<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 MDP11849

Description Mediator of RNA polymerase II transcription subunit 13
SequenceMNRNFVRIGKWFVKPYEKDEKPINKSEHLSCSFTFFLHGDSNVCTSVEINQHQPVYLLSEEHITLAQQSNSPFQVILSPFGLNGTLTGQAFKMSDSATKKLIGEWKQFYPISCCSKEMSEEKQEDMDWEDDSLAAVEVLVAGVRMIYPACFVLVPQSDIPTPSSVGSSHCSASCLGVHQVPASTRDPAMSSVTLTPPTSPEEVQTVDPQSAQKWVKFSSVSDGFSTDSTSHHGGKIPRKLANHVVDRVWQECNMNRAQNKRKYSASSGGLCEDEIANKVASWDFVEVTQRTSCSCLRHKNPKPRNAGQQGQAPSCQQQVLPKHKTNEKQEKSEKPQKRPLTPFHHRVSISDDVGMDTDSASQRLVISAPDSQVRFSNIRTNDVAKTPQMHATEMANSPQPPPLSPHPCDVVDEGVTKTPSTPQSQHFYQMPTPDPLVPTKPMEDRIDSLSQSFPPQFQEAVEPTVYVGTAVNLEEDEANIAWKYYKVPKKKDVEFLPPQLPSDKFKDDPVGPFGQESVTSVTELMVQCKKPLKVSDELVQQYQIKNQYLSAIVPDAEQEPKIDPYAFVEGDEEFLFPDKKDRQNSDREAGKKHKAEDGTPSVTVLSHEEDAMSLFSPSIKQDAPRPNSHARPPSTSLIYDSDLAVSYTDLDNLFNSDEDELTPGSKKSANGSDDKANCKESKTGNLDPLSCISTADLHKMYPTPPSLEQHILGFSPMNMNNKEYGSMDTTPGGTVLEGSSSSIGAQFKIEVDEGFCSPKPSEIKDFSYVYKPENCQVLVGCSMFAPLKTLPSQCLPPIKLPEECIYRQSWTVGKLDLLPSGPSMPFIKEGDGNNMDQEYGPAYTPQTHTSFGMPPSSAPPSNSGAGILPSPSTPRFPTPRTPRTPRTPRGTGGPASAQGSVKYENSDLYSPASTPSTCRPLNSVEPATVPSVPEAHSLYVNLILSESVMNLFKDCNFDSCCICVCNMNIKGADVGVYIPDPTQEAQYRCTCGFSAVMNRKFGNNSGLFLEDELDIIGRNTDCGKEAEKRFEALRATSTEHGGLKESEKLPDELILLLQDQCTNLFSPFGVTDQDPFPKIGVISNWVRVEERDCCNDCYLALEHGRQFMDNMSGGKVDEALVKSSCLHPWSKRNDVSMQCSQDILRMLLSLQPVLQDAIQKKRTVRPWGVQGPLTWQQFHKMAGRGSYGTDESPEPLPIPTFLLGYDYDFLVLSPFALPHWERLMLEPYGSQRDIAYVVLCPENEALLNGAKSFFRDLTAIYESCRLGLHRPISRLLTDGIMRVGSTASKKLSEKLVAEWFSQAADGDHEAFSKLKLYAQVCLFDLGPYLASQPLDSSLLSQPNLVAPTNQSLITPPQMANTGNANTPSATLASSASSTMTMTSGVAISTSLTTANSTLTTTSSSSSSSLNSGVSSNKLPSFPPFGSMNSSGTGPMSAQASTVQSGQLGGQPSSALQTTGIAGESSSLPTQPHPDVSESTMDRDKVGIPTDGDSHAITYPPAIVVYIIDPFTYENKDESTNSSNVWTLGLLRCFLEMVQTLPPHIKSTVSAQIVPCQYLLQPVKHEDRQIYTQHLKSLAFSVFTQCRRPLPTSTNVKTLTGFGPGLAMETALKSPDRPECIRLYTPPFILAPVKDKQTELGETFGEAGQKYNVLFVGYCLSHDQRWILASCTDLYGELLETCIINIDVPNRARRKKGSARRFGLQKLWEWCLGLVQMSSLPWRVVIGRLGRIGHGELKDWSCLLSRRNLQSLSKRLKDMCRMCGISAADSPSILSACLVAMEPQGSFVIMPDSVSTGSVFGRSTTLNMQTSQLNTPQDTSCTHILVFPTSASVQVASATYTTENLDLAFNPNNDGADGMGIFDLLDTGDDLDPDIINILPASPTTSPVHSPGSHYPHGGDAGKGQGTDRLLSTESHDEVTNILQQPLALGYFVSTAKAGPLPDWFWSACPQAQYQCPLFLKASLHLHVPSVQSDELLHSKHSHPLDSNQTSDVLRFVLEQYNALSWLTCDPAIQDRRSCLPIHFVVLNQLYNFIMNML
Length2037
PositionMiddle
OrganismDipodomys ordii (Ord's kangaroo rat)
KingdomMetazoa
LineageEukaryota> Metazoa> Chordata> Craniata> Vertebrata> Euteleostomi> Mammalia> Eutheria> Euarchontoglires> Glires> Rodentia> Castorimorpha> Heteromyidae> Dipodomyinae> Dipodomys.
Aromaticity0.07
Grand average of hydropathy-0.408
Instability index52.38
Isoelectric point5.46
Molecular weight223715.96
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: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

