<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 MDP28960

Description Mediator of RNA polymerase II transcription subunit 13
SequenceMSASFVPNGASLEDCHCNLFCLADLTGIKWKKYVWQGPTSAPILFPVTEEDPILSSFSRCLKADVLGVWRRDQRPGRRELWIFWWGEDPSFADLIHHDLSEEEDGVWENGLSYECRTLLFKAVHNLLERCLMNRNFVRIGKWFVKPYEKDEKPINKSEHLSCSFTFFLHGDSNVCTSVEINQHQPVYLLSEEHITLAQQSNSPFQVILCPFGLNGTLTGQAFKMSDSATKKLIGEWKQFYPISCCLKEMSEEKQEDMDWEDDSLAAVEVLVAGVRMIYPACFVLVPQSDIPTPSPVGSTHCSSSCLGVHQVPASTRDPAMSSVTLTPPTSPEEVQTVDPQSAQKWVKFSSVSDGFNSDSTSHHGGKIPRKLANHVVDRVWQECNMNRAQNKRKYSASSGGLCEEATAAKVASWDFVEATQRTNCSCLRHKNLKSRNAGQQGQAPSLGQQQQILPKHKTNEKQEKSEKPQKRPLTPFHHRVSVSDDVGMDADSASQRLVISAPDSQVRFSNIRTNDVAKTPQMHGTEMANSPQPPPLSPHPCDVVDEGVTKTPSTPQSQHFYQMPTPDPLVPSKPMEDRIDSLSQSFPPQYQEAVEPTVYVGTAVNLEEDEANIAWKYYKVPKKKDVEFLPPQLPSDKFKDDPVGPFGQENVTSVTEYQIKNQYLSAIASDAEQEPKIDPYAFVEGDEEFLFPDKKDRQNSEREAGKKHKVEDGTSSVTVLSHEEDAMSLFSPSIKQDAPRPTSHARPPSTSLIYDSDLAVSYTDLDNLFNSDEDELTPGSKKSANGSDDKASCKESKTGNLDPLSCISTADLHKMYPTPPSLEQHIMGFSPMNMNNKEYGSMDTTPGGTVLEGNSSSIGAQFKIEVDEGFCSPKPSEIKDFSYVYKPENCQILVGCSMFAPLKTLPSQYLPPIKLPEECIYRQSWTVGKLELLSSGPAMPFIKEGDGSNMDQEYGPAYTPQTHTSFGMPPSSAPPSNSGAGILPSPSTPRFPTPRTPRTPRTPRGAGGPASAQGSVKYENSDLYSPASTPSTCRPLNSVEPATVPSIPEAHSLYVNLILSESVMNLFKDCNFDSCCICVCNMNIKGADVGVYIPDPTQEAQYRCTCGFSAVMNRKFGNNSGLFLEDELDIIGRNTDCGKEAEKRFEALRATSAEHVNGGLKESEKLSDDLILLLQDQCTNLFSPFGAADQDPFPKSGIISNWVRVEERDCCNDCYLALEHGRQFMDNMSGGKVDEALVKSSCLHPWSKRNDVSMQCSQDILRMLLSLQPVLQDAIQKKRTVRPWGVQGPLTWQQFHKMAGRGSYGTDESPEPLPIPTFLLGYDYDYLVLSPFALPYWERLMLEPYGSQRDIAYVVLCPENEALLNGAKSFFRDLTAIYESCRLGQHRPISRLLTDGIMRVGSTASKKLSEKLVAEWFSQAADGNNEAFSKLKLYAQVCRYDLGPYLASLPLDSSLLSQPNLVAPTSQSLITPPPMTNTGNANTPSATLASAASSAMTMTSGVAISTSVATANSTLTTASTSSSSSSNLNSGVPSNKLPSFPPFGSMNSNAAGSMSTQANTVQSGQLGGQQTSALQTPGISGESSSLPTQPHPDVSESTMDRDKVGIPTDGDSHAVTYPPAIVVYIIDPFTYENTDESTNSSSVWTLGLLRCFLEMVQTLPPHIKSTVSVQIIPCQYLLQPVKHEDREIYPQHLKSLAFSAFTQCRRPLPTSTNVKTLTGFGPGLAMETALRSPDRPECIPLYALPFILPVKDKARRKKSSARKFGLQKLWEWCLGLVQMSSLPWRVVIGRLGRIGHGELKDWSCLLSRRNLQSLSKRLKDMCRMCGISAADSPSILSACLVAMEPQGSFVIMPDSVSTGSVFGRSTTLNMQTSQLNTPQDTSCTHILVFPTSASVQVASATYTTENLDLAFNPNNDGADGMGIFDLLDTGDDLDPDIINILPASPTGSPVHSPGSHYPHGGDAGKGQSTDRLLSTEPHEEVPNILQQPLALGYFVSTAKAGPLPDWFWSACPQAQYQCPLFLKASLHLHVPSVQSDELLHSKHSHPLDSNQTSDVLRFVLEQYNALSWLTCDPAIQDRRSCLPIHFVVLNQLYNFIMNML
Length2100
PositionMiddle
OrganismPongo abelii (Sumatran orangutan) (Pongo pygmaeus abelii)
KingdomMetazoa
LineageEukaryota> Metazoa> Chordata> Craniata> Vertebrata> Euteleostomi> Mammalia> Eutheria> Euarchontoglires> Primates> Haplorrhini> Catarrhini> Hominidae> Pongo.
Aromaticity0.08
Grand average of hydropathy-0.404
Instability index53.31
Isoelectric point5.43
Molecular weight230929.91
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: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

