<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 MDP26906

Description Mediator of RNA polymerase II transcription subunit 13
SequenceMNRNFVRIGKWFVKPYEKDEKPINKSEHLSCSFTFFLHGDSNVCTSVEINQHQPVYLLSEEHVTLAQQSNSPFQVILSPFGLNGTLTGQAFKMSDSATKKLIGEWKQFYPISCGLKEMSEEKQEDMDWEDDSLAAVEVLVAGVRMIYPACFVLVPQSDIPTPSSVGSSHCSASCLGIHQVPASTRDPAMSSVTLTPPTSPEEVQSVDPQSAQKWVKFSSVSDGFSTDSTSHHGGKIPRKLANHVVDRVWQECNMNRLQNKRKYSATSSGLCEEETADKIGSWDFVEATQRTSCSCLRHKSLKTRNTGQQGQAPSLGQQQQILPKHKTNEKQEKSEKPQKRPLTPFHHRVSISDDIGMDTDSASQRLVISAADSQVRFTNIRTNDVAKTPQMHGTELANSPQPPPLSPHPCDVVDEGVTKTPSTPQSQHFYQMPTPDPLVPTKPMEDRIDSLSQSFPPPFQEAVEPTVYVGTAVSLEEDEANVAWKYYKVPKKKDVEFLPPQLPNDKFKDDPVGPFGQESVTSVTELMVQCKKPLKVSDEIVQQYQIKNQYLSAIASDTEQEPKIDPYAFVEGDEEFIFTDKKDRQNSEREAGKKHKVEDGTSAVTVLSHEEDAMSLFSPSKQDAPRPANHARPPSTSLIYDSDLAVSYTDLDNLFNSDEDELTPGSKKSASGSDDKASSKESKTGSLDPLSCISTADLHKMYPTPPSLEQHIMGFSPMNMNNKEYGSMDPTPGGTVLEGSSSSVGTQFRIEVEEGFCSPKPSEIKDFSYVYKPENCQVLVGCSMFAPLKTLPSHCLPPIKLPEECVYRQSWTVGKLDLLPSGPSMPFIKEGDGSNLDQDYGPAYTPQIHTSFGMPPSSAPPSNGGAGILPSPSTPRFPTPRTPRTPRTPRGAGGPASAQGSVKYENSDLYSPASTPSTCRPLNSVEPATVPSIPEAHSLYVNLILSESVMNLFKDCNFDSCCICVCNMNIKGADVGVYIPDPTQEAQYRCTCGFSAVMNRKFGNNSGLFLEDELDIIGRNTDCGKEAEKRFEALRASSVENVNGSLKESEKVPDELILLLQDQCTNLFSPFGAADHDPFPKAGISSNWVRVEERDCCSDCCLALEHGRQFMDNMSGGKVDEALVRSSCLHPWAKQNDASVQCSQDILRMLLSLQPVLQDAIQKKRTVRPWGVQGPLTWQQFHKMAGRGSYGTDESPEPLPIPTFLLGYDYDFLVLSPFALPYWEKLMLEPYGSQRDIAYVVLCPENEALLNGARSFFRDLTAIYESCRLGQHRPISRLLTDGIMKVGATASKKLSEKFVTEWFSQAADGNNEAFSKLKLYAQVCRYDLGPYLASQPLDSSLLSQPNLVAPPNQSLVTAPQMTNTGNANAPSATLASAASSTMTLTPGVAISTSVATANSTLTTTSSSSSSSMSSGVSSNKLPSFPPFGSMNTSGTGSMSAQGSTVQSGQLGGQQSSSLQAAGISGESASLPTQPHPDVSESTMDRDKVGIPTDGDSHAITYPPAIVVYIIDPFTYENKDESTSSSNVWTLGLLRCFLEMLQTLPPHIKSTVSVQIVPCQYLLQPVKHDDRQIYSQHLKSLAFSAFTQCRRPLPTSTNVKTLTGFGPGLAMETALKSPDRPECIRLYTPPFILAPVKDKQTELGETFGEAGQKYNVLFVGYCLSHDQRWILASCTDLYGELLETCIINIDVPNRARRKKGSARRFGLQKLWEWCLGLVQMSSLPWRVVIGRLGRIGHGELKDWSCLLSRRNLQSLSKRLKDMCRMCGISAADSPSILSACLVAMEPQGSFVIMPDSVSTGSVFGRSTTLNMQTPQLNTPQDTSCTHILVFPTSASVQVASATYTTENLDLAFNPNNDGADGMGIFDLLDTGDDLDPDIINILPASPTTSPVHSPGSHYPHGGDAGKGQGTDRLLSTESHDEVTNILQQPLALGYFVSTAKAGPLPDWFWSACPQAQYQCPLFLKASLHLHVPSVQSDELLHSKHSHPLDSNQTSDVLRFVLEQYNALSWLTCDPAIQDRRSCLPIHFVVLNQLYNFIMNML
Length2040
PositionMiddle
OrganismRattus norvegicus (Rat)
KingdomMetazoa
LineageEukaryota> Metazoa> Chordata> Craniata> Vertebrata> Euteleostomi> Mammalia> Eutheria> Euarchontoglires> Glires> Rodentia> Myomorpha> Muroidea> Muridae> Murinae> Rattus.
Aromaticity0.07
Grand average of hydropathy-0.400
Instability index53.30
Isoelectric point5.44
Molecular weight223504.44
Publications
PubMed=15057822
PubMed=15632090
PubMed=22673903

