<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 MDP03861

Description Mediator of RNA polymerase II transcription subunit 13
SequenceMPEFPSPSSPAGGGRRRMLNNADNKPDLHGTMNDPYYYDCRILVDATPEKSSRKKSTFVRHFSCTSSHALVKIAAAIVDPRAVVLHGREPHGEQGGGGATGERGHSRSRAERTDPTTTAPFFSGSNRRQVADLFRRPPSSFSDVFGMLIRDPRCYVYSCIGYLKGELQNVSWFQFLPVEPDPSTASERSSKAEQKDALNNIVLSAHLHLQSEGFLSTWTNSFVGPWDPSQGEHNPVVSNGLWVAPGNLEEVAAALCQALRNSLERRAQPTIEFVFAATEEAIFVHVIISARYMRNLCSDDIEKVLTHSPRSVGEGLPVIVAPSGMLGRLVGCCPSDLVRQVYSSKLSAATLPGFTQPTMCQLRGQSYYVEVALGFPAATTDKVPESENNQIKKELDSAKDPQLSADEHQKLESADSVPVLERTFIYPPEAVMVPMVHQAFVRFSSKRMCSQACVGNSSWEGWPFWNFSPSSYFRNSSCLGSSRGLGVNSNFLRLRRQKNSNYSSMASSISSVSSTSNGSEHAVAAEGGDLSADADSMACHQSDLPSNIAGSKMVSKRPRSEIPEVSSRAGKESVDNNQGVNGQGRCSWGWDEEGVAMDINLLISEFGDFSDFFQEEELDFGEPPGTAESHSLVIPGPDCGDATFTDSPSTAMDIPEQRFSPVGLSSLEVFNHQTVAPIHDVVSKVQEPQKDIASPTSSQSVVLSSGRSSHLTRAEALLTYAPEYAAIEISTGETPTSLFTNPYQPRSIKPGSSSFNSRVYSYDAAQSSQMESGEDKPEKSVRLASGNLSRDIGSSNLYTVVQVGKKESDKGLKNTDIQSGKEEASRPISGETSLDSSVVSQRKSDSMFNAGYFLLSMKTALATEMECIKFQAAMCRIRHTLLSLSSKASAELKSALSSLVHTDVSNKLDLVPKYDIKRKENIPARLSIDVDHEVYDRSLENVGVWKPVGTPKGPTHLESFSAKTYTGTSQGLPVKRQPIVDLLSAMALIVQQSTSFVDIALDMDDGDGSFFWLSLDEQKRRGFSCDPSMVHAGCGGILGTCHSKDCAGVDLVDPLSAEVSDSSVISLLQSDIKAALKTAFANMDGPLLVTDWCRGRSNAAEYASMGDAYSFQHPTGDIRESSSSISIGGDSMSPPQSSHVISNDRGTSELEHHRGYHRVRPTVAVLPLPSLLVGYQDDWLKTSANCLSLWEKAPLEPYASPKPVTYYALCPDIEMLTSAATDFFLQLGTIYEVCKLGTHSPQNSGGQMELSPGKYLSSGLVLTECPDQVKIGNGHSSSISSTSEYVQALSRNWTVKSFVTSLTRVIKDIKLNSSILANQKESTSGPCTVIYVVCPFPEPSAVLETLVECSVALGSVMLSPERERKSFLYSQVAKALNCNASVDESSASNVVMLSGFSIPKLVLQIVTVETLLRLHKPNNELAVLKDMAFTVYNKARRIPKAISTSDMFQSPAYMGRSQSTMMHATSPGPTLWKECLVPRMSGSTLSRETEFDASMRSSVTWDNSWPGRAGGFMDPNKIPDVCVQDDRKYAFEPLFILAEPGSVDYSSGMESSKSGVDASGSGIYSSISGGGSDSGASASALLEGSDNDNAASLHCCYGWTEDWRWLVCIWTDSKGELLDSLIFPFGGISSRQDTKVLQSLFIQILQHGCQIMSSAPESSNTRPRDVIITRIGGFLELEIQEWQKAIYSFGGNEVKKWPVQLRRSIPEGIPSNSNGPALQQQDMGLMQDRNMPSSPSPLYSPHAKSSFMKGALGQSGNKKQILVEQAGMDSSKGSLHLVRSISLVAISQDHSLHLTCQADLLTRPTPGEGNQTSSGPSSYLEGFTPVKSIGSMSASYLLVPSPSMRYLSPATLQLPTCLTSESPPLAHLLHSKGTAIPLAMGYVVSKAVPPVRKDSARLANEDRPSVLSVSIIDHYGGSIAAVQEKMSRGSGKQTRNFTQEAAGRDHETEMHNVLEAVAAELHSLSWMTVSPVYMERRSALPSHCDMVLRLRRLLHYADRHLSQSTEKGDVA
Length2011
PositionKinase
OrganismOryza rufipogon (Brownbeard rice) (Asian wild rice)
KingdomViridiplantae
LineageEukaryota> Viridiplantae> Streptophyta> Embryophyta> Tracheophyta> Spermatophyta> Magnoliopsida> Liliopsida> Poales> Poaceae> BOP clade> Oryzoideae> Oryzeae> Oryzinae> Oryza.
Aromaticity0.07
Grand average of hydropathy-0.310
Instability index56.48
Isoelectric point5.85
Molecular weight218226.03
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

