<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 MDP32253

Description Mediator of RNA polymerase II transcription subunit 13 (Fragment)
SequenceMWTNVFRIGGLHNVSWFQFLPSETELNPGSDRSSRAEQNDVATYLVLSSHLRLQKEGFLTTWTNSFVGPWDPSQGLYNPDEKIKLWLFLPGRHSSITDKAQAAVPKLRVVASGIWVAPGDSEEISVALSQSLRNCIERSLTGLSYMRFGDVFSKFSPQSEEYLRRGQPTVEFIFAATEEAVFVHVIISAKNVRTLSSGDAERLLKSSLKNSSYRLPVIVSPHGMRGSLTGFCPNDLVKQVYFSSGNLRTSSGYIGLSSHVGHGSSLINGNHSYVEVTLGCCQSRNENTSQINSTFAVNLPHNQCPEPSVGSKDHRKGEQDLLSVCEKKFIYPAEAVLVPILQSSFAKFSLKRFWLQNWIGPSLAGSSLFMHWAGDFDSLGASGNKSDGFYEKGGYNSSGSSRNSSISSTSSASSGSGWRMTRTGDLDADADSLTCRQSGLTCNDDRPKMGSKRPRTGMGESFGQVGIENDQIGWDWDDDDDDDDDREVGMDIKALLSEFGDFGDFFENDALPFGEPPGTAESHALMFPPDSVDVGSSPVDMMDVSDQIVLPVGFSSFESFNPVPPIIDECLIKSQDVLNSSITSVPPNQMPVSSTGEFDHLMKAEAMMTFAPEYGAVEAPMSEISPTFFKSPYLPKSHKVESSNSRTSNYVYGATPPATDSDGAADKILYGSKAGIGKNDCRTLFQLKKHYIQVEGRKGQLPTVISDNNSTKEGVSQSKHSKHSAANAVKIVQGKKTNGISAVVSTLLYSKTLLATDVGSVMFQAFMCRMRHIAASSKHNSPASLTRLSGNFFLNQLPNEPSTLTDNISARNEIYKKDIPTRIAGDFDGGMIDGHMSAPVGVWRTVSVPKTAKPASSPNIEAGSSLPHSSFSEDSLLSYGQRQPLQELLDGIALLVQQATSFVDLALDSDCGDGPYGWLALEELWRRELSCGPSAVHAGCGGTLASCHSLDIAGVKLVDPLSAEVFPSSVITLLQSDIKTALKSAFGQSDGPLSVTDWCKGRNQSGDGGSISEGSTAESALTEVSIDGAKGDETTQSQDIYSSELLRPTLFVLPSPSILVGYQDDWLKISTNSLPHWEKAPFEPYALPKNINYTVVCPDIDPLTCAAADFFQQLGTVYEMCRLGTHLPQSLGNQMETDAGKLSSSGFVLLDYPQSMKIESNNTSLLGSLSDYFLSLSNGWNVSSYLKSLSKALKGIKLGSYLYTNQKEGSGSPCMVVYIVCPFPDPSAVLRTIVESSIALGSVIQSDRDRRSILNSQVARAFGSSAAVDETSISHIPVLSGFNVPKLVLQVVSVDSIFRITSPSFNELVILKDTAFSVYNKARRISRGVPNDAFLSSSLSGRSTSALTPMSSISGIWKDCVGSRMTGSTHPRDGEMDVSLRTGGWDTSWQIPRSGGLSCDPNRNGDFYLNDEIFYLFEPLFILSEPGSVERGVSPSFGGLGSESSKPIPEDGGRGSGAGLNSMEGITSGSNSQGDASQLEGKAIPSLHCSYGWTEDWRWLVSIWTDARGELLDTHIFPFGGISSRQDTKGLQCLFVQVLQQGCQILQACSSPDNGSYKPRNFVITRIGNFFELEYQEWQKAIYSAGGPEIKKWPIQLRRSAPSGIASNSNGSSLQQQDLSLIQERASSTSTLYSSHSKPSTFVKGSMGQSAGRKQIMGGQTISGTPRGLFQWVHSISFASISLDHSLHFVLPAELVSAGGGQSSTGMSSVNYIEGFTPVKSIGSTAFSYMMIPSPNMRFLHPSPLQLPTCLTAESPPLAHLLHSKGCAIPLSTGFVVSKAVPSMRKDSRINIKEEWPSVLSVSLVDYYGGYGHAHDKILQGSMKQGGGTKETRDFEVESHIILESIAAELHALSWMTVSPVYLDRRTALPFHCDMVLRLRRLLHFADKELSRLPDKSGDHLTAIYCLHRNFLSSCYRFLS
Length1920
PositionKinase
OrganismCapsella rubella
KingdomViridiplantae
LineageEukaryota> Viridiplantae> Streptophyta> Embryophyta> Tracheophyta> Spermatophyta> Magnoliopsida> eudicotyledons> Gunneridae> Pentapetalae> rosids> malvids> Brassicales> Brassicaceae> Camelineae> Capsella.
Aromaticity0.08
Grand average of hydropathy-0.243
Instability index49.26
Isoelectric point5.78
Molecular weight208268.72
Publications
PubMed=23749190

