<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 MDP11851

Description Mediator of RNA polymerase II transcription subunit 13
SequenceMDKNFVRIGKWFVRPYEKDEKPVNKSEHLSCAFTFFLHGESNVCTSVEIAQHQPIYLINEEHIHMAQSSPAPFQVLVSPYGLNGTLTGQAYKMSDPATRKLIEEWQYFYPMVLKKKDELKEEEELGYDDDFPVAVEVIVGGVRMVYPSAFVLISQNDIPVPQSVVNAGGQITVGQQGLGSVKDPSNCGIPLTPPTSPEQAVVGESGGMQSATSHLGSQDGGMITMHSPKRSGKIPPNLHNHMVHRVWKECILNRAQSKRSQMSTPALEEEPANSPAAWGFVDPTQRVSCSCSRHKLLKRCAVGPNRPPTISQPGFSAGPSSASSLPPPASSKHKTTERQEKGDKLQKRPLIPFHHRPSVAEELCMEPDTSGQKLGLAGMDSSLEVSSSRKYDKQMAVPSRNTSKQMNLNPMDSPRSPISPLPPTLSPQPRGQEAESLDPPSVPVNPALYGNGLELQQLSTLDDRTVLVGQRLPLLAEVSETALYTGIGPSHLESSGKWWQSFRLPSSDDAEFRPPELQGERCDTRIEGPSESTALQRLLAQPNKRFKIWQDKQPQMQPLHFLDPSPLSQQPGDGLGEVNDPYTFEDGDIKYIFTANKKCKQGTEKDSLKKSKSEDGFGTKDVTTPGHSTPVPDGKNAMSIFSSATKTDVRQDNAAGRAGSSSLTQVTDLAPSLHDLDNIFDNSDDDELGAVSPALRSSKMPTIGTEDRPLGKDGRAAVPYPPIADLQRMFPTPPSLEQHPAFSPVMTYKDGILPETVTALGMMESPAVSMVSTHLPEFKMEVEDGLGSPKPEEIKDFSYVHRPPPFQPFVGSSMFAPLKMLPSHCLLPLKIPDACLFRPSWAIPPKIEQLPLPSAATFVRDGYNNVPSVGSLADPDYLNTPQMNTPVTLNSAAPASNSGAGVLPSPATPRFSVPTPRTPRTPRTPRGGGTASGQGSVKYDSTDQGSPASTPSTTRPLNSVEPATMQPIPEAHSLYVTLILSDSVMNIFKDRNFDSCCICACNMNIKGADVGLYIPDSSNEDQYRCTCGFSAIMNRKLGYNSGLFLEDELDIFGKNSDIGQAAERRLMMCQSTFLPQMEGARKSLEPPISLLLLLQNQHTQPFASLSFLDYISSNNRQTIPCVSWSYDRVQADNNDYWTECFNALEQGRQYVDNLTGGKIDEALVRSATVHSWPHSNVLDISMLSSQDVVRMLLSLQPFLQDAIQKKRTGRTWENIQHVQGPLTWQQFHKMAGRGTYGSEESPEPLPIPTLLVGYDKDFLTVSPFSLPFWERLLLDPYGGRRDVAYIVVCPENEALLEGAKTFFRDLSAVYEMCKLGQHKPICKVLRDGIMRVGKTVAQKLADELVSEWFNQPWSGEENDNHSRLKLYAQVCRHHLAPYLATLQLDSSLLTPPKYQPPPPAAQGQATPGTAGPLAPNSGSAAPPAGSAFNPTSNSNSANPAASTSSAGSSGPPVSSAASAPGINQMSTTSSSGFSGGVGGQNPSSGGGSIDRTQGNIACGGDPEQGSSTQPYQDGQDSVTERERIGIPTEPDSADSQAYPPAVVIYMVDPFTYTAEEDSTSGNFWLLSLMRCYTEMLDNLPEHMRNSFILQIVPCQYMLQTMKDEQVVYIQYLKSMAFSVYCQCRRPLPTQIHIKSLTGFGPAASIEMTLKNPERPSPIQLYSPPFILAPIKEKQTEQGETLGEASQKYNVLFVGYCLSHDQRWLLASCTDLHGELLETCIVNIALPNRSRKSKVSARKIGLQKLWEWCIGIVQMTSLPWRVVIGRLGRLGHGELKDWSILLGECSLQTISKQLKDVCRMCGISAADSPSILSACLVAMEPQGSFVVMPDAVTMGSVFGRSTALNMQSSQLNTPQDASCTHILVFPTSSTIQVAPANYPNEDGFSPNNDDMFVDLPFPDDMDNDIGILITGNLHSSPNSSPAPSPGSPSGIGVGSHFQHSRSQGERLLSREAPEELKQQPLALGYFVSTAKAEKLPQWFWSSCPQAQNQCPLFLKASLHHHISVAQTDELLPVRNSQRVPHPLDSKTTSDVLRFVLEQYNALSWLTCNPATQDRTSCLPVHFVVLTQLYNAIMNIL
Length2075
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 index58.83
Isoelectric point5.70
Molecular weight226834.03
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. 