>MDP03861
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|     134.62|      47|     367|     725|     776|       1
---------------------------------------------------------------------------
  725-  774 (70.30/70.20)	AAIEISTGETPTSL.FTNPYqpRSIKPGSSSFNSRVYSYDaAQSSQME.....SGE
  779-  831 (64.31/43.48)	KSVRLASGNLSRDIgSSNLY..TVVQVGKKESDKGLKNTD.IQSGKEEasrpiSGE
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|     140.47|      43|     369|    1509|    1599|       3
---------------------------------------------------------------------------
 1509- 1552 (75.22/40.76)	AGGFMDPNKIP..DVCVQDDRKyAFEPLFI.LAEPGSVDYSSGMESS
 1614- 1659 (65.25/56.93)	KGELLDSLIFPfgGISSRQDTK.VLQSLFIqILQHGCQIMSSAPESS
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|     295.44|      97|     730|     360|     469|       4
---------------------------------------------------------------------------
  360-  469 (147.72/146.10)	CqlRGQSYYVEVA.LG....FPAATTDkVPESeNNQIKKELDSAKDPQLSadeHqkLESAD.SVPVLE..RTF..IYPPEAVMvPMvHQAFVRFSSKRMCSQA.CVgnSSWEGWPFWNF.SP
 1093- 1201 (147.72/101.41)	C..RGRSNAAEYAsMGdaysFQHPTGD.IRES.SSSISIGGDSMSPPQSS...H..VISNDrGTSELEhhRGYhrVRPTVAVL.PL.PSLLVGYQDDWLKTSAnCL..SLWEKAPLEPYaSP
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      60.58|      22|     727|     837|     867|       5
---------------------------------------------------------------------------
  837-  866 (23.23/35.41)	SVVSQRKSDsmFNAgyfllSMKTALAtEME
 1063- 1084 (37.35/17.31)	SVISLLQSD..IKA.....ALKTAFA.NMD
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             3|     130.47|      34|     369|    1560|    1599|       6
---------------------------------------------------------------------------
    8-   29 (36.19/11.90)	SSPAGGGR......RRML..NNADNKPDLH.....
 1565- 1599 (57.60/41.94)	SSISGGGSDSGASASALLEGSDNDNAASLHcCYGW
 1943- 1966 (36.68/15.11)	......GRDHETEMHNVLEAV....AAELH.SLSW
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      55.57|      18|     370|     638|     661|       8
---------------------------------------------------------------------------
  605-  623 (29.92/15.02)	EFGD..FSDfFQEEELDFGE....P
  638-  661 (25.65/27.89)	DCGDatFTD.SPSTAMDIPEqrfsP
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      73.78|      20|     734|     939|     973|      13
---------------------------------------------------------------------------
  951-  970 (36.66/44.21)	PKGPTHLESFSAKTYTGTSQ
 1439- 1458 (37.12/ 9.58)	PKAISTSDMFQSPAYMGRSQ
---------------------------------------------------------------------------




































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 MDP03861 with Med13 domain of Kingdom Viridiplantae
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