<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 MDP28845

Description Mediator of RNA polymerase II transcription subunit 13
SequenceMSSCFVPNGASLEDCHSNLFCLADLTGIKWKRYVWQGPTSAPILFPVTEEDPILSSFSRCLKADVLSVWRRDQRPGRRELWIFWWGDDPNFADLIHHDLSEEEDGVWENGLSYECRTLLFKAVHNLLERCLMNRNFVRIGKWFVKPYEKDEKPINKSEHLSCSFTFFLHGDSNVCTSVEISQHQPVYLLSEEHLTLAQQSNNPFQVILSPFGLNGTLTGQSFKLSDSSTKKLIGEWKQFYPVTSNLKEGSEEKQEEMDWEDDSLAAVEVLVAGVRMVYPACFVLVPQTDIPAPSSVGAPHCSTACLGVHQVPASTRDPAMSSVTLTPPTSPEEVQTVDAQSAQKWVKFSSVSDGFISDSTSHHGGKIPRKLANQVVDRVWQECNMNRAQNKRKYSATSNGLCEEETADKVASWDFVEATQRTNCNCSRHKNLKPRNSGQQGQAPPVGPQQPAAPKHKTNEKQDKGDKPQKRPLTPFHHRVSISDDVAMEADSASQRLVMAAPDSQVRFANIRTADGAKPPQLHGAELANSPQPPPLSPHPCDGADEGVPKAPSTPQSQHFYQMPTPDPLVPTKAMEDRLDGLSQPFSAAFPEVIEPTVYVGTAVNLEEDEADTTWKYYKVPKKKDVEFLPPQLPNDKLRDDPVIPAGQENVTSVTELMVQCRKPLKVSDELVQQYQSKNQYLTAVATEADQEPEIDPYAFVDGDVEFLFPDSKKDRQNIEREVGKKHKAEDGTSSVTVLSHEGEDAMSLFSPSVKQDAQRLAAHARTASTSLFHETDLVVSYTDLDNLFNSDEDELTPGSKRTVNGTDDKSNCKEAKTGNLDPLSCISTADLHKMYPTPPSLEQHIMGFSPMNMNNKEYGSMDTTLGGTVLEGNSSTVGAQFRIEVDEGFCSPKPAEIKDYSYVYKPENCQALVGCSMFAPLKTLPSQCLPPIKLPEECIYRQSWTVGKLDLLPPGPAMPFIKDGDGSTMDQEYGPAYTPQTHTPFGMPPSSAPPSNGGAGILPSPSTPRFPTPRTPRTPRTPRGAGGPASAQGSVKYENSDLYSPASTPSTCRPLNSVEPATVPSIPEAHSLYVNLILSESVMNLFKDCNFDSCCICVCNMNIKGADVGVYIPDPTQEAQYRCTCGFSAVMNRKFGNSSGLFLEDELDILGRNTECGKEAEKRFEALRATSIEHGSGGLKEPEKLPDDLILLLQDQCTNLFSPFGAADQDSIAKVGAVSNLVRVEERDCCNDCYLALEHGRQFMDNMSGGKVDEALVKTTCLHHWSKRNVVDVSMQCSQDILRMLLSLQPVLQDAIQKKRTVRSWGVQGPLTWQQFHKMAGRGSYGTDESPEPLPIPTFLLGYDYDFLVLSPFALPYWERLMLEPYGSQRDVAYVVVCPENEALLNGAKSFFRDLTAIYESCRLGQHRPICKLLPDGIMRVGPTASKKLSEKLVTEWFSQTANANNDAFSKLKLYAQVCRYELGPYLASQPLDNSLLSQTNLVPPSSQAASALPPVTAPAANPNTPSSAPAAPASSTIAVTSSSAMSSAATTANSTLTTTAPSSSSASLGSGIPTSKPSSFPPFSNINNTTPASLPTQAAPVPNGQTGGQQQQPTLQTAGMSGDTAAAPAQPHPEVSESTMDRDKVGVPTDGDSHAITYPPAIVVYIIDPFTYEKKDENSSSSSLWTLGLLRCFLEMVQVLPPHIKNIISVQIVPCQYLLQPVKHEDRQIYTQHLKSLAFSAFTQCRRPLPTSTNVKTLTGFGPGLAMETALRSPDRPECIRLYTPPFILAPVKDKQTELGETFGEAGQKYNVLFVGYCLSHDQRWLLASCTDLYGEQLETCIINIDVPNRARRKKGSARRLGLQKLWEWCLGLVQMSSLPWRVVIGRLGRIGHGELKDWSCLLSRRNLQSLSKRLKDMCRMCGISAADSPSILSACLVAMEPQGSFIIMPDSVSTGSVFGRSTTLNMQTSQLNTPQDTSCTHILVFPTSASVQVASSTYTTENLDLAFNTNNDGADGMGIFDLLDTGDDLDPDIINILPASPGGSPVHSPGSHYPHGGDMGKGQGTDRLLSTESHDEVTNILQQPLALGYFVSTAKAGPLPDWFWSACPQAQNQCPLFLKASLHLHVPSVQSDELLHSKHSHPLDSNQTSDVLRFVLEQYNALSWLTCDPATQDRRSCLPIHFVVLNQLYNFIMNML
Length2179
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-0.391
Instability index52.14
Isoelectric point5.41
Molecular weight239067.14
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:Ensembl
nucleoplasm	GO:0005654	IEA:Ensembl

