<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 MDP04106

Description Mediator of RNA polymerase II transcription subunit 13
SequenceMQFPMRWSLLVGVTPCLSSLLLFCALWISRCLMDKNFVRIGKWFVRPYDKDEKPVNKSEHLSCAFTFFLHGESNVCTSVEIAQHQPIYVINEEHLHMAQSSPAPFQVLVSPYGLNGTLTGHAYKMSDPAARKLIEEWQCFYPMVLRKKEEPREEAELEYDDDFPVAVEVIVGGVRMVYPSAFVLISQNDIPVPQSGTSAGGHVTIAQQGLGSVKDPSNCGMPLTPPTSPEQVVIGESGVQSAASHLGSHDGGMIATHSPKRSKKIPPKLHSHMVHRVWKECILNRAQSKRSQMSAPAGEEEPAHSPAAWDFVDPTQRVSCSCSRHKLLKRCAVGPSRPPTLSQPGFSAGPPPPSSLPPPASSKHKTTERQEKGDKLQKRPLVPFHHRPSVAEELCMEQDAPGQKLGLAGIDSSLEVSSSRKYDKQMAVPSRNTSKQMDLNPMDSPHSPISPLPPTLSPQPRGQETESLDPPSVPVNPALYGNGLDLQQLSALEDRTVLVGQRLPLMAEASETALYSGLRPSYTESSDRWWQSFRLPPSEDAEFRPPELQGEGFHTVLDVSPESTALQRLLAQPNKRFKIWQDEQPQVQPLPFLDPSPLSQQPGDTLGEVNDPYTFEDGDIKYIFTANKKCKQGTEKDSLKKNKSEDGFGTKDVTTPGHSTPVPDGKNAMSIFSSATKTDVRQDNAAGRAGSGSLTQVTDLAPSLHDLDNIFDNSDDDELGAVSPALRSSKMPTVGTEERPPGKDGRAAGPYPPTVADLQRMFPTPPSLEQHPAFSPVMNYKDGVSSETVTALGMLESPVVSMVPTHLTEFRMEVEDGLGSPKPEDIKDFSYVHRVPQFQPFVGSSMFAPLKTLPSHCLLPLKTPDACLFRPSWAVPPKMEQLPMPPAASSIRDGYNNVPSVGSLADADYLNTPQMNTPVTLNSAAPASNSGAGVLPSPATPRFSVPTPRTPRTPRTPRGGGTASGQGSVKYDSTDQGSPASTPSTTRPLNSVEPATMQPIPEAHSLYVTLILSDSVMNVFKDRNFDSCCICACNMNVKGADVGLYIPDSSKEDQYRCTCGFSAIVNRRLGYNSGLFLEDELDIFGKNSDIGQAAERRLMMCQTSCQSTLLPQVEGARKAPEPPVSLLLLLQNQHTQPFASLSFLDYISSSSRHALPCVSWTYDRVQADNNDYWTECVNALEQGRQYVDNPTGGKVDEALVRSATVHCWPHSNVLDTSMLSSQDVVRMLLSLQPFLQDAIQKKRTGRTWENIQHVQGPLTWQQFHKMAGRGTYGSEESPEPLPIPTLLVGYDKEFLTISPFSLPFWERLLLEPYGGHRDVAYIVVCPENEALLEGAKTFFRDLSAVYEMCRLGQHKPICKVLRDGIMRVGKTVAQKLTEELVSEWFNQPWSSEESDNHSRLKLYAQVCRHHLAPYLATLQLDSGLLMPPKHQSPPAEAQGQATPGNAGSSSSGSGAPPAGSAFNPTSSSSAASSSSSCSGPPGSSATSAPGITQMSTTSSSGFSGGVGGQNPSAGGSSTDGTPGNVACGDAEHAQSCAQPSQDGQDSVTERERIGIPTEPDSADSHAYPPAVVIYMVDPFTYTAEEDSSSGNFWLLSLMRCYTEMLDHIPEHMRSSFILQIVPCQYMLQTVKDEHVFYIQYLKSMAFSVYCQCRRPLPTQIHIKSLTGFGPAASIEMTLKNPERPSPIQLYSPPFILAPIKDKQTEPGEAFGEASQKYNVLFVGYCLSHDQRWLLASCTDLHGELLETCVVNIALPSRSRKSKVSARKIGLQKLWEWCLGIVQMTSLPWRVVIGRLGRLGHGELKDWSILLGECSLQTISKQLKDVCRMCGISAADSPSILSACLVAMEPQGSFVVMPDAVTMGSVFGRSTALNMQSSQLNTPQDASCTHILVFPTSSTIQVAPANYPNEDGFSPNNDDMFVDLPFPDDMDNDIGILMTGNLHSSPNSSPVPSPGSPSGIGVGSHFQHSRSQGERLLSREAPEELKQQPLALGYFVSTAKAENLPQWFWSSCPQARNQCPLFLKASLHHHISVAQTDELLPVRNSQRAPHPLDSKTTSDVLRFVLEQYNALSWLTCNPATQDRTSCLPVHFVVLTQLYNAIMNML
Length2104
PositionMiddle
OrganismRattus norvegicus (Rat)
KingdomMetazoa
LineageEukaryota> Metazoa> Chordata> Craniata> Vertebrata> Euteleostomi> Mammalia> Eutheria> Euarchontoglires> Glires> Rodentia> Myomorpha> Muroidea> Muridae> Murinae> Rattus.
Aromaticity0.07
Grand average of hydropathy-0.377
Instability index61.97
Isoelectric point5.78
Molecular weight229761.22
Publications
PubMed=15057822
PubMed=22673903