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

>MDP32253
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No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|     355.88|     113|     123|     980|    1102|       1
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  980- 1102 (176.10/121.64)	TALKSAFGQSDGplSVTDWCKgrnqSGDGGSISEGSTAESALTEVSIDGAKGDETTQSQDIYSSEL.LRPTL..FVLpspSILVGYQ.DDWLKISTNSLPHWEKAPF......EPYALPKNINYtVVCPDIDP
 1104- 1226 (179.79/99.40)	TCAAADFFQQLG..TVYEMCR....LGTHLPQSLGNQMETDAGKLSSSGFVLLDYPQSMKIESNNTsLLGSLsdYFL...SLSNGWNvSSYLKSLSKALKGIKLGSYlytnqkEGSGSPCMVVY.IVCPFPDP
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|     395.98|     131|     448|    1237|    1384|       2
---------------------------------------------------------------------------
 1237- 1384 (182.71/131.77)	SIALGSvIQSDRDRRSILNSQVARAFGSSAAVDETSISHIpvlSGF...................NVPKLVLQVVSVDSIFRITSPSFNELVILKDTAFSVyNKARRISRGVPN...DAFLssSLSGRSTSALtpmsSISGIwkDCVGsrmtGSTHPRDGEMDVSLRTGG
 1675- 1827 (213.27/110.53)	SISFAS.ISLDHSLHFVLPAELVSAGGGQSSTGMSSVNYI...EGFtpvksigstafsymmipspNMRFLHPSPLQLPTCLTAESPPLAHLLHSKGCAIPL.STGFVVSKAVPSmrkDSRI..NIKEEWPSVL....SVSLV..DYYG....GYGHAHDKILQGSMKQGG
---------------------------------------------------------------------------
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No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|     243.63|      75|     713|      89|     260|       3
---------------------------------------------------------------------------
  171-  251 (116.59/59.83)	EFIFAAteEAVFVHVIISAKNVRTLSSGDAERLLKSSLKNSSYRLPVI..VSPHGMRGSLT.GFcpndLVKQVYFSSGNLRTSS
  328-  405 (127.03/63.42)	KFIYPA..EAVLVPILQSSFAKFSLKRFWLQNWIGPSLAGSSLFMHWAgdFDSLGASGNKSdGF....YEKGGYNSSGSSRNSS
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|     126.06|      37|     429|     253|     292|       4
---------------------------------------------------------------------------
  253-  292 (62.66/40.92)	YIGLSSHVGHGSSLINGNHSYVEvtlGCCQSRNENTSQIN
  691-  727 (63.41/34.82)	YIQVEGRKGQLPTVISDNNSTKE...GVSQSKHSKHSAAN
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             3|     159.45|      61|     429|     406|     543|       5
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  406-  442 (51.82/74.10)	.......................................................ISSTSSASSGSGWR....MTRTGDLDADADSLTCRQ.SGLTC
  503-  538 (21.93/12.84)	GDFFENDALPF.GEP......PGtaeshalmfppdSVDVGSSP......................................................
 1405- 1489 (85.69/21.28)	GDFYLNDEIFYlFEPlfilsePG............SVERGVSPsfgglgsesskpIPEDGGRGSGAGLNsmegITSGSNSQGDASQLEGKAiPSLHC
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|     112.84|      37|     262|     584|     624|       6
---------------------------------------------------------------------------
  584-  624 (58.97/45.26)	SVPPNQMPVSS....TG.EFDHLMKAEAMMTfapEYGAvEAPMSEI
  847-  888 (53.87/29.37)	SVPKTAKPASSpnieAGsSLPHSSFSEDSLL...SYGQ.RQPLQEL
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      82.07|      25|     776|     768|     793|       7
---------------------------------------------------------------------------
  768-  793 (42.73/26.96)	CRMRHIAASSKHNS..PAS..LTRLsGNFF
 1543- 1571 (39.34/20.25)	CQILQACSSPDNGSykPRNfvITRI.GNFF
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|     115.21|      32|     573|     916|     955|       8
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  916-  955 (50.48/51.13)	YGWlalEELWRRELScgpsaVHAGCGGTLASCHSLDIAGV
 1491- 1522 (64.73/41.32)	YGW...TEDWRWLVS.....IWTDARGELLDTHIFPFGGI
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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 MDP32253 with Med13 domain of Kingdom Viridiplantae
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