<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 MDP19831

Description Mediator of RNA polymerase II transcription subunit 1
SequenceMQIRKMAAVQSSSPVADSSQGGTAAGSERPRAEDGSESEKQSRIMTLLERLYCKHSSSRSWQETSKVIRQAMEKRGAVNTGGHQLLLNCLETLQRALKVSTLPSMTDRLESIARQNMLGSHLSPSHTECYITSDMFYVEVHMDKSGKLMDVKVAHHGENPVSCPELIQHLRDKNFDEFSKHLKGLVNLYNLPGDNKLKTKMYLALQSLELDLTKMMHMFRIATNANTVETILHGSVGLLTSRSGGHLVSLQCYVSPNDIFEEEKAAHLNTDVNIPHTLGVSVSVTVEGTTSVYKLPIAPLITGSHPVDNKGTPSFSSITNSNCVDLPACFFLKMNCLMPFSLSYIKKMGSTTGIPVFETAPTLSPLYDLIIKSQLREEGGASPPSAQSMRFYASLPGQQHCYFLNGDAPVQDGRSLQGALVSKIPFRHPAQVPALLDIIRHQAAYNTLIGSCVKKACIKEDTPGLLQFEVCPLTDSSFSVSFQHPVNESLVCVVMEVIDSMQVACKLYKGLSDALICTDDFITKVVQRCMSIPVTMRAIRRKAETIQADTPALSLIAETVEIMVKKNLPPTGSPGYMGMGTGPDGSNPMGLPLNSGNNSVVCVGGNGSFQGPITSMFNMGRTGQGSSCIDTMGQVGGQQQAMQQQHQQSQSHGSDDFNKVTQNPILTSLLQITGSVGSSPTPQQPQPHQTPPTTTSPASNTKNHPMLMNLLKDNPSQDFAALYSSSPLERQNSSGSPRTDNQGQPCSGTKGKKKRLRGSDKGVMGAAGGMSMKQSQQQVVDMTQHHHLTSHSEDDFHRELFSMDVDASQNPIFDVSLPGDGLDTPHSITPAPSQCGTPPPGPGMQYHPQCHVQPQIQVQSQSQGSIPRMVRLSSSDSIGPDINDILSDIPDQANKGSNIGHGQHLMTSEDGGSLGTPVRDSSSSGQGSTVFEADLFNTNSNENPFTDAADLIAEAATATTPNSDTSSTNFFPDTDFNPELLSGQGSFSQTYFEDSSPSPDPDLELVKSFSGGSQQNTPTGTPQNPASHGQNTPETSLKDPFEIGIFGGNGGGGKPLMAPASDIADSHHAHTGGGQSPLIGIVVAGNDFKNVDAKAKQQQMRTKEDHVGGSSGQGMVSACSSEMKQVKRSRTPSSEGKSKDKPAKRKKLEPDAKSPSHSAGGRPYTPPCGSATSVGLVSTGGSKSPGSVGRSQTPPGGATPPIPKITIQIPRALTGGKTSSHGGYTSSSSTSGGTGNTIGTSNSKSHHSSSSGKIKSSKLESSVGQGNIAKQSSAAGTGSGIPSQSKVSSMGMGTGKPSSSPITKHGLSSSGGGGSSGSGSGIKNKPQGGKPPGSLMNPNIKPNISPSHSRSGGSDKLSSPMKQGQVPGTPPSSKAKSPIGSGSGSGGNKCSSGGGVGSKSLSSSSSNSASTSCASSTGSSSSGSMPFSSNGQSQYGSSGGNCSGGGGGGGCGNNPNAKGKSPSRNKKPSLTAVIDKLKSVGSGGNGGEEIESCGGSSGVGQQNTVPTSSKHSMSSQGGEFLSKRDKIDKDGKSKMSGSGGNSSDKKMIDAKSNTMTGTGVAKIIISKPEGGSPSIKSKVTLQKPGEGSGDGGIRSQHSGHKASPLFSGSTPKHDRSSPSHSRSPGCTPMNPDSESESGSSSVAEKSHQNSPSSDDDQTMRLHQPIQDYMSSISISQSEKHKKHKKEKKKQKDRERDKERDKEKEKKKSMSCGPSHTVKTDNWSRSPISSETSVSLLSSERSSRPSPVYMHTEDDDLMDSALTGNLEPFK
Length1769
PositionMiddle
OrganismDanio rerio (Zebrafish) (Brachydanio rerio)
KingdomMetazoa
LineageEukaryota> Metazoa> Chordata> Craniata> Vertebrata> Euteleostomi> Actinopterygii> Neopterygii> Teleostei> Ostariophysi> Cypriniformes> Danionidae> Danioninae> Danio.
Aromaticity0.04
Grand average of hydropathy-0.630
Instability index55.35
Isoelectric point8.74
Molecular weight185354.36
Publications
PubMed=23594743