>MDP28960
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             4|     767.44|     270|     300|     473|     769|       1
---------------------------------------------------------------------------
  473-  628 (180.99/95.26)	....................................................................................................................................................................LTPFHHR.VSVSDDVGMDADSASQRLvisAPdsqvrFSNIRTNDVAK...TP.............QMHGTE...MAN............................SPQPPPLSPHPCDV.......VDEG.VTKTPSTPQSQHFYQMPT.PDPLVPSKPME.DRI......DSLSQSFPPQ.YQEAVEPTVYVGTAVNLEEDeaNIAWKYYKVPKkkdVEF
  629-  932 (378.81/194.55)	LPPQLPSDKFKDDPVGPFGQENVTSVTEYQIKNQYLSAIASDAEQEPKIDPYAfvEGDEEFL.......FPDKKDRQN..SEREAGkkhkvedGTSSV..TVLSHEEDamsLFSPSIKQDAPRPTSHARP......PSTSLIYdSDLAVSYTDLdNLFnsdedeLTPGSKKsANGSDDKASCKESKTGNL...DP.....LSCISTADLHKmypTPpsleqhimgfspmNMNNKEygsMDT............................TPGGTVLEGNSSSIgaqfkieVDEGfCSPKPSEIKDFSYVYKPE.NCQILVGCSMF.APL......KTL....PSQ.YL....P......PIKLPEE..CIYRQSWTVGK...LEL
  933- 1067 (127.15/49.81)	LS.........SGPAMPFIKEGDGSNMDQEYGPAYTPQTHTSFGMPPSSAPPS..NSGAGILpspstprFPTPRTPRTprTPRGAG.......GPASAqgSVKYENSD...LYSPASTPSTCRPLNSVEPatvpsiPEAHSLY.VNLILSESVM.NLF...................................................................................................................................................................................................................................
 1528- 1634 (80.49/29.35)	LNSGVPSNKLPSFP..PFGSMN...........................................................................................................................................................................................................................snaagsmstqantvqsgqlggqqtsalqTPG...ISGESSSL............................PTqPHPDVSESTMDrDKVgiptdgDSHAVTYPPAiVVYIIDPFTYENT..........................
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      78.09|      24|     298|    1552|    1575|       4
---------------------------------------------------------------------------
 1552- 1575 (41.74/25.84)	GSMSTQANTVQSGQLGGQ......QTSALQ
 1847- 1876 (36.35/21.44)	GSFVIMPDSVSTGSVFGRsttlnmQTSQLN
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             3|     136.20|      40|     720|     383|     431|       5
---------------------------------------------------------------------------
  383-  431 (59.14/52.33)	CNMNRaqnkrKYSASSGGLCEEAT........AAKVASWDFvEATQRTNCsclRHKN
 1080- 1107 (21.58/ 6.05)	CNMNI.....K.GADVGVYIPDPTqeaqyrctCG.......................
 1112- 1157 (55.48/29.09)	..MNR.....KFGNNSGLFLEDELdiigrntdCGKEAEKRF.EALRATSA...EHVN
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      65.52|      20|     409|    1384|    1422|       7
---------------------------------------------------------------------------
  217-  236 (36.03/13.23)	LTGQAFKMSDSATK....KLIGEW
 1393- 1416 (29.50/28.60)	LTDGIMRVGSTASKklseKLVAEW
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      82.14|      24|     410|    1471|    1497|       9
---------------------------------------------------------------------------
  292-  322 (39.41/16.58)	TPSPVGSThcsssclGVHQVPASTRDPAMSS
 1471- 1494 (42.73/19.02)	TPPPMTNT.......GNANTPSATLASAASS
---------------------------------------------------------------------------




































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 MDP28960 with Med13 domain of Kingdom Metazoa
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