<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 MDP11854

Description Mediator of RNA polymerase II transcription subunit 13
SequenceMDKNFVRIGKWFVRPYEKDEKPVNKSEHLSCAFTFFLHGESNVCTSVEIAQHQPIYLINEEHIHMAQSSPAPFQVLVSPYGLNGTLTGQAYKMSDPATRKLIEEWQYFYPMVLKKKDELKEEEELGYDDDFPVAVEVIVGGVRMVYPSAFVLISQNDIPVPQSVVNAGGQITVGQQGLGSVKDPSNCGIPLTPPTSPEQAVVGESGGMQSATSHLGSQDGGMITMHSPKRSGKIPPNLHNHMVHRVWKECILNRAQSKRSQMSTPALEEEPANSPAAWGFVDPTQRVSCSCSRHKLLKRCAVGPNRPPTISQPGFSAGPSSASSLPPPASSKHKTTERQEKGDKLQKRPLIPFHHRPSVAEELCMEPDTSGQKLGLAGMDSSLEVSSSRKYDKQMAVPSRNTSKQMNLNPMDSPRSPISPLPPTLSPQPRGQEAESLDPPSVPVNPALYGNGLELQQLSTLDDRTVLVGQRLPLLAEVSETALYTGIGPSHLESSGKWWQSFRLPSSDDAEFRPPELQGERCDTRIEGPSESTALQRLLAQPNKRFKIWQDKQPQMQPLHFLDPSPLSQQPGDGLGEVNDPYTFEDGDIKYIFTANKKCKQGTEKDSLKKSKSEDGFGTKDVTTPGHSTPVPDGKNAMSIFSSATKTDVRQDNAAGRAGSSSLTQVTDLAPSLHDLDNIFDNSDDDELGAVSPALRSSKMPTIGTEDRPLGKDGRAAVPYPPTVADLQRMFPTPPSLEQHPAFSPVMTYKDGILPETVTALGMMESPAVSMVSTHLPEFKMEVEDGLGSPKPEEIKDFSYVHRPPPFQPFVGSSMFAPLKMLPSHCLLPLKIPDACLFRPSWAIPPKIEQLPLPSAATFVRDGYNNVPSVGSLADPDYLNTPQMNTPVTLNSAAPASNSGAGVLPSPATPRFSVPTPRTPRTPRTPRGGGTASGQGSVKYDSTDQGSPASTPSTTRPLNSVEPATMQPIPEAHSLYVTLILSDSVMNIFKDRNFDSCCICACNMNIKGADVGLYIPDSSNEDQYRCTCGFSAIMNRKLGYNSGLFLEDELDIFGKNSDIGQAAERRLMMCQSTFLPQMEGARKSLEPPISLLLLLQNQHTQPFASLSFLDYISSNNRQTIPCVSWSYDRVQADNNDYWTECFNALEQGRQYVDNLTGGKIDEALVRSATVHSWPHSNVLDISMLSSQDVVRMLLSLQPFLQDAIQKKRTGRTWENIQHVQGPLTWQQFHKMAGRGTYGSEESPEPLPIPTLLVGYDKDFLTVSPFSLPFWERLLLDPYGGRRDVAYIVVCPENEALLEGAKTFFRDLSAVYEMCKLGQHKPICKVLRDGIMRVGKTVAQKLADELVSEWFNQPWSGEENDNHSRLKLYAQVCRHHLAPYLATLQLDSSLLTPPKYQPPPPAAQGQATPGTAGPLAPNSGSAAPPAGSAFNPTSNSNSANPAASTSSAGSSGPPVSSAASAPGINQMSTTSSSGFSGGVGGQNPSSGGGSIDRTQGNIACGGDPEQGSSTQPYQDGQDSVTERERIGIPTEPDSADSQAYPPAVVIYMVDPFTYTAEEDSTSGNFWLLSLMRCYTEMLDNLPEHMRNSFILQIVPCQYMLQTMKDEQVVYIQYLKSMAFSVYCQCRRPLPTQIHIKSLTGFGPAASIEMTLKNPERPSPIQLYSPPFILAPIKEKQTEQGETLGEASQKYNVLFVGYCLSHDQRWLLASCTDLHGELLETCIVNIALPNRSRKSKVSARKIGLQKLWEWCIGIVQMTSLPWRVVIGRLGRLGHGELKDWSILLGECSLQTISKQLKDVCRMCGISAADSPSILSACLVAMEPQGSFVVMPDAVTMGSVFGRSTALNMQSSQLNTPQDASCTHILVFPTSSTIQVAPANYPNEDGFSPNNDDMFVDLPFPDDMDNDIGILITGNLHSSPNSSPAPSPGSPSGIGVGSHFQHSRSQGERLLSREAPEELKQQPLALGYFVSTAKAEKLPQWFWSSCPQAQNQCPLFLKASLHHHISVAQTDELLPVRNSQRVPHPLDSKTTSDVLRFVLEQYNALSWLTCNPATQDRTSCLPVHFVVLTQLYNAIMNIL
Length2076
PositionMiddle
OrganismDipodomys ordii (Ord's kangaroo rat)
KingdomMetazoa
LineageEukaryota> Metazoa> Chordata> Craniata> Vertebrata> Euteleostomi> Mammalia> Eutheria> Euarchontoglires> Glires> Rodentia> Castorimorpha> Heteromyidae> Dipodomyinae> Dipodomys.
Aromaticity0.07
Grand average of hydropathy-0.399
Instability index58.80
Isoelectric point5.70
Molecular weight226921.11
Publications