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	IBA:GO_Central

GO - Biological Function
retinoic acid receptor binding	GO:0042974	IBA:GO_Central
thyroid hormone receptor binding	GO:0046966	IBA:GO_Central
transcription coregulator activity	GO:0003712	IBA:GO_Central
vitamin D receptor binding	GO:0042809	IBA:GO_Central

GO - Biological Process
cellular response to thyroid hormone stimulus	GO:0097067	IBA:GO_Central
regulation of transcription by RNA polymerase II	GO:0006357	IBA:GO_Central









Interaction





Binary Interactions











Repeat regions





Repeats

>MDP19831
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No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             8|    1289.82|     168|     170|    1160|    1327|       1
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  569-  674 (113.23/22.99)	......PPTGS.........................PGYMGMG.TG......PDGSNP.........MGLP..LNSGNNSvvCVGG.......................................NGSFQG.PITSMFNMGRTGQGS..........scIDTMGQVGGQQQAMQ....Q................QHQ......Q...SQSHGSddfN.......KV.TQ..NP.I.LTS.LLQITG..........................
  675-  826 (161.56/35.83)	............................SVGSSP.TPQQPQPHQTP......P.TTTS...PASN.TKNHPMLMNLLKDN..PSQDFAALYSSSPlERQNS.............SGSPRTDNQ..GQPCSGtKGKKKRLRGS.DKGV............M....GAAGGMSMKQ....S................QQQ.....VV...DMTQHH...H.......LT.SH..SE.D.DFHrELFSMDV...DASqnpifdvSLPGDGL.DTPH
  843- 1026 (187.30/42.66)	GMQ.YHPQCHVQPQI..QV........QSQSQGS.IPRMVRLSSSD......SIG..P...DINDILSDIPDQANKGSNI..GHGQHLMTSEDGG.SLGTP.............V.......R..DSSSSG.Q.GSTVFEADLFNTNsnenpftdaadlIAEAATATTPNSDTS....StnffpdtdfnpellsgQGS.....FS...QTYFED...S.......SP.SP..DP.D.LEL..VKSFSG...GSQ.......QNTPTGTPQNPA
 1027- 1160 (154.26/33.89)	SHGQNTPE......................TSLK.DPFEIGIFGGN......GGGGKPlmaPASDIA.DSHHAHTGGGQS..PLIGIVVA........GND.............FKNVDAKAK..QQQM...RTKEDHVGGSSGQGM............VSACSS......EM.....K................QVK.....RS...RTPSSE...G.......KS.KD..KP.A.KRK.KLEPDAK...SPS.......HSAG........
 1161- 1327 (281.85/67.77)	.GRPYTPPCGSATSV..GL........VSTGGSK.SPGSVGRSQTP......PGGATP...PIPKITIQIPRALTGGKTS..SHGGYTSSSSTSG.GTGNT.............IGTSNSKSH..HSSSSG.KIKSSKLESSVGQGN............IAKQSSAAGTGSGIP....S................QSK.....VS...SMGMGT...G.......KP.SS..SP.I.TKH.GLSSSGG...GGS.......SGSGSGIKNKPQ
 1328- 1456 (152.09/33.31)	GGKP...P.GS.......LmnpnikpnISPSHSR.SGGS.DKLSSPmkqgqvPG..TP...P.............SSKAK..SPIG..SGSGSGG.NKC............................SSGG.GVGSKSLSSS..SSN............SASTSCASSTGS.........................S.......S...SGSM..............PfSS..NG.Q.SQY.G..SSGGncsGGG.......GGGGCG..NNPN
 1465- 1598 (132.20/28.03)	NKKP......SLTAVidKL........KSVG....SGGN...................................GGEEIE..SCGG......SSGvGQQNT.............VPTS.SK.H..SMSSQG.....GEFLSK..RDK............IDKDGKSKMSGSGGN....S................SDKkmidaKS...NTMTGT...GvakiiisKPeGG..SPsIkSKV.TLQKPGE...G.........SGDG.GIRSQHS
 1599- 1750 (107.34/21.43)	.........GHKAS...PL........FSGSTPKhDRSSPSHSRSP........GCTP...MNPD.......SESESGSS..SVAEKSHQNSPSS.DDDQTmrlhqpiqdymssISISQSEKHkkHKKEKK.KQKDRERDKERDKEK............EKKKSMSCGPSHTVKtdnwS................RSP.....ISsetSVSLLS...S.......ER.SSrpSP.V.YMH.................................
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|     159.99|      47|     270|     124|     173|       2
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  124-  173 (75.79/61.07)	PSHTECYITSDMFYVEVHMDKSGKLMDvKVAHhgENPVSCPELIQHLRDK
  396-  442 (84.20/55.73)	PGQQHCYFLNGDAPVQDGRSLQGALVS.KIPF..RHPAQVPALLDIIRHQ
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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 MDP19831 with Med1 domain of Kingdom Metazoa
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