Function

Annotated function Component of the Mediator complex, a coactivator involved in the 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	ISO:RGD

GO - Biological Function
transcription coregulator activity	GO:0003712	IBA:GO_Central

GO - Biological Process
regulation of transcription by RNA polymerase II	GO:0006357	IBA:GO_Central









Interaction





Binary Interactions











Repeat regions





Repeats

>MDP04106
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             4|     118.40|      19|      22|    1446|    1464|       1
---------------------------------------------------------------------------
  348-  362 (23.26/ 6.66)	AGPPPPSSLPPPASS.....
 1446- 1464 (36.27/15.53)	AGSSSSGSGAPPAGSAFN.P
 1471- 1489 (30.01/11.27)	ASSSSSCSG.PPGSSATSaP
 1493- 1511 (28.85/10.47)	QMSTTSSSGFSGGVGGQN.P
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      70.46|      20|      21|     846|     866|       2
---------------------------------------------------------------------------
  846-  866 (34.56/16.21)	MFAPLKTLPSHC.LLPLkTPDA
  868-  888 (35.89/13.66)	LFRPSWAVPPKMeQLPM.PPAA
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             5|     608.11|     158|     254|     188|     345|       3
---------------------------------------------------------------------------
  188-  276 (116.98/53.60)	....................................................................................................................................................................NDIPVPQS..GTSAGGHVTIAQQG..LGSVKDPSNC..GMPLTPPTSP.......................EQVVIGE.SGVQSAASHLGSHDG.GMI.ATHS.PKRSKKIPPKLHSHMVHR
  277-  345 (87.03/37.65)	VWKECILNRAQS.KRSQMSAPAGEEEPA.HS.PAAWDFVDP....TQ..R.VSCSCSRHKLLK..RCAVG.P...SRPPTLS.QPG........................................................................................................................................................................................................
  424-  528 (62.68/24.68)	......................................................................................fsagppppsslpppasskhktterqekgdklqkrplvpfhhrpsvaeelcmeqdapgqklglagidsslevsssrkydKQMAVPSR..NTS.......KQMD..LNPMDSPHSP..ISPLPPTLSPqprgqetesldppsvpvnpalygNGLDLQQlSALEDRTVLVGQRLP.LMAeASET.ALYSGLRPSYTESS..DR
  529-  673 (168.00/80.77)	WWQSFRL..PPS.EDAEFRPPELQGEGF.HT...VLD.VSPestaLQ..RlLAQPNKRFKIWQdeQPQVQ.PlpfLDPSPLSqQPG......................................................................................................dtLGEVNDPYTFedGDIKYIFTAN.......................KKCKQGT.E..KDSLKKNKSEDGfGTK.DVTT.PGHSTPVPDGKNAMSIFS
  680-  844 (173.43/83.66)	VRQDNAAGRAGSgSLTQVTDLA....PSlHDlDNIFDNSDD....DElgA.VSPALRSSKM.....PTVGtE...ERPP..G.KDG................................................................raagpypptvadlqRMFPTPPSleQHPAFSPVMNYKDG..VSS.ETVTAL..GMLESPVVSM.......................VPTHLTE.FRME.VEDGLGSPKP.EDI.KDFSyVHRVPQFQPFVGS.....
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      84.06|      26|      26|     931|     956|       4
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  931-  956 (46.15/24.11)	GAGVLPSPATPRFSVPTPRTP.RTPRT
  959-  985 (37.91/18.17)	GGGTASGQGSVKYDSTDQGSPaSTPST
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      63.97|      21|      26|    1588|    1613|       5
---------------------------------------------------------------------------
 1586- 1611 (32.31/37.13)	DSSSgnfWLLSLMRC.YteMLDHI.PEH
 1612- 1634 (31.66/19.32)	MRSS...FILQIVPCqY..MLQTVkDEH
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      87.79|      27|      28|    1964|    1991|       6
---------------------------------------------------------------------------
 1964- 1991 (41.86/35.58)	HFQhSRSQGERL...LSREAPEELKQQPLAL
 1993- 2022 (45.94/32.97)	YFV.STAKAENLpqwFWSSCPQARNQCPLFL
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      81.03|      23|      28|    1029|    1055|       7
---------------------------------------------------------------------------
 1026- 1048 (46.21/32.60)	DSC.CICACNMNVK...GADVGLYIPD
 1053- 1079 (34.83/14.70)	DQYrCTCGFSAIVNrrlGYNSGLFLED
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      59.07|      18|      28|    1913|    1935|       9
---------------------------------------------------------------------------
 1913- 1935 (24.82/22.09)	SPNNDdmfvDLPFPDDmDNDIGI
 1944- 1961 (34.25/14.90)	SPNSS....PVPSPGS.PSGIGV
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      57.87|      16|      19|    1408|    1423|      10
---------------------------------------------------------------------------
 1408- 1423 (28.29/17.20)	RHHLAPYLATLQLDSG
 1429- 1444 (29.58/18.40)	KHQSPPAEAQGQATPG
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|     232.08|      74|    1269|      54|     133|      11
---------------------------------------------------------------------------
   54-  133 (114.57/104.18)	PVNKSeHLSCAFTFFlHGESNVCTSVEIAQHQPI.YVINEEHLHMAQSSPAPF.QVLVSPYgLNGTLTGhayKMSDPAAR.KL
 1326- 1402 (117.52/82.76)	PENEA.LLEGAKTFF.RDLSAVYEMCRLGQHKPIcKVLRDGIMRVGKTVAQKLtEELVSEW.FNQPWSS...EESDNHSRlKL
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|     151.55|      47|     665|    1167|    1216|      12
---------------------------------------------------------------------------
 1167- 1216 (75.45/66.21)	ADNNDYWTECVNALE.QGrQYVDNPTGGKVDEALVRSATVHCwpHSNVLDT
 1834- 1881 (76.10/52.58)	ADSPSILSACLVAMEpQG.SFVVMPDAVTMGSVFGRSTALNM..QSSQLNT
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      51.52|      16|      17|    1125|    1140|      13
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 1125- 1140 (27.36/18.12)	SLLLLL..QNQHTQPFAS
 1142- 1159 (24.16/14.93)	SFLDYIssSSRHALPCVS
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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 MDP04106 with Med13 domain of Kingdom Metazoa
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