<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 MDP03645

Description Mediator of RNA polymerase II transcription subunit 13
SequenceMPEFPSPSSPAGGGRRRTLNNADNKPDLHGTMNDPYYYDCRILVDATPEKSSRKKSTFVRHFSCTSSHALVKIAAAIVDPRAVVLHGREPHGEQGGGGATGERGHSRSRAERTDPTTTAPFFSGSNRRQVADLFRRPPSSFSDVFGMLIRDPRCYVYSCIGYLKGELQNVSWFQFLPVEPDPSTASERSSKAEQKDALNNIVLSAHLHLQSEGFLSTWTNSFVGPWDPSQGEHNPVVSNGLWVAPGNLEEVAAALCQALRNSLERRAQPTIEFVFAATEEAIFVHVIISARYMRNLCSDDIEKVLTYSPRSVGEGLPVIVAPSGMLGRLVGCCPSDLVRQVYSSKLSAATLPGFTQPTMCQLRGQSYYVEVALGFPAATTDKVPESENNQIKKELDSAKDPQLSADEHQKLESADSVPVLERTFIYPPEAVMVPMVHQAFVRFSSKRMCSQACVGNSSWEGWPFWNFSPSSYFRNSSCLGSSRGLGVNSNFLRLRRQKNSNYSSMASSISSVSSTSNGSEHAVAAEGGDLSADADSMACHQSDLPSNIAGSKMVSKRPRSEIPEVSSRAGKESVDNNQGVNGQGRCSWGWDEEGVAMDINLLISEFGDFSDFFQEEELDFGEPPGTAESHSLVIPGPDCGDATFTDSPSTAMDIPEQRFSPVGLSSLEVFNHQTVAPIHDVVSKVQEPQKDIASPTSSQSVVLSSGRSSHLTRAEALLTYAPEYAAIEISTGETPTSLFTNPYQPRSIKPGSSSFNSRVYSYDAAQSSQMESGEDKPEKSVRLASGNLSRDIGSSNLYTVVQVGKKESDKGLKNTDIQSGKEEASRPISGETSLDSSVVSQRKSDSMFNAGYFLLSMKTALATEMECIKFQAAMCRIRHTLLSLSSKASAELKSALSSLVHTDVSNKLDLVPKYDIKRKENIPARLSIDVDHEVYDRSLENVGVWKPVGTPKGPTHLESFSAKTYTGTSQGLPVKRQPIVDLLSAMALIVQQSTSFVDIALDMDDGDGSFFWLSLDEQKRRGFSCDPSMVHAGCGGILGTCHSKDCAGVDLVDPLSAEVSDSSVISLLQSDIKAALKTAFANMDGPLLVTDWCRGRSNAAEYASMGDAYSFQHPTGDIRESSSSISIGGDSMSPPQSSHVISNDRGTSELEHHRGYHRVRPTVAVLPLPSLLVGYQDDWLKTSANCLSLWEKAPLEPYALPKPVTYYALCPDIEMLTSAATDFFLQLGTIYEVCKLGTHSPQNSGGQMELSPGKYLSSGLVLTECPDQVKIGNGHSSSISSTSEYLQALSRNWTVKSFVTSLTRVIKDIKLNSSILANQKESTSGPCTVIYVVCPFPEPSAVLETLVECSVALGSVMLSPERERKSFLYSQVAKALNCNASVDESSASNVVMLSGFSIPKLVLQIVTVETLLRLHKPNNELAVLKDMAFTVYNKARRIPKAISTSDMFQSPAYMGRSQSTMMHATSPGPTLWKECLVPRMSGSTLSRETEFDASMRSSVTWDNSWPCRAGGFMDPNKIPDVCVQDDRKYAFEPLFILAEPGSVDYSSGMESSKSGVDASGSGIYSSISGGGSDSGASASALLEGSDNDNAASLHCCYGWTEDWRWLVCIWTDSKGELLDSLIFPFGGISSRQDTKVLQSLFIQILQHGCQIMSSAPESSNTRPRDVIITRIGGFLELEIQEWQKAIYSFGGNEVKKWPVQLRRSIPEGIPSNSNGPALQQQDMGLMQDRNMPSSPSPLYSPHAKSSFMKGALGQSGNKKQILVEQAGMDSSKGSLHLVRSISLVAISQDHSLHLTCQADLLTRPTPGEGNQTSSGPSSYLEGFTPVKSIGSMSASYLLVPSPSMRYLSPATLQLPTCLTSESPPLAHLLHSKGTAIPLAMGYVVSKAVPPVRKDSARLANEDRPSVLSVSIIDHYGGSIAAVQEKMSRGSGKQTRNFTQEAAGRDHETEMHNVLEAVAAELHSLSWMTVSPVYMERRSALPSHCDMVLRLRRLLHYADRHLSQSTEKGDVA
Length2011
PositionKinase
OrganismOryza nivara (Indian wild rice) (Oryza sativa f. spontanea)
KingdomViridiplantae
LineageEukaryota> Viridiplantae> Streptophyta> Embryophyta> Tracheophyta> Spermatophyta> Magnoliopsida> Liliopsida> Poales> Poaceae> BOP clade> Oryzoideae> Oryzeae> Oryzinae> Oryza.
Aromaticity0.07
Grand average of hydropathy-0.307
Instability index56.48
Isoelectric point5.84
Molecular weight218308.17
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

>MDP03645
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|     134.62|      47|     367|     725|     776|       1
---------------------------------------------------------------------------
  725-  774 (70.30/71.17)	AAIEISTGETPTSL.FTNPYqpRSIKPGSSSFNSRVYSYDaAQSSQME.....SGE
  779-  831 (64.31/44.08)	KSVRLASGNLSRDIgSSNLY..TVVQVGKKESDKGLKNTD.IQSGKEEasrpiSGE
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|     319.93|     101|     370|    1467|    1599|       3
---------------------------------------------------------------------------
  432-  537 (161.37/69.85)	MVPMVHQAFVrfsSKRMCSQACVGNS.SWE.GWPFW..NFSPSSYFRNsSCLGSSRGLGVNSNFLrLRRQKNSNYSS.MASSISSVSSTSNGSEHAVAAEGGDLSADADSM
 1476- 1581 (158.56/125.39)	LVPRMSGSTL...SRETEFDASMRSSvTWDnSWPCRagGFMDPNKIPD.VCVQDDRKYAFEPLFI.LAEPGSVDYSSgMESSKSGVDASGSGIYSSISGGGSDSGASASAL
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|     183.54|      63|     728|     344|     431|       5
---------------------------------------------------------------------------
  360-  431 (90.79/95.18)	CqlRGQSYYVEVA.LG....FPAATTDkVPESeNNQIKKELDSAKDPQLSadeHqkLESAD.SVPVLE..RTF..IYPPEAV
 1093- 1165 (92.74/45.30)	C..RGRSNAAEYAsMGdaysFQHPTGD.IRES.SSSISIGGDSMSPPQSS...H..VISNDrGTSELEhhRGYhrVRPTVAV
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      55.57|      18|     367|     638|     661|       6
---------------------------------------------------------------------------
  605-  623 (29.92/14.63)	EFGD..FSDfFQEEELDFGE....P
  638-  661 (25.65/27.21)	DCGDatFTD.SPSTAMDIPEqrfsP
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      66.88|      23|     727|    1031|    1072|      15
---------------------------------------------------------------------------
  539-  562 (36.79/10.62)	CHQSDL..P..SNIAGSKMVSKRpRSEI
 1046- 1072 (30.09/45.81)	CAGVDLvdPlsAEVSDSSVISLL.QSDI
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      73.78|      20|     728|     939|     973|      16
---------------------------------------------------------------------------
  951-  970 (36.66/40.91)	PKGPTHLESFSAKTYTGTSQ
 1439- 1458 (37.12/ 8.81)	PKAISTSDMFQSPAYMGRSQ
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|     157.08|      49|     155|    1713|    1790|      19
---------------------------------------------------------------------------
    1-   63 (79.53/38.29)	MPEFPSP.SSPAGGGR..RRTLNNADNKPdlhgtmndpyyydcRILVDATPEKSSRKKSTFVRHFS
 1731- 1782 (77.56/60.61)	MPSSPSPlYSPHAKSSfmKGALGQSGNKK..............QILVEQAGMDSSKGSLHLVRSIS
---------------------------------------------------------------------------




































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 MDP03645 with Med13 domain of Kingdom Viridiplantae
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