<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 MDP22258

Description Mediator of RNA polymerase II transcription subunit 13
SequenceMSSCSVPNGASLEDCHSNLFYLADLTGIKWKMFVWQGPTSAPILFPVTEEDPILCSFSRCLKADVLSVWRRSQRPGRRELWLFWWGDDPNFTELIHHELTAGDDGLWENGLPYECRTLLFKAIHNLLERCLMNRSