<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 MDP16908

Description Mediator of RNA polymerase II transcription subunit 13
SequenceMSSCFVPNGASLEDCHSNLFCLADLTGIKWKRYVWQGPTSAPILFPVTEEDPILSSFSRCLKADVLSVWRRDQRPGRRELWIFWWGDDPNFADLIHHDLSEEEDGVWENGLSYECRTLLFKAVHNLLERCLMNRNFVRIGKWFVKPYEKDEKPINKSEHLSCSFTFFLHGDSNVCTSVEISQHQPVYLLSEEHLTLAQQSNSPFQVILSPFGLNGTLTGQSFKLSDSSTKKLIGEWKQFYPVTSNLKEGSEEKQEEMDWEDDSLAAVEVLVAGVRMVYPACFVLVPQTDIPAPSTVGASHCSTTCLGVHQVPPSTRDPAMSSVTLTPPTSPEEVQTVDAQSAQKWVKFSSVSDGLISDSTSHHGGKIPRKLANQVVDRVWQECNMNRAQNKRKYSATSNGLCDEETADKVASWDFVEATQRTNCNCSRHKNLKPRNSGQQGQAPPVGQQQQVAPKHKTNEKQDKGDKPQKRPLTPFHHRVSISDDVAMEADSASQRLVMTAPDSQVRFSNIRTNDVAKTPQMHNAEMANSPQPPPLSPHPCDVVDEGVAKAPSTPQSQHFYQMPTPDPLVPTKTMEDRLDGLSQPFPAPFPEVIEPTMYVGTAVNLEEDEADTTWKYYKVPKKKDVEFLPPQLPNDKLRDDPVIPAGQENVTSVTELMVQCRKPLKVSDELVQQYQSKNQYLAAVATEADQEPEIDPYAFVDGDVEFLFPDSKKDRQNMEREAGKKHKAEDGTSSVTVLSHEGEDAMSLFSPSVKQDAQRIAAHARTASTSLFHETDLVVSYTDLDNLFNSDEDELTPGSKRTVNGADDKSNCKEAKAGNLDPLSCISTADLHKMYPTPPSLEQHIMGFSPMNMNNKEYGSMDTTLGGTVLEGNSSSVGAQFRIEVDEGFCSPKPAEIKDYSYVYKPENCQALVGCSMFAPLKTLPSQCLPPIKLPEECIYRQSWTVGKLDLLPPGPAMPFIKDGDGSTMDQEYGPAYTPQTHTPFGMPPSSAPPSNSGAGILPSPSTPRFPTPRTPRTPRTPRGAGGPASAQGSVKYENSDLYSPASTPSTCRPLNSVEPATVPSIPEAHSLYVNLILSESVMNLFKDCNFDSCCICVCNMNIKGADVGVYIPDPTQEAQYRCTCGFSAVMNRKFGNSSGLFLEDELDILGRNTECGKEAEKRFEALRATSVEHGSGGLKEPEKLPDELILLLQDQCTNLFSPFGAADQESIPKVGAVSNLVRVEERDCCNDCYLALEHGRQFMDNMSGGKVDEALVKTTCLHHWSKRNVVDVSMQCSQDILRMLLSLQPVLQDAIQKKRTVRSWGVQGPLTWQQFHKMAGRGSYGTDESPEPLPIPTFLLGYDYDFLVLSPFALPYWERLMLEPYGSQRDVAYVVVCPENEALLNGAKSFFRDLTAIYESCRLGQHRPICKLLPDGIMRVGPTASKKLSEKLVTEWFSQTANANNEAFSKLKLYAQVCRYELGPYLASQPLDNSLLSQTNLVPPSSQPAPALPAVTAGAGNPNTPXVTATSNSAMSSAATTANSTLTTTAPASSSATIGSGMPTNKPSSFPPFPSMNNTAPASLPAQAATVQNGQAGGQQQQPALQTAGMAGDAASAPAQPHPEVSESTMDRDKVGVPTDGDSHAITYPPAIVVYIIDPFTYEKKDENSSSSSLWTLGLLRCFLEMVQVLPPNIKNIISVQIVPCQYLLQPVKHEDRQIYTQHLKSLAFSAFTQCRRPLPTSTNVKTLTGFGPGLAMETALKSPDRPECIRLYTPPFILAPVKDKQTELGETFGEAGQKYNVLFVGYCLSHDQRWLLASCTDLYGEQLETCIINIDVPNRARRKKGSARRLGLQKLWEWCLGLVQMSSLPWRVVIGRLGRIGHGELKDWSCLLSRRNLQSLSKRLKDMCRMCGISAADSPSILSACLVAMEPQGSFIIMPDSVSTGSVFGRSTTLNMQTSQLNTPQDTSCTHILVFPTSASVQVASSTYTTENLDLAFNTNNDGADGMGIFDLLDTGDDLDPDIINILPASPTGSPVHSPGSHYPHGGDMGKGQGTDRLLSTESHDEVTNILQQPLALGYFVSTAKAGPLPDWFWSACPQAQNQCPLFLKASLHLHVPSVQSDELLHSKHSHPLDSNQTSDVLRFVLEQYNALSWLTCDPATQDRRSCLPIHFVVLNQLYNFIMNML
Length2169
PositionMiddle
OrganismColumba livia (Rock dove)
KingdomMetazoa
LineageEukaryota> Metazoa> Chordata> Craniata> Vertebrata> Euteleostomi> Archelosauria> Archosauria> Dinosauria> Saurischia> Theropoda> Coelurosauria> Aves> Neognathae> Columbiformes> Columbidae> Columba.
Aromaticity0.07
Grand average of hydropathy-0.400
Instability index51.49
Isoelectric point5.40
Molecular weight238447.69
Publications
PubMed=23371554