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

>MDP11851
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             5|     181.94|      28|      28|     899|     926|       1
---------------------------------------------------------------------------
  277-  320 (33.93/11.67)	AWGFVDPTQRV.ScscsrhkllkrcavgpnR.PP.TISQPGF.....SAGPS
  880-  907 (40.32/15.38)	TPQMNTPVTLN.S.................AAPA.SNSGAGV.....LPSPA
  908-  935 (47.26/19.40)	TPRFSVPTPRT.P.................RTPR.TPRGGGT.....ASGQG
 1425- 1452 (31.99/10.55)	GSAF.NPTSNSnS.................ANPAaSTSSAG......SSGPP
 1459- 1487 (28.45/ 8.50)	APGINQMSTTS.S.................SGFS.....GGVggqnpSSGGG
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             3|      94.23|      23|      28|    1895|    1922|       2
---------------------------------------------------------------------------
 1874- 1889 (25.57/ 6.51)	PANYPNEDGF..........SPN.....NDD..
 1897- 1922 (39.63/30.68)	PDDMDNDIGIlitGN..LHSSPN.....SSPAP
 1924- 1952 (29.03/ 8.97)	PGS.PSGIGV...GShfQHSRSQgerllSREAP
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      88.55|      25|      28|     992|    1016|       3
---------------------------------------------------------------------------
  992- 1016 (51.64/32.46)	NFDSC.CICACN..MNIK.GADVGLYIPD
 1019- 1047 (36.91/21.09)	NEDQYrCTCGFSaiMNRKlGYNSGLFLED
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      69.74|      20|      21|     831|     850|       4
---------------------------------------------------------------------------
  831-  850 (39.09/19.58)	IPDACLF.RPSWAIPPKIEQL
  852-  872 (30.65/13.78)	LPSAATFvRDGYNNVPSVGSL
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      57.24|      17|      21|    1095|    1115|       6
---------------------------------------------------------------------------
 1098- 1115 (27.69/22.62)	HTQPFASLSFlDYI.SSNN
 1117- 1134 (29.55/11.20)	QTIPCVSWSY.DRVqADNN
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      54.33|      16|      20|     422|     437|       8
---------------------------------------------------------------------------
  422-  437 (29.96/12.79)	PPTLSPQP....RGQEAESL
  439-  458 (24.37/ 8.95)	PPSVPVNPalygNGLELQQL
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      38.39|      11|      21|    1505|    1517|       9
---------------------------------------------------------------------------
 1505- 1517 (16.92/12.75)	GSSTQPyqDGQDS
 1525- 1535 (21.47/ 9.09)	GIPTEP..DSADS
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      50.51|      14|      21|    1241|    1254|      10
---------------------------------------------------------------------------
 1241- 1254 (27.59/16.70)	SPEPLPI..PTLLVGY
 1262- 1277 (22.92/12.23)	SPFSLPFweRLLLDPY
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             3|     114.92|      25|      28|     760|     786|      11
---------------------------------------------------------------------------
  688-  714 (33.36/13.53)	LGAV.SPA..LRSSKMPTIG..TEdrplGKDG
  726-  751 (39.92/18.58)	LQRM.FPTPPSLEQH.PAFSpvMT....YKDG
  760-  785 (41.63/23.70)	LGMMeSPAVSMVSTHLPEFK..ME....VEDG
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      73.79|      23|      27|    1607|    1632|      12
---------------------------------------------------------------------------
 1610- 1632 (44.34/38.20)	QYLKSM..AFSVYCQCR...RPLPTQIH
 1634- 1661 (29.45/13.64)	KSLTGFgpAASIEMTLKnpeRPSPIQLY
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      52.88|      15|      22|    1557|    1577|      13
---------------------------------------------------------------------------
 1562- 1577 (24.55/30.82)	NFWLLSLMRCyTEMLD
 1585- 1599 (28.32/12.83)	NSFILQIVPC.QYMLQ
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      86.38|      27|      29|    1719|    1747|      14
---------------------------------------------------------------------------
 1719- 1747 (44.15/36.39)	C..IVNI.ALPNRSRKSKVSarKIGLQKLWEW
 1748- 1777 (42.22/27.79)	CigIVQMtSLPWRVVIGRLG..RLGHGELKDW
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|     239.52|      74|    1265|      22|     101|      15
---------------------------------------------------------------------------
   22-  101 (115.18/105.72)	PVNKSeHLSCAFTFFlHGESNVCTSVEIAQHQPIYLINEEHIHMAQSSPAP..FQVLVSPYgLNGTLTGQAykmSDPATR.KL
 1290- 1366 (124.34/89.08)	PENEA.LLEGAKTFF.RDLSAVYEMCKLGQHKPICKVLRDGIMRVGKTVAQklADELVSEW.FNQPWSGEE...NDNHSRlKL
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      46.79|      13|      22|    1817|    1829|      17
---------------------------------------------------------------------------
 1817- 1829 (24.21/13.75)	AMEPQGSFVVMPD
 1842- 1854 (22.58/12.28)	ALNMQSSQLNTPQ
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      96.77|      33|      36|     136|     169|      18
---------------------------------------------------------------------------
  136-  169 (54.40/32.59)	EVIVG..GVRMVY.PSAF.VLISQNDIPvPQSVV.NAGG
  170-  207 (42.37/20.51)	QITVGqqGLGSVKdPSNCgIPLTPPTSP.EQAVVgESGG
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      67.99|      21|    1338|     327|     347|      21
---------------------------------------------------------------------------
  327-  347 (38.65/22.87)	PP...ASSKHKTTERQEK.GDKLQK
 1663- 1687 (29.34/15.47)	PPfilAPIKEKQTEQGETlGEASQK
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      87.60|      25|     394|     217|     242|      22
---------------------------------------------------------------------------
  217-  242 (45.32/29.82)	SQDG.GMITMHSPKRSGKIPPNlHNHM
  613-  638 (42.28/23.12)	SEDGfGTKDVTTPGHSTPVPDG.KNAM
---------------------------------------------------------------------------




































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 MDP11851 with Med13 domain of Kingdom Metazoa
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