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	ISO:RGD
nucleoplasm	GO:0005654	IEA:Ensembl
nucleus	GO:0005634	IDA:RGD

GO - Biological Function
thyroid hormone receptor binding	GO:0046966	ISO:RGD
transcription coactivator activity	GO:0003713	ISO:RGD
transcription coregulator activity	GO:0003712	ISO:RGD

GO - Biological Process
cholesterol homeostasis	GO:0042632	ISO:RGD
negative regulation of DNA-binding transcription factor activity	GO:0043433	ISO:RGD
positive regulation of transcription by RNA polymerase II	GO:0045944	ISO:RGD
positive regulation of transcription initiation from RNA polymerase II promoter	GO:0060261	ISO:RGD
positive regulation of transcription, DNA-templated	GO:0045893	ISO:RGD
regulation of transcription by RNA polymerase II	GO:0006357	IBA:GO_Central
triglyceride homeostasis	GO:0070328	ISO:RGD









Interaction





Binary Interactions











Repeat regions





Repeats

>MDP26906
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             3|     807.34|     237|     326|     198|     514|       1
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   17-  197 (156.13/50.03)	........................................................................................................................................EKDEKPINKS....EH.LSCSFTFFLHGD............SNV.CTSVEINQhqpVYLLSEEHVTlaQQSNSPFQVI..........................LSPFGLNgtltgqafkMS....DSATKKL..IGEWKQFYPISCGL..KEMSEEK.QEDmdwEDDSLAavevlvagvrMIYPACF..VLVPQSDIPTPSSVGSSHCSAScLGIHQVPaSTRDpamssVT..LTPP.........
  198-  509 (350.51/254.52)	TSPEE..VQSVDPqsaqkwvkfSSVSDgfstdstshhggkiprklanHVVDrvwqecnmnRLQNKRKYSATSSGlcEEETADKIGSWDFVEatqrtscsclrhkslktrntgqqgqapslGQQQQILPKHKTNEKQEKSEKPQKRPLtpfHHrVSISDDIGMDTDSASQRLVISAADSQVRFTNIRTND...VAKTPQMHGT..ELANSPQPPP..........................LSPHPCD.........VV....DEGVTKTPSTPQSQHFYQMPTPD..PLVPTKP.MED...RIDSLS..........QSFPPPFQEAVEPTVYVGTAVSLEEDEANVA.WKYYKVP.KKKD.....VE..FLPPQlPNDkFKD
  521-  766 (300.69/127.36)	TSVTElmVQCKKP.........LKVSD....................EIVQ.........QYQIKNQYLSAIAS..DTEQEPKIDPYAFVE.............................GDEEFIFTDKKDRQNSER.EAGKKHKV................EDGTSAVTVLSHEEDAMSLFSPSKQD....APRP.........ANHARPPStsliydsdlavsytdldnlfnsdedeLTPGSKK.........SAsgsdDKASSKESKTGSLDPLSCISTADlhKMYPTPPsLEQ...HIMGFS.........pMNMNNKEYGSMDPT..PGGTV.LEGSSSSVG.TQF......RIE.....VEegFCSPK.PSE.IKD
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             3|     288.55|      76|     202|    1535|    1629|       2
---------------------------------------------------------------------------
 1535- 1612 (130.09/75.50)	CFL..EMLQTLPPHIKSTvsVQIVPCQYLLQPV..........................KHDD.RQIYSQHLKSL.AFSAFTQCRRPLPTSTNVKTLTGFGPGLAMET
