<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 MDP28440

Description Mediator of RNA polymerase II transcription subunit 13 (Fragment)
SequenceFLQADLTGIKWKRYVWQGPTSAPILFPVTEEDPILSSFSRCLKADVLSVWRRDQRPGRRELWIFWWGEDPNFADLIHHDLSEEEDGVWENGLSYECRTLLFKAVHNLLERCLMNRNFVRIGKWFVKPYEKDEKPVNKSEHLSCSFTFFLHGDSNVCTSVEINQHQSVYLLSEEHITLAQQSNSPFQVILSPFGLNGTLTGQAFKMSDSATKKLIGEWKQFYPISCCLKEMSEEKQEDMDWEDDSLAAVEVLVAGVRMIYPACFVLVPQSDIPTPSSVGSSHCSASCLGVHQVPASTRDPAMSSVTLTPPTSPEEVQTVDPQSAQKWVKFSSVSDGFNSDSTSHHGGKVPQKLASHVVDRVWQECNMNRAQNKRKYSASLGGLNEEEIPDKVACWDFVEATQRTSCSCSRHKNLKPRNTGQQGQAPSLNQQQQVLPKHKTNEKQEKNEKPQKRPLTPFHHRVSISDDVGMDADSASQRLVISAPDSQVRFSNLRTNDVAKTPQMHGTEMANSPQPPPLSPHPCDVADEGVTKTPSTPQSQHFYQIPTPDPLVPTKPMEDRIDTLSQSFPPQFQETVEPTVYVGTAVNLEEDEANTAWKYYKVPKKKDVEFLPPQLPNDKFKDDPVGPFGQESVTSVTELMVQCKKPLKVSDELVQQYQIKNQYISAIASDTEKEPKIDPYAFVEGDEEFLFPDKKDRQNSEREAGKKHKVEDGTSSVTVLSHEEDAMSLFSPSVKQDAPRPSNHARPPSTSLIYDSDLAVSYTDLDNLFNSDEDELTPGSKKSATGSDDKASCKESKTGNLDPLSCISTADLHKMYPTPPSLEQHIMGFSPMNMNNKDYGSMDTTPGGTVLDGNSSSIGAQFKIEVDEGFCSPKPSEIKDFSYVYKPENCQVLVGCSMFAPLKNLPSQCLPPIKLPEECIYRQSWTVGKLELLPSGSTMPFIKEGDGSNMDQEYGPAYTPQTHTSFGMPPSSAPPSNSGAGILPSPSTPRFPTPRTPRTPRTPRGAGGPASAQGSVKYENSDLYSPASTPSTCRPLNSVEPATVPSIPEAHSLYVNLILSESVMNLFKDCNFDSCCICVCNMNIKGADVGVYIPDPMQEAQYRCTCGFSAVMNRKFGNNSGLFLEDELDIIGRNTDCGKEAEKRFEALRATSAEHISGGLKESEKLPDELILLLQDQCTNLFSPFGASDQDPFPKIGVISNWVRVEERDCCNDCYLALEHGRQFMDNMSGGKVDEALVKSSCLHPWSKRNDVSMQYSQDILRMLLSLQPVLQDAIQKKRTVRPWGVQGPLTWQQFHKMAGRGSYGTDESPEPLPIPTFLLGYDYDFLVLSPFALPYWERLMLEPYGSQRDIAYVVLCPENEALLHGAKSFFRDLTAIYESCRLGQHRPISQLLMDGIMRVGSAASKKLSEKIVAEWFSQTADGNNEAFSKLKLYAQVCKYDLGPYLASQPLDSSLLSQPNLVTPTSQSLITPPQMTNTGNANTSSATLASTASSTMTMTSGVAISSSVATANSTLTTSSSSSSSNSNSGVSSNKVPSFPPFGSMNSSGTGSMSTQANTVQSGQLGGQQSSALQTAGISGDSSSLPTQPHPDVSESTMDRDKVGIPTDGDSHAITYPPAIVVYIIDPFTYEDKDESTNSSNVWTLGLLRCFLEMVQTLPPHIKSTVSVQIVPCQYLLQPVKHEDRQIYTQHLKSLAFSAFTQCRRPLPTSTNVKTLTGFGPGLAMETALKSPDRPECIRLYTPPFILAPVKDKQTELGETFGEAGQKYNVLFVGYCLSHDQRWILASCTDLYGELLETCIINIDVPNRARRKKGSARRFGLQKLWEWCLGLVQMSSLPWRVVIGRLGRIGHGELKDWSCLLSRRNLQSLSKRLKDMCRMCGISAADSPSILSACLVAMEPQGSFVIMPDSVSTGSVFGRSTTLNMQTSQLNTPQDTSCTHILVFPTSASVQVASATYTTENLDLAFNPNNDGADGMGIFDLLDTPDDLDPDIINILPASPTASPVHSPGSHYPHGGDTGKGQSTDRLLSTESHDEVTNILQQPLALGYFVSTAKAGPLPDWFWSACPQAQYQCPLFLKASLHLHVPSVQSDELLHSKHSHPLDSNQTSDVLRFVLEQYNALSWLTCDPAIQDRRSCLPIHFVVLNQLYNFIMNML
Length2153
PositionMiddle
OrganismHeterocephalus glaber (Naked mole rat)
KingdomMetazoa
LineageEukaryota> Metazoa> Chordata> Craniata> Vertebrata> Euteleostomi> Mammalia> Eutheria> Euarchontoglires> Glires> Rodentia> Hystricomorpha> Bathyergidae> Heterocephalus.
Aromaticity0.08
Grand average of hydropathy-0.423
Instability index52.13
Isoelectric point5.40
Molecular weight237578.16
Publications
PubMed=21993625