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. 


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

>MDP11854
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             4|     150.22|      28|      28|     900|     927|       1
---------------------------------------------------------------------------
  308-  329 (30.67/ 8.17)	......P....TISQPGFSAGPSS..ASSLPPPA
  409-  441 (30.01/ 7.83)	.NPMDSPrspiSPLPPTLSPQPRGqeAESLDPPS
  881-  908 (43.78/15.01)	TPQMNTP....VTLNSAAPASNSG..AGVLPSPA
  909-  936 (45.76/16.04)	TPRFSVP....TPRTPRTPRTPRG..GGTASGQG
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             3|      94.23|      23|      28|    1896|    1923|       2
---------------------------------------------------------------------------
 1875- 1890 (25.57/ 7.20)	PANYPNEDGF..........SPN.....NDD..
 1898- 1923 (39.63/33.43)	PDDMDNDIGIlitGN..LHSSPN.....SSPAP
 1925- 1953 (29.03/ 9.88)	PGS.PSGIGV...GShfQHSRSQgerllSREAP
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             3|      85.99|      21|      22|    1431|    1451|       3
---------------------------------------------------------------------------
 1417- 1433 (26.15/12.22)	NSGSA...AP.....PAGSAF.....nPTS
 1434- 1455 (34.85/19.31)	NSNSA...NPAASTSSAGSSG.....pPVS
 1456- 1485 (24.99/11.27)	SAASApgiNQMSTTSSSGFSGgvggqnPSS
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      88.55|      25|      28|     993|    1017|       4
---------------------------------------------------------------------------
  993- 1017 (51.64/34.17)	NFDSC.CICACN..MNIK.GADVGLYIPD
 1020- 1048 (36.91/22.18)	NEDQYrCTCGFSaiMNRKlGYNSGLFLED
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      69.74|      20|      20|     832|     851|       5
---------------------------------------------------------------------------
  832-  851 (39.09/27.16)	IPDACLF.RPSWAIPPKIEQL
  853-  873 (30.65/19.17)	LPSAATFvRDGYNNVPSVGSL
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      51.42|      13|      22|    1096|    1108|       7
---------------------------------------------------------------------------
 1096- 1108 (24.59/15.52)	QNQHTQPFASLSF
 1115- 1127 (26.83/17.74)	NNRQTIPCVSWSY
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      50.51|      14|      22|    1242|    1255|       9
---------------------------------------------------------------------------
 1242- 1255 (27.59/12.31)	SPEPLPI..PTLLVGY
 1263- 1278 (22.92/ 8.95)	SPFSLPFweRLLLDPY
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             3|     139.63|      34|      37|     721|     756|      10
---------------------------------------------------------------------------
  721-  754 (62.23/26.33)	PPTVADLQRM.FPTPP..SLEQH.PAFSPV.MTYKDGIL
  758-  787 (27.07/11.50)	...VTALGMMeSPAVS..MVSTHlPEFK...MEVEDGL.
  792-  828 (50.34/19.27)	PEEIKDFSYV.HRPPPfqPFVGS.SMFAPLkMLPSHCLL
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|     239.52|      74|    1266|      22|     101|      11
---------------------------------------------------------------------------
   22-  101 (115.18/101.51)	PVNKSeHLSCAFTFFlHGESNVCTSVEIAQHQPIYLINEEHIHMAQSSPAP..FQVLVSPYgLNGTLTGQAykmSDPATR.KL
 1291- 1367 (124.34/85.54)	PENEA.LLEGAKTFF.RDLSAVYEMCKLGQHKPICKVLRDGIMRVGKTVAQklADELVSEW.FNQPWSGEE...NDNHSRlKL
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             3|     111.93|      28|      41|     174|     214|      12
---------------------------------------------------------------------------
  174-  201 (52.94/24.48)	GQQ..GLGSVKDPSNCGIPLTPPTSPEQ....AV
  216-  236 (23.17/24.27)	GSQdgGMITMHSPKRSG..KIPP...........
 1513- 1543 (35.82/14.17)	.QD..GQDSVTERERIGIPTEPDSADSQayppAV
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      75.00|      25|      37|     488|     518|      14
---------------------------------------------------------------------------
  488-  518 (34.43/37.24)	GPShlESSGkwWQsfRLPSSDDAEF.....RPPELQ
  528-  557 (40.57/21.34)	GPS..ESTA..LQ..RLLAQPNKRFkiwqdKQPQMQ
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      52.88|      15|      22|    1558|    1578|      15
---------------------------------------------------------------------------
 1563- 1578 (24.55/27.77)	NFWLLSLMRCyTEMLD
 1586- 1600 (28.32/11.56)	NSFILQIVPC.QYMLQ
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      47.34|      12|      27|    1739|    1750|      16
---------------------------------------------------------------------------
 1739- 1750 (24.58/18.39)	KIGLQKLWEWCI
 1769- 1780 (22.75/16.34)	RLGHGELKDWSI
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|     110.96|      35|     111|     558|     602|      18
---------------------------------------------------------------------------
  559-  596 (50.81/36.42)	LHFLDpSPLSQQPGDGLGEVNdPyTFEDGDIKYIFTAN
  673-  707 (60.15/26.97)	LHDLD.NIFDNSDDDELGAVS.P.ALRSSKMPTIGTED
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      46.79|      13|      26|    1818|    1830|      20
---------------------------------------------------------------------------
 1818- 1830 (24.21/17.46)	AMEPQGSFVVMPD
 1843- 1855 (22.58/15.60)	ALNMQSSQLNTPQ
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      51.57|      16|    1313|     332|     347|      21
---------------------------------------------------------------------------
  332-  347 (28.29/21.05)	KHKTTERQEK.GDKLQK
 1672- 1688 (23.27/15.78)	KEKQTEQGETlGEASQK
---------------------------------------------------------------------------




