GO - Biological Function
thyroid hormone receptor binding	GO:0046966	IEA:Ensembl
transcription coactivator activity	GO:0003713	IEA:Ensembl

GO - Biological Process
cholesterol homeostasis	GO:0042632	IEA:Ensembl
negative regulation of DNA-binding transcription factor activity	GO:0043433	IEA:Ensembl
positive regulation of transcription initiation from RNA polymerase II promoter	GO:0060261	IEA:Ensembl
triglyceride homeostasis	GO:0070328	IEA:Ensembl









Interaction





Binary Interactions











Repeat regions





Repeats

>MDP28845
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             3|     197.51|      52|      62|     466|     520|       1
---------------------------------------------------------------------------
  466-  501 (41.60/16.07)	...........................DKPQKRPLTPfHHRVSISDDVAMEADSA..SQRLV.MAA
  502-  565 (74.06/32.68)	PDSQVRFanIRTADGAKPPqlhgaelaNSPQPPPLSP..HPCDGADEGVPKAPSTpqSQHFYqMPT
  955- 1005 (81.85/32.96)	PGPAMPF..IKDGDGSTMD......qeYGPAYTPQT..HTPFGMPPSSAPPSNGG..AG..I.LPS
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      73.03|      25|      40|    1413|    1451|       2
---------------------------------------------------------------------------
 1413- 1437 (42.59/43.82)	KL.LPDGIMR..VGP.TASKKLSEKLVTE
 1452- 1480 (30.44/ 7.38)	KLkLYAQVCRyeLGPyLASQPLDNSLLSQ
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             3|     120.97|      34|      40|    1118|    1157|       3
---------------------------------------------------------------------------
 1098- 1116 (29.87/13.16)	......CVCN....MNIK.GADVGVY.....IPD..........P
 1118- 1157 (54.79/45.35)	QEAQYRCTCGFSAVMNRKFGNSSGLF.....LEDELdILgrnteC
 1159- 1192 (36.31/16.22)	KEAEKR....FEALRATSIEHGSGGLkepekLPDDL.IL......
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      69.09|      19|      40|     382|     400|       4
---------------------------------------------------------------------------
  382-  400 (34.48/22.31)	ECNMNRAQNKRKYSATSNG
  423-  441 (34.62/22.44)	NCNCSRHKNLKPRNSGQQG
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      51.87|      18|      40|     702|     719|       5
---------------------------------------------------------------------------
  702-  719 (33.26/20.03)	DG............DVEFLF.PDSKKDRQNI
  731-  761 (18.62/ 7.62)	DGtssvtvlshegeDAMSLFsPSVKQDAQRL
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      44.71|      12|      40|     848|     859|       6
---------------------------------------------------------------------------
  848-  859 (25.24/14.46)	GF.SPMNMNNKEY
  889-  901 (19.46/ 9.30)	GFcSPKPAEIKDY
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      89.51|      29|      30|    1525|    1553|       7
---------------------------------------------------------------------------
 1525- 1553 (44.38/23.10)	SAMSSAATTANSTLTTTAP.SSSSASLGSG
 1557- 1586 (45.13/23.65)	SKPSSFPPFSNINNTTPASlPTQAAPVPNG
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      97.26|      31|     420|    1330|    1379|       8
---------------------------------------------------------------------------
  625-  661 (47.42/15.86)	DVEFL...PPQLPN.DKLRDDPVipAGQENVTSVtelmVQC
 1345- 1379 (49.83/28.71)	DYDFLvlsPFALPYwERLMLEPY..GSQRDVAYV....VVC
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             3|     301.98|      81|     719|    1010|    1090|      11
---------------------------------------------------------------------------
  291-  331 (35.32/10.18)	..PAPSSVGAPHCSTACLGvhqvPASTRDPA.......MSSVTLTPPTSP............................................
 1010- 1090 (143.35/63.17)	RFPTPRTPRTPRTPRGAGG....PASAQGSV.....KYENSDLYSPASTPSTCRPLNSVEPATVPSIPEA....HSLYVNLILSESVMNLFKDC
 1728- 1812 (123.31/53.34)	RRPLP.TSTNVKTLTGF.G....PGLAMETAlrspdRPECIRLYTP...PFILAPVKDKQTELGETFGEAgqkyNVLFVGYCLSHDQRWLLASC
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      84.53|      23|     518|    1292|    1314|      13
---------------------------------------------------------------------------
 1292- 1314 (42.26/28.64)	VLQDAIQKKRTVRSWGVQGPLTW
 1829- 1851 (42.26/28.64)	VPNRARRKKGSARRLGLQKLWEW
---------------------------------------------------------------------------




































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 MDP28845 with Med13 domain of Kingdom Metazoa
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