 1744- 1812 (100.69/50.79)	CLLsrRNLQSLSKRLKDM.......CR.MCGIS..........................AADS.PSILSACLVAMePQGSFV....IMPDSVSTGSVFGRSTTLNMQT
 1865- 1944 (57.78/38.57)	DLL..DTGDDLDPDI.....INILPASPTTSPVhspgshyphggdagkgqgtdrllsteSHDEvTNILQQPL.AL.GYFVSTAKAGPLP...................
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      89.49|      29|     202|    1250|    1287|       3
---------------------------------------------------------------------------
 1250- 1278 (48.60/36.67)	LNGARSFFRD.LTAIYESCRLGQHRPISRL
 1288- 1317 (40.88/15.40)	ATASKKLSEKfVTEWFSQAADGNNEAFSKL
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             3|     122.92|      26|      32|     819|     844|       4
---------------------------------------------------------------------------
  819-  844 (46.88/19.15)	LPSGPSMPFIKEGDGSNLDQD.YGPAY
  854-  877 (42.21/16.54)	MPPSSAPP..SNGGAGILPSP.STPRF
  888-  913 (33.83/11.86)	TPRGAGGPASAQGSVKYENSDlYSPA.
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|     101.59|      34|      39|     985|    1023|       7
---------------------------------------------------------------------------
  985- 1023 (51.05/58.80)	EAQYRctcgFSAVMNRKFGNNSGLFLE.....DELdIIGRNTDC
 1026- 1064 (50.54/37.70)	EAEKR....FEALRASSVENVNGSLKEsekvpDEL.ILLLQDQC
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      55.15|      17|     355|     780|     799|       8
---------------------------------------------------------------------------
  780-  799 (23.88/21.74)	VGCSMfAPLKTLPShcLPPI
 1140- 1156 (31.26/14.70)	VQCSQ.DILRMLLS..LQPV
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      72.99|      19|     532|    1160|    1178|       9
---------------------------------------------------------------------------
 1160- 1178 (37.08/24.37)	AIQKKRTVRPWGVQGPLTW
 1694- 1712 (35.90/23.33)	ARRKKGSARRFGLQKLWEW
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      57.85|      17|      17|    1437|    1453|      10
---------------------------------------------------------------------------
 1437- 1453 (29.70/16.01)	SMSAQGSTVQSGQLGGQ
 1457- 1473 (28.15/14.78)	SLQAAGISGESASLPTQ
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      84.31|      33|      39|    1345|    1380|      14
---------------------------------------------------------------------------
 1338- 1378 (38.65/27.69)	DSsllsqPNLVAppNQSLVTApQMTNTGNANAPSATLASAA
 1379- 1416 (45.65/21.30)	SStmtltPGVAI..STSVATA.NSTLTTTSSSSSSSMSSGV
---------------------------------------------------------------------------




































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 MDP26906 with Med13 domain of Kingdom Metazoa
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