>MDP11849
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             3|     610.42|     242|     327|     296|     622|       1
---------------------------------------------------------------------------
  300-  385 (34.17/23.57)	...........................................................................................................................................................................................................................................................................NPKPRNagqQGQAPSCQ...QQVLPKHKTN.EKQEKSEKPQkrpLTPFHHR.VSISDDVGMDTDSASQRLvisAPdsqvrFSNIRTNDVAK
  397-  699 (343.49/255.54)	SPQPPPLSPH....................PCDVVDEGvtkTPSTPQSQhfYQMPTPDPLVPTKPMEdrIDSLSQSFPPqfqEAVEptVYVGTAV.............NLEEDEANIAWKYYKVPKkkdVEFLP..PQLP....SD.KFKDDPVGP.FGQESVTSVTelMVQCKKPLKVSDelvqqyqiknqylSAIVPdAEQEPKidpyafvegdeeflFPDKKDRQNSDREAGkkhkaeDGTPSVTVLSHEEDAMSLFSPsikqdAPRPNS...HARPPSTSliyDSDLAVSYTDlDNLFNSDEDE...LTPGSKKsANGSDDKANCKESKTGNL...DP.....LSCISTADLHK
  701-  911 (232.76/98.64)	YPTPPSLEQHilgfspmnmnnkeygsmdttPGGTVLEG...SSSSIGAQ..FKIEVDEGFCSPKPSE..IKDFSYVYKP...ENCQ..VLVGCSMfaplktlpsqclpPIKLPEECIYRQSWTVGK...LDLLPsgPSMPfikeGDgNNMDQEYGPaYTPQTHTSFG..MPPSSAPPSNSG.............AGILP.SPSTPR..............FPTPRTPRTPRTPRG......TGGPASAQGSVKYENSDLYSP................................................................................................
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             3|     181.59|      49|     844|    1118|    1166|       2
---------------------------------------------------------------------------
 1118- 1166 (88.20/53.83)	EALVKSSCLHPWSKRNDVSMQCSQDILRMLL....SLQ.PVLQD.AIQKKRTVRP
 1945- 1971 (26.69/10.59)	...........WSACPQAQYQCPL.FLKASL....HLHvPSVQ............
 1973- 2020 (66.70/38.72)	DELLHSKHSHPLD.....SNQTS.DVLRFVLeqynALS.WLTCDpAIQDRRSCLP
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      89.56|      25|     844|     963|     998|       3
---------------------------------------------------------------------------
  971-  995 (46.51/40.53)	GADVGVYIPDPTQEAQYRCTCGFSA
 1002- 1026 (43.05/13.94)	GNNSGLFLEDELDIIGRNTDCGKEA
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             3|     119.27|      31|     844|    1043|    1080|       4
---------------------------------------------------------------------------
   58-   91 (30.81/ 8.47)	.....LSEEHITLAQQSNSPfqvILSPFGlngtLTGQ.AF
 1045- 1076 (52.76/38.50)	ES.EKLPDELILLLQDQCTN...LFSPFG....VTDQdPF
 1191- 1217 (35.70/11.40)	ESpEPLPIPTFLLGYDYDFL...VLSPFA....L......
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      42.64|      14|      26|    1377|    1391|       6
---------------------------------------------------------------------------
 1377- 1391 (19.66/15.02)	STMTMTSGVAiSTSL
 1405- 1418 (22.98/12.64)	SSSSLNSGVS.SNKL
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|     256.60|      78|     322|    1480|    1562|       9
---------------------------------------------------------------------------
 1480- 1562 (135.07/90.34)	MDRDKVGIPTDGD.SHAITYPPAIVVYIID.PFTYENKDESTNSSNVWTLGL.LRCFLEMVQTLPPHIkstvsAQIVPCQYLLQPV
 1807- 1887 (121.53/72.11)	MQTSQLNTPQDTScTHILVFPTSASVQVASaTYTTENLDLAFNPNNDGADGMgIFDLLDTGDDLDPDI.....INILPASPTTSPV
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|     207.51|      69|    1427|     151|     270|      10
---------------------------------------------------------------------------
  195-  270 (111.28/142.20)	TPP..TSP.EEVQT.VDPQSAQKWVKFSSVSDGFstdSTSHHGGKIprkLAN..HVVDRVWQEC..NM...NRAQnKRKYSASSGGL
 1624- 1703 (96.23/41.23)	TPPfiLAPvKDKQTeLGETFGEAGQKYNVLFVGY...CLSHDQRWI...LASctDLYGELLETCiiNIdvpNRAR.RKKGSARRFGL
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      61.63|      18|      29|    1705|    1722|      11
---------------------------------------------------------------------------
 1705- 1722 (37.52/24.46)	KLWEW.C.LGLVQMSSLPWR
 1735- 1754 (24.11/12.88)	ELKDWsClLSRRNLQSLSKR
---------------------------------------------------------------------------




































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 MDP11849 with Med13 domain of Kingdom Metazoa
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