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

>MDP16908
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             6|     236.65|      35|      40|     979|    1014|       1
---------------------------------------------------------------------------
  519-  556 (37.12/ 9.28)	TPQM.HnaemanSP..Q.P.PPLSPhPC....DvVDEGVAKAP.STPQ...
  558-  588 (37.74/11.61)	.....Q......HFYQM.PtPDPLV.PT....K.TMEDRLDGL.SQP.FPA
  979- 1013 (71.72/26.69)	TPQT.H......TPFGM.P.PSSAP.PS....N.SGAGILPSP.STPRFPT
 1016- 1054 (35.11/ 9.91)	TPRTpR......TPRGAgG.PASAQ.GSvkyeN.SD...LYSPaSTPSTCR
 1485- 1507 (28.13/ 6.78)	.P...........PSSQ.P.APALP.AV....T.AGAG...NP.NTP....
 1583- 1604 (26.84/ 6.13)	................Q.Q.PAL...QT....A.GMAG..DAA.SAPAQPH
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|     107.27|      35|      40|    1118|    1157|       2
---------------------------------------------------------------------------
 1118- 1157 (52.70/47.01)	QEAQYRctcgFSAVMNRKFGNSSGLF.....LEDELdILGRNTEC
 1159- 1198 (54.57/32.13)	KEAEKR....FEALRATSVEHGSGGLkepekLPDEL.ILLLQDQC
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|     481.62|     157|     265|      46|     233|       3
---------------------------------------------------------------------------
   46-  233 (248.06/201.00)	PVTEEDPILSSFSRCLKADVLSVWRRDQRPGRRelWI.FWWGDDPNFAD.LIHH......DLSEE.EDGVWenglsyecrtllfkavhnllERCLMN.....RNFV.............RIGKW.FVKPYEKDEKPINKSEHLSCSFTfflhGDSNvcTSVEISQHQPVyllSEEHLTLAQQ..SNSPFQVILSPFGLNGTLTGQSFKLSDSSTKKLI
  312-  498 (233.56/135.49)	PPSTRDPAMSSVTLTPPTSPEEVQTVDAQSAQK..WVkFSSVSDGLISDsTSHHggkiprKLANQvVDRVW....................QECNMNraqnkRKYSatsnglcdeetadKVASWdFVEATQRTNCNCSRHKNLKPRNS....GQQG..QAPPVGQQQQV...APKHKTNEKQdkGDKPQKRPLTPFHHRVSISDDVAMEADSASQRLV
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      44.52|      12|      40|     848|     859|       4
---------------------------------------------------------------------------
  848-  859 (25.08/12.98)	GF.SPMNMNNKEY
  889-  901 (19.44/ 8.41)	GFcSPKPAEIKDY
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      34.02|      10|      40|     708|     717|       5
---------------------------------------------------------------------------
  708-  717 (19.49/11.44)	LF.PDSKKDRQ
  749-  759 (14.53/ 6.36)	LFsPSVKQDAQ
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|     145.64|      46|    1054|     660|     706|       6