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: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

>MDP28440
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No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|     131.50|      38|     202|    1705|    1742|       1
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 1705- 1742 (68.19/41.11)	LPTSTNVKTLTGFGPGLAMETA.LKSPDRPECIRLYTPP
 1905- 1943 (63.30/37.56)	MPDSVSTGSVFGRSTTLNMQTSqLNTPQDTSCTHILVFP
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             3|     849.17|     252|     388|     172|     557|       2
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  266-  537 (403.66/363.05)	VPQsDIPTPSS.........VGSSHCSASCLGVHQVPASTRDpamssvTLTpPTSPEEVQTVDPQSAQKWVKFSSVsDGFNSDSTS..HHGGKVPQKLASHVVDrvWQECNMNRaQNKRKYSASLGGL....NEEEIPD..KVacwdfvEATQrTSCS..CSRHKNL....KPRNT....GQQGQAPSLNQQQQVLPKHKTNEKQEKNEKPQKRPLTPFHHRVSiSDDVG.MD.ADSASQRLVISAPDSQVRFSNL.RTNDVAKTPQMHGT.EMANSPQPPPLSPHPCDVA.DEGVTKTPSTPQ
  733-  989 (351.26/152.90)	VKQ.DAPRPSNharppstslIYDSDLAVSYTDLDNLFNSDED......ELT.PGSKKSATGSDDKASCKESKTGNL.DPLSCISTAdlHKMYPTPPSLEQHIMG..FSPMNMNN.KDYGSMDTTPGGTvldgNSSSIGAqfKI......EVDE.GFCSpkPSEIKDFsyvyKPENCqvlvGCSMFAPLKNLPSQCLP.............PIKLPEECIYRQ...SWTVGkLElLPSGSTMPFIKEGDG....SNMdQEYGPAYTPQTHTSfGMPPSSAPPSNS........GAGILPSPSTPR
 1400- 1506 (94.25/13.63)	.......................................................................................................................................................................................GSAASKKLSEKIVAEWFSQTADGNNEAFSKLKL...YAQVC.KYDLG....PYLASQPL.DSSLLSQPNLVTP.TSQSLITPPQMTNT.GNANTSSATLASTASSTMTmTSGVAISSS...
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|     187.61|      57|     533|     633|     689|       5
---------------------------------------------------------------------------
  633-  689 (98.86/58.40)	TSVTELMVQCKKPLKVSDELV..QQYQIKNQYISAIASDTEKEPKI................DPYAFVEGDEEFL
 1150- 1224 (88.75/51.64)	TSAEHISGGLKESEKLPDELIllLQDQCTNLFSPFGASDQDPFPKIgvisnwvrveerdccnDCYLALEHGRQFM
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      48.14|      13|      15|    1008|    1020|       6
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 1008- 1020 (22.98/10.99)	PASAQGSVKYENS
 1025- 1037 (25.16/12.79)	PASTPSTCRPLNS
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|     109.18|      32|     544|    1045|    1096|       7
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 1059- 1096 (53.06/63.90)	SESVMNLFK...DCNFDSCCIcvcnmNIKGADVgVYIPDPM
 1592- 1626 (56.11/24.59)	SESTMDRDKvgiPTDGDSHAI.....TYPPAIV.VYIIDPF
---------------------------------------------------------------------------
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No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      86.39|      23|     544|    1269|    1291|      10
---------------------------------------------------------------------------
 1269- 1291 (43.28/29.91)	VLQDAIQKKRTVRPWGVQGPLTW
 1803- 1825 (43.11/29.76)	VPNRARRKKGSARRFGLQKLWEW
---------------------------------------------------------------------------




































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 MDP28440 with Med13 domain of Kingdom Metazoa
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