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 MDP11854 with Med13 domain of Kingdom Metazoa


     
       
      
        
        
        


      
      
   
   

      

      














Intrinsically Disordered Regions








IDR SequenceStartStop




1) CAVGPNRPPTISQPGFSAGPSSASSLPPPASSKHKTTERQEKGDKLQKRPLIPFHHRPSVAEELCMEPDTSGQKLGLAGMDSSLEVSSSRKYDKQMAVPSRNTSKQMNLNPMDSPRSPISPLPPTLSPQPRGQEAESLDPPSVPVNPALYGNGLEL
2) GTEKDSLKKSKSEDGFGTKDVTTPGHSTPVPDGKNAMSIFSSATKTDVRQDNAAGRAGSSSLTQVTD
3) KDPSNCGIPLTPPTSPEQAVVGESGGMQSATSHLGSQDGGMITMHSPKRSGKIPPNLH
4) LITGNLHSSPNSSPAPSPGSPSGIGVGSHFQHSRSQGERLLSREAP
5) PSLHDLDNIFDNSDDDELGAVSPALRSSKMPTIGTEDRPLGKDGRAAVP
6) SLLTPPKYQPPPPAAQGQATPGTAGPLAPNSGSAAPPAGSAFNPTSNSNSANPAASTSSAGSSGPPVSSAASAPGINQMSTTSSSGFSGGVGGQNPSSGGGSIDRTQGNIACGGDPEQGSSTQPYQDGQDSVTERERIGIPTEPDSA
7) VGSLADPDYLNTPQMNTPVTLNSAAPASNSGAGVLPSPATPRFSVPTPRTPRTPRTPRGGGTASGQGSVKYDSTDQGSPASTPSTTRPLNSVEPATMQ
300
602
182
1908
671
1388
870
455
668
239
1953
719
1534
967










Molecular Recognition Features






MoRF SequenceStartStop




1) KRFKIWQ
544
550