVQEKMSRGSGKQTRNFTQEAAGRDHETEMHNVLEAVAAELHSLSWMTVSPVYMERRSALPSHCDMVLRLRRLLHYADRHLSQSTEKGDVA
Length2055
PositionKinase
OrganismOryza glaberrima (African rice)
KingdomViridiplantae
LineageEukaryota> Viridiplantae> Streptophyta> Embryophyta> Tracheophyta> Spermatophyta> Magnoliopsida> Liliopsida> Poales> Poaceae> BOP clade> Oryzoideae> Oryzeae> Oryzinae> Oryza.
Aromaticity0.07
Grand average of hydropathy-0.296
Instability index56.10
Isoelectric point5.98
Molecular weight223124.85
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. 


ECO:0000256	RuleBase:RU364134

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

>MDP29506
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|    1238.76|     404|     485|     641|    1088|       1
---------------------------------------------------------------------------
  641- 1088 (620.64/411.40)	MDINLLISEF....GDFSDFFQE.EELDFGEPPGTA.ESHSLVIPGpdcGDAtfTDSPSTAMDIPEQRfspvGLSSLEvfNHQTVAPIHDVVSKVQEPQ.....KDIASPTSSQSVVLSSGRSSHLTRAEALLTYAPEYAAIEISTGeTPTSLFTNPYQPRSI.KPGSSSFNSRVYSYDAAQSSQMESG...EDKPEKsVRLASGNlSRDIGSSNLY..................TVVQVGKKESDKGLKNTDIQSGKEEASRPISGETslDSSVVsqrksdsmfnagyfllsmktaLATEMEC.IKFQAAMC...RIRHTLL......SLSSKASAELKSALSSLVHTDVSnkldlVPK..YDIKRKENIpARLSIDVDHEVYDRSLENVGVWKPVGTPKGPTHLESFSAKTYTGTSQGLPVKRQPIVDLLSAMALIVQQSTSFVDIALDMDDG.DGSFFWLSLDEQKRRGFsCDPSMVHAGC..................GGI...LGMCHSK
 1127- 1597 (618.12/328.45)	MDGPLLVTDWcrgrSNAAEYASMgDAYSFQHPTGDIrESSSSISIG...GDS..MSPPQSSHVISNDR....GTSELE..HHRGYHRVRPTVAVLPLPSllvgyQDDWLKTSANCLSLWEKAPLEPYASPKPVTYYALCPDIEMLTS.AATDFFLQLGTIYEVcKLGTHSPQNSGGQMELSPGKYLSSGlvlTECPDQ.VKIGNGH.SSSISSTSEYlqalsrnwtvksfvtsltRVIKDIKLNSSILANQKESTSGPCTVIYVVCPFP..EPSAV.....................LETLVECsVALGSVMLspeRERKSFLysqvakALNCNASVDESSASNVVMLSGFS.....IPKlvLQIVTVETL.LRLHKPNNELAVLKDMAFTVYNKARRIPKAISTSDMFQSPAYMGRSQSTMMHATSPGPTLWKECLVPRMSGSTLSRETEFDASmRSSVTWDNSWPGRAGGF.MDPNKIPDVCvqddrkyafeplfilaepGSVdysSGMESSK
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      82.98|      27|     509|    1089|    1115|       2
---------------------------------------------------------------------------
 1089- 1115 (46.21/24.20)	DCAGVDLVDPLSAEVSDS..SVISLLQ.SD
 1601- 1630 (36.77/17.66)	DASGSGIYSSISGGGSDSgaSASALLEgSD
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|     205.85|      66|    1493|     330|     406|       3
---------------------------------------------------------------------------
  330-  406 (97.68/87.38)	VIISARYMRNL.CSDDIekvLTHsPrSVGEGLPVIVAPSGMlgrLVGCCPsdlVRQVYSSKLSAATLPG....FTQPTMCQL
 1828- 1898 (108.17/64.95)	VAISQDHSLHLtCQADL...LTR.P.TPGEGNQTSSGPSSY...LEGFTP...VKSIGSMSASYLLVPSpsmrYLSPATLQL
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             3|     101.10|      26|      29|     573|     599|       4
---------------------------------------------------------------------------
  548-  567 (24.05/ 8.19)	.......SMASSIS.SVSSTSNGSEHAV
  573-  599 (38.89/22.40)	DLsADADSMACHQS.DLPSNIAGSKMVS
  605-  631 (38.16/17.88)	EI.PEVSSRAGKESvDNNQGVNGQGRCS
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|     256.43|      77|    1606|      23|     109|       5
---------------------------------------------------------------------------
   23-  109 (114.47/93.96)	DNKPDLHGTMNdpYYYDCRILVDATPEKSSRKKSTFVRHFSCTSSHALVKIAAAIVdprAVVLHgrepHGEQGGGGATgERGHSRSR
 1632- 1708 (141.96/84.66)	DNAASLHCCYG..WTEDWRWLVCIWTDSKGELLDSLIFPFGGISSRQDTKVLQSLF...IQILQ....HGCQIMSSAP.ESSNTRPR
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      81.86|      22|      22|     484|     505|       7
---------------------------------------------------------------------------
  484-  505 (43.32/23.65)	FVRFS.SKRMCSQACVGNSSWEG
  508-  530 (38.54/20.22)	FWNFSpSSYFRNSSCLGSSRGLG
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      71.93|      22|    1793|     199|     222|       8
---------------------------------------------------------------------------
  199-  222 (32.66/29.93)	HAIgLACVkKGELQNVSWFQFLPV
 1995- 2016 (39.26/24.91)	HNV.LEAV.AAELHSLSWMTVSPV
---------------------------------------------------------------------------




































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 MDP29506 with Med13 domain of Kingdom Viridiplantae


     
       
      
        
        
        


      
      
   
   

      

      














Intrinsically Disordered Regions








IDR SequenceStartStop




1) GIPSNSNGPALQQQDMGLMQDRNMPSSPSPLYSPHAKSSF
2) IAGSKMVSKRPRSEIPEVSSRAGKESVDNNQGVNGQGRCS
3) MPEFPSPSSPAGGGRRRTLNNADNKPDLHGT
4) QEEELDFGEPPGTAESHSLVIPGPDCGDATFTDSPSTAMDIPEQR
5) QEKMSRGSGKQTRNFTQEAAGRDHETEMHN
6) VLHGREPHGEQGGGGATGERGHSRSRAERTDPTTTAPF
1752
592
1
658
1967
84
1791
631
31
702
1996
121










Molecular Recognition Features






MoRF SequenceStartStop




1) YYYDCRILV
36
44