<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 MDP28848

Description Mediator of RNA polymerase II transcription subunit 13
SequenceAELTGIKWRRYNFEGHGDCGPIISAPAQDDPILLSFIRCLQANLLCVWRRDVKPDCKELWIFWWGDEPNLVDVIHRELHMVEEGFWENGLSYECRTLLFKAIHNLLERCLMDKNFVRIGKWFIRPYDKDEKPVNKSEHLSCAFTFFLHGESNVCTSVEIAQHQPIYLITEEHIQMAQSSPSPFQVLVSPYGLNGTLTGQSYKMSDPATRKLMEEWQYFYPMVLKKKEGMKEEKELGYDNDFPVAVEVIVGGVRMVYPSAFVLISQSDIPVSQSAASAAGHINVGQQGLGSVKDPVSTCGMPLTPPTSPEQAVMGESGCSQSSISHPAVQEGTVSVHSPKKSSKITPKFHNRIVHRVWKECILNRAQSKRNQITTANLEEEVPNNSVSWDFVDPVQRVSCSCSRHKVFKQRCTGASGRPPTLPQPGFTVGTAAASALPPPASSKHKTTERQDKGEKLQKRPLMPFHHRPSMTEELCMEQDTAGQKLGLAGMESSLEVPSSRKYEKPLSLPARNASKQINMNPMDSPHSPTSPLPPTLSPQPRGQEAENLDPPSVPVNPALYGSGLELQPLPSLDDRTVLVGQRLPLMAEVSETALYCGITQSNEAVDVWRAYSVPSSDDPEFRPPELPCERYDGRMEVNPDSTALKRFLAQPNKRFKILEEQKPVQTLNYLDPLPLLQPPGEGWGDTSDPYTFEDGDIKYSFTVNKKCKLGAEKDPLKKNKSEDGIGSKEIPPTGHSTSVPDGKDAMSIFSSAPKTDPRQDSAAGRAGSGSLTQVTDLAPSLHDLDNIFDNSDEDELGAVSPALRSSKLPAAGSEERPLGKDSRTAVPYPPTVADLQRMFPTPPSLEQHPAFSPVMSYKDGISSETVTALGMMESPMVNMVPTQLAEFKMEVEDGLGSPKPEEIKDFSYVHKVPSFQPFVGSSLFAPLKILPSQCLLPLKIPDACIFRPSWAVPPKIEQLPLPPAATFIRDGYNNVPSVGSLADQDYLQMSTPQMSTPVMLNSAAPASNSGAGVLPSPATPRFSVPTPRTPRTPRTPRGGGTASGQGSVKYDSTDQGSPASTPSTTRPLNSVEPGTVQPIPEAHSLYVTLILSDSVLNIFKDRNFDSCCICACNMNIKGADVGLYIPDSSNEDQYRCTCGFSAIMNRKLGYNSGLFIEDELDIFGKTSDIGQAAERRLMICQSNLFSQMGEGARRSQEPPMSLLLLLQNQHTQPFTSLSCLDYMASNNRQTLPCVNLSYDRLQADSNDSWVECFNALEQGRQYVDNPTGGKVDEALVRSATVHSWPHSNVLDISMLSSQDVVRMLLSLQPFLQDAIQKKRTGRTWENIQHVQGPLTWQQFHKMAGRGTYGSEESPEPLPIPTLLVGYDKDFLTISPFSLPFWERLLLDPYGGHRDVAYIVVCPENEALLDGAKTFFRDLSAVYEMCRLGQHKPICKVLRDGIMRVGKSVAQKLTDELVSEWFSQPWGSEDCDNHSRLKLYAQVCRHHLAPYLATLQLDSSLLLPPKYQTPAPSQPQAAPGSSGPAPSSASSCLSAAAGAPATGSSFSSTPSAGTTSLPAGSASSSGSSVPQLSASSATPGASQMGTSSTPGFSGTAGSGQGGGAAGGAAERSQGSAGPGTDTEPGPTLPPQQQEGQEGTSERERIGVPTEPDAADSNAYPPAVVIYMVDPFTYTADEESASTNFWLLSLMRCYTEMLDNLPENMRNSFILQIVPCQYMLQTMKDEQVFYIQHLKSLAFSVYCQCRRPLPTQIHIKSLTGFGPAASIEMTLKNPERPSPIQLYSPPFILAPIKDKQTELGETFGEASQKYNVLFVGYCLSHDQRWLLASCTDLHGELLETCIVNIDLPSRSRRSKLSARKIGLQKLWEWCIGIVQMTSLPWRVVIGRLGRLGHGELKDWSILLGECSLQTISKQLKEVCRMCGISAADSPSILSACLVAMEPQGSFVVMPDAVTMGSVFGRSTALNLQSSQLNTPQDASCTHILVFPTSATIQVAPANYPNEDGFSPTNDDMFDLPFPDDMDNDIRILITGNLHSSPNSSPVPSPGSPSGTGVGSHYHHSRSQGERLLSREAPEELKQQPLALGYFVSTAKAENLPQWFWSSCPQAQNQCPLFLKASLHHHISVAQTDELLPARNSQRVPHPLDSKTTSDVLRFVLEQYNALSWLTCNPATQDRSSCLPVHFVVLTQLYNAIMNIL
Length2194
PositionMiddle
OrganismTaeniopygia guttata (Zebra finch) (Poephila guttata)
KingdomMetazoa
LineageEukaryota> Metazoa> Chordata> Craniata> Vertebrata> Euteleostomi> Archelosauria> Archosauria> Dinosauria> Saurischia> Theropoda> Coelurosauria> Aves> Neognathae> Passeriformes> Passeroidea> Estrildidae> Estrildinae> Taeniopygia.
Aromaticity0.07
Grand average of hydropathy-0.361
Instability index60.08
Isoelectric point5.62
Molecular weight240157.33
Publications
PubMed=20360741