---------------------------------------------------------------------------
  660-  706 (77.03/52.68)	QCRKPLKVSDElVQQYQSKNQYLA.AVATEADQEPE.IDPYA..FVDGDVE
 1716- 1765 (68.61/42.12)	QCRRPLPTSTN.VKTLTGFGPGLAmETALKSPDRPEcIRLYTppFILAPVK
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      46.66|      15|      44|    1423|    1437|       7
---------------------------------------------------------------------------
 1423- 1437 (24.76/14.02)	GP.TASKKLSEKLVTE
 1465- 1480 (21.90/11.42)	GPyLASQPLDNSLLSQ
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|     105.15|      31|     525|    1080|    1116|      10
---------------------------------------------------------------------------
 1080- 1116 (51.00/47.89)	SESVMNLFK...DCNFDSCCIcvcnmNIKGADVgVYIPDP
 1608- 1641 (54.15/32.02)	SESTMDRDKvgvPTDGDSHAI.....TYPPAIV.VYIIDP
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      89.58|      28|     719|     625|     654|      11
---------------------------------------------------------------------------
  625-  654 (46.17/31.46)	DVEFL...PPQLPN.DKLRDDPVipAGQENVTSV
 1345- 1376 (43.41/23.07)	DYDFLvlsPFALPYwERLMLEPY..GSQRDVAYV
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      32.34|      10|      31|    1533|    1543|      15
---------------------------------------------------------------------------
 1533- 1543 (13.81/12.36)	PAsSSATIGSG
 1567- 1576 (18.53/10.95)	PA.QAATVQNG
---------------------------------------------------------------------------




































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 MDP16908 with Med13 domain of Kingdom Metazoa


     
       
      
        
        
        


      
      
   
   

      

      














Intrinsically Disordered Regions








IDR SequenceStartStop




1) DSKKDRQNMEREAGKKHKAEDGTSSVTVLSHE
2) GPAMPFIKDGDGSTMDQEYGPAYTPQTHTPFGMPPSSAPPSNSGAGILPSPSTPRFPTPRTPRTPRTPRGAGGPASAQGSVKYENS
3) GSPVHSPGSHYPHGGDMGKGQGTDRLLSTESH
4) LSQTNLVPPSSQPAPALPAVTAGAGNPNTPXVTATSNSAMSSAATTANSTLTTTAPASSSATIGSGMPTNKPSSFPPFPSMNNTAPASLPAQAATVQNGQAGGQQQQPALQTAGMAGDAASAPAQPHPEVSESTMDRDKVGVPTDGD
5) NCNCSRHKNLKPRNSGQQGQAPPVGQQQQVAPKHKTNEKQDKGDKPQKRPLTPFHHRVSISDDVAMEADSASQRLVMTAPDSQVRFSNIRTNDVAKTPQMHNAEMANSPQPPPLSPHPCDVVDEGVAKAPSTPQSQHFYQMPTPDPLVPTKTMEDRLDGLSQPFPA
711
956
2016
1478
423
742
1041
2047
1624
588










Molecular Recognition Features






MoRF SequenceStartStop




1) MSLYLLWRD
1
9