<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 MDP03421

Description Mediator of RNA polymerase II transcription subunit 13
SequenceMPEFPSPSSPAGGGRRRTLNNADNKPDLHGTMNDPYYYDCRILVDATPEKSSRKKSTFVRHFSCTSSHALVKIAAAIVDPRAVVLHGREPHGEQGGGGATGERGHSRSRAERTGHHHRPLLLRFKPAASRRPLPPPTEQLLRWNPNLLYLISQIEGELQNVSWFQFLPVEPDPSTASERSSKAEQKDALNNIVLSAHLHLQSEGFLSTWTNSFVGPWDPSQGEHNPVVSNGLWVAPGNLEEVAAALCQALRNSLERRAQPTIEFVFAATEEAIFVHVIISARYVRNLCSDDIEKVLTHSPRSVGEGLPVIVAPSGMLGRLVGCCPSDLVRQVYSSKLSAATLPGFTQPTMCQLRGQSYYVEVALGFPAATTDKVPESENNQIKKELDSAKDPQLSADEHQKLESADSVPVLERTFIYPPEAVMVPMVHQAFVRFSSKRMCSQACVGNSSWEGWPFWNFSPSSYFRNSSCLGSSRGLGVNSNFLRLRRQKNSNYNSMASSISSVSSTSNGSEHAVAAEGGDLSADADSMACHQSDLPSNIAGSKMVSKRPRSEIPEVSSRAGKESVDNNQGVNGQGRCSWGWDEEGVAMDINLLISEFGDFSDFFQEEELDFGEPPGTAESHSLVIPGPDCGDATFTDSPSTAMDIPEQRFSPVGLSSLEVFNHQTVAPIHDVVSKVQEPQKDIASPTSSQSVVLSSGRSSHLTRAEALLTYAPEYAAIEISTGETPTSLFTNPYQPRSIKPGSSSFNSRVYSYDAAQSSQMESGEDKPEKSVRLASGNLSRDIGSSNLYTVVQVGKKESDKGLKNTDIQSGKEEASRPISGETSLDSSVVSQRKSDSMFNAGYFLLSMKTALATEMECIKFQAAMCRIRHTLLSLSSKASSELKSALSSLVHTDVSNKLDLVPKYDIKRKENIPARLSIDVDHEVYDRSLENVGVWKPVGTPKGPTHLESFSAKTYTGTSQGLPVKRQPIVDLLSAMALIVQQSTSFVDIALDMDDGDGSFFWLSLDEQKRRGFSCDPSMVHAGCGGILGTCHSKDCAGVDLVDPLSAEVSDSSVISLLQSDIKAALKTAFANMDGPLLVTDWCRGRSNAAEYASMGDAYSFQHPTGDIRESSSSISIGGDSMSPPQSSHVISNDRGTSELEHHRGYHRVRPTVAVLPLPSLLVGYQDDWLKTSANCLSLWEKAPLEPYASPKPVTYYALCPDIEMLTSAATDFFLQLGTIYEVCKLGTHSPQNSGGQMELSPGKYLSSGLVLTECPDQVKIGNGHSSSISSTSEYLQALSRNWTVKSFVTSLTRVIKDIKLNSSILANQKESTSGPCTVIYVVCPFPEPSAVLETLVECSVALGSVMLSPERERKSFLYSQVAKALNCNASVDESSASNVVMLSGFSIPKLVLQIVTVETLLRLHKPNNELAVLKDMAFTVYNKARRIPKAISTSDMFQSPAYMGRSQSTMMHATSPGPTLWKECLVPRMSGSTLSRETEFDASMRSSVTWDNSWPGRAGGFMDPNKIPDVCVQDDRKYAFEPLFILAEPGSVDYSSGMESSKSGVDASGSGIYSSISGGGSDSGASASALLEGSDNDNAASLHCCYGWTEDWRWLVCIWTDSKGELLDSLIFPFGGISSRQDTKVLQSLFIQILQHGCQIMSSAPESSNTRPRDVIITRIGGFLELEIQEWQKAIYSFGGNEVKKWPVQLRRSIPEGIPSNSNGPALQQQDMGLMQDRNMPSSPSPLYSPHAKSSFMKGALGQSGNKKQILVEQAGMDSSKGSLHLVRSISLVAISQDHSLHLTCQADLLTRPTPGEGNQTSSGPSSYLEGFTPVKSIGSMSASYLLVPSPSMRYLSPATLQLPTCLTSESPPLAHLLHSKGTAIPLAMGYVVSKAVPPVRKDSARLANEDRPSVLSVSIIDHYGGSIAAVQEKMSRGSGKQTRNFTQEAAGRDHETEMHNVLEAVAAELHSLSWMTVSPVYLERRSALPSHCDMVLRLRRLLHYADRHLSQSTEKGDVA
Length2002
PositionKinase
OrganismOryza glumipatula
KingdomViridiplantae
LineageEukaryota> Viridiplantae> Streptophyta> Embryophyta> Tracheophyta> Spermatophyta> Magnoliopsida> Liliopsida> Poales> Poaceae> BOP clade> Oryzoideae> Oryzeae> Oryzinae> Oryza.
Aromaticity0.07
Grand average of hydropathy-0.318
Instability index57.26
Isoelectric point5.92
Molecular weight217343.08
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

>MDP03421
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No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      58.65|      18|      37|     639|     657|       1
---------------------------------------------------------------------------
  639-  657 (28.23/19.42)	PSTAMDIPEQRFSPVgLSS
  679-  696 (30.42/15.94)	PQKDIASPTSSQSVV.LSS
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             3|     161.41|      40|      57|     987|    1027|       2
---------------------------------------------------------------------------
  987- 1027 (69.89/41.33)	FVDiALDMDDGDGSFFWLSLDEQK...RRGF.SCD.PSMVHAGCGG
 1042- 1086 (54.27/27.43)	LVD.PLSAEVSDSSVISLLQSDIKaalKTAFaNMDgPLLVTDWCRG
 1488- 1513 (37.25/16.25)	............SSVTWDNSWPGR...AGGF..MD.PNKIPDVC..
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      73.58|      20|     508|     942|     961|       3
---------------------------------------------------------------------------
  942-  961 (37.53/22.98)	PKGPTHLESFSAKTYTGTSQ
 1430- 1449 (36.05/21.74)	PKAISTSDMFQSPAYMGRSQ
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|     153.04|      49|     508|     710|     789|       4
---------------------------------------------------------------------------
  735-  788 (69.73/92.63)	QPRSIkPGSSsfnSRVYSyDAAQSSQMES..GEDKPEKSVRLASGNLSRDIGSSNL
 1718- 1768 (83.31/36.56)	QDRNM.PSSP...SPLYS.PHAKSSFMKGalGQSGNKKQILVEQAGMDSSKGSLHL
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|     113.15|      36|     611|     589|     627|       5
---------------------------------------------------------------------------
  589-  627 (57.42/47.87)	DINLLISEFGDFsdFFQ....EEELDFG..EPPGTAESHSLViPG
 1203- 1244 (55.73/35.15)	DIEMLTSAATDF..FLQlgtiYEVCKLGthSPQNSGGQMELS.PG
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      74.62|      24|      59|    1769|    1797|       6
---------------------------------------------------------------------------
 1769- 1797 (33.84/42.22)	VRSISLVAISqDHSLHL.TCqadlLTRPTP
 1830- 1854 (40.78/30.53)	VPSPSMRYLS.PATLQLpTC....LTSESP
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|     310.06|      97|    1551|       8|     114|       7
---------------------------------------------------------------------------
    8-  114 (150.37/148.34)	SSPAGGG.....RRRTL...NNADNKPDLHGTMNdpYYYDCRILVDATPEKSSRKKSTFVRHFSCTSSHALVKIAAAIVdprAVVLHgrepHGEQGGGGATgERGHSRSR...AERTG
 1556- 1663 (159.69/121.54)	SSISGGGsdsgaSASALlegSDNDNAASLHCCYG..WTEDWRWLVCIWTDSKGELLDSLIFPFGGISSRQDTKVLQSLF...IQILQ....HGCQIMSSAP.ESSNTRPRdviITRIG
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|     185.13|      60|    1551|     365|     424|       8
---------------------------------------------------------------------------
  365-  424 (102.26/82.36)	GFPAATTDKVPESENNQIKKELDSAKDPQLSADEHQKLE..SAD.......SV.PV.LERTFIYPPEAVMV
 1908- 1978 (82.87/64.88)	GSIAAVQEKMSRGSGKQTRNFTQEAAGRDHETEMHNVLEavAAElhslswmTVsPVyLERRSALPSHCDMV
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|     105.90|      35|      59|    1315|    1354|      12
---------------------------------------------------------------------------
 1315- 1354 (52.71/40.39)	SGPCTVIyVVCPFPEPSAVLETL.VECSVALGsvmlSPERE
 1376- 1411 (53.19/27.90)	SSASNVV.MLSGFSIPKLVLQIVtVETLLRLH....KPNNE
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      81.86|      22|      22|     431|     452|      19
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  431-  452 (43.32/24.23)	FVRFS.SKRMCSQACVGNSSWEG
  455-  477 (38.54/20.70)	FWNFSpSSYFRNSSCLGSSRGLG
---------------------------------------------------------------------------




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 MDP03421 with Med13 domain of Kingdom Viridiplantae

Intrinsically Disordered Regions

IDR SequenceStartStop
1) AVVLHGREPHGEQGGGGATGERGHSRSRAERTGHHHRPLLLRFKPAAS
2) GIPSNSNGPALQQQDMGLMQDRNMPSSPSPLYSPHAKSSF
3) IAGSKMVSKRPRSEIPEVSSRAGKESVDNNQGVNGQGRCS
4) QEEELDFGEPPGTAESHSLVIPGPDCGDATFTDSPSTAMDIPEQR
5) QEKMSRGSGKQTRNFTQEAAGRDHETEMHN
82
1699
539
605
1914
129
1738
578
649
1943

Molecular Recognition Features

MoRF SequenceStartStop
1) LLLRF
2) YYYDCRILV
120
36
124
44