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. 
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

>MDP28848
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No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             4|     193.91|      36|      37|    1514|    1549|       1
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 1021- 1073 (36.36/11.86)	RFSVP..tprtprtprtprgGGTASGQGSvkydSTdqGSPASTPSTTRPLNSVEP
 1514- 1549 (64.13/26.65)	PQAAPGS.............SGPAPSSAS....SC..LSAAAGAPATGSSFSSTP
 1553- 1578 (37.67/12.56)	TTSLP...............AGSASSSGS....SVpqLSAS..........SATP
 1585- 1617 (55.76/22.19)	TSSTPGF.............SGTAGSGQG.........GGAAGGAAERSQGSAGP
---------------------------------------------------------------------------
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No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      89.80|      25|      28|    1103|    1127|       3
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 1103- 1127 (52.19/35.61)	NFDSC.CICACN..MNIK.GADVGLYIPD
 1130- 1158 (37.60/23.38)	NEDQYrCTCGFSaiMNRKlGYNSGLFIED
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No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             3|      76.69|      17|      18|    1224|    1240|       4
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 1207- 1221 (20.95/ 9.54)	..QNQHTQPFTS.LSCLD
 1224- 1240 (30.36/17.51)	ASNNRQTLPCVN.LSYDR
 1243- 1260 (25.38/13.30)	ADSNDSWVECFNaLEQGR
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No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             3|     105.27|      25|      28|    1961|    1985|       5
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 1937- 1961 (38.58/18.72)	AMEPQGSFVVMPDAV..TMGS....VFGRST
 1962- 1986 (41.61/20.80)	ALNLQSSQLNTPQDA..SCTH....ILVFPT
 1987- 2016 (25.08/ 9.44)	SATIQVAPANYPNEDgfSPTNddmfDLPFP.
---------------------------------------------------------------------------
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No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      65.07|      19|      20|     924|     943|       6
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  924-  943 (31.31/16.98)	FAPLKILPSQC.LLPLKiPDA
  946-  965 (33.76/14.65)	FRPSWAVPPKIeQLPLP.PAA
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             4|     141.20|      23|      34|    2071|    2093|       7
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  418-  436 (31.80/15.36)	PPTL.PQP.......GFTVGTAAASAL
  453-  474 (37.12/19.29)	GEKLQKRPL.....MPFHHRPSMTEEL
 2071- 2093 (38.78/20.52)	PEELKQQPL....ALGYFVSTAKAENL
 2102- 2128 (33.50/16.61)	PQAQNQCPLflkaSLHHHISVAQTDEL
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No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      77.16|      20|      34|      18|      37|       8
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   18-   37 (36.37/19.61)	DCGPIISAPAQDDPILLSFI
   55-   74 (40.79/22.93)	DCKELWIFWWGDEPNLVDVI
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             3|     221.02|      58|     424|     288|     349|       9
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  288-  345 (101.62/46.69)	LGSVKDPVST......CGMPLTPPTSPEQAVM.GESGCSQ.SSISHPAVQEGTVS.VHSPKKSSKIT
  709-  772 (84.79/37.13)	LGAEKDPLKKnksedgIGSKEIPPTGHSTSVPdGKDAMSI.FS.SAPKTDPRQDS.AAGRAGSGSLT
 1625- 1661 (34.61/10.91)	.......................PTLPPQQQE.GQEGTSErERIGVPTEPDAADSnAYPPA......
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      65.16|      20|      27|    1725|    1751|      10
---------------------------------------------------------------------------
 1731- 1750 (40.11/29.49)	HLKSL.....AFSVYCQCR...RPLPTQ
 1752- 1779 (25.06/ 7.96)	HIKSLtgfgpAASIEMTLKnpeRPSPIQ
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      94.10|      28|      33|    1840|    1869|      11
---------------------------------------------------------------------------
 1840- 1869 (46.42/40.60)	IVNI.DLPSRSRRSKLSarKIGLQKLWEWCI
 1871- 1899 (47.68/34.31)	IVQMtSLPWRVVIGRLG..RLGHGELKDWSI
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      52.48|      17|      37|     842|     863|      12
---------------------------------------------------------------------------
  842-  863 (21.92/25.50)	PPSLEQhpaFSpvMSYKDGISS
  881-  897 (30.56/15.86)	PTQLAE...FK..MEVEDGLGS
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      41.28|      12|      34|     481|     492|      13
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  481-  492 (19.79/11.16)	AGQKLGLAGMES
  513-  524 (21.49/12.79)	ASKQINMNPMDS
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|     170.57|      52|    1267|     139|     191|      14
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  139-  191 (91.82/73.43)	LSCAFTFFlHGESNVCTSVEIAQHQPIYLITEEHI.QMAQSSPSPF.QVLVS.....PYG
 1408- 1466 (78.75/57.36)	LDGAKTFF.RDLSAVYEMCRLGQHKPICKVLRDGImRVGKSVAQKLtDELVSewfsqPWG
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---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      62.95|      17|    1319|     808|     824|      16
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  808-  824 (30.71/19.10)	LPAAGSEERPLGKDSRT
 2129- 2145 (32.24/20.51)	LPARNSQRVPHPLDSKT
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No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      49.60|      17|      21|    1675|    1695|      21
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 1675- 1692 (26.17/25.45)	DE..ESASTNFwLLSLMRC.Y
 1697- 1716 (23.43/ 7.54)	DNlpENMRNSF.ILQIVPCqY
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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 MDP28848 with Med13 domain of Kingdom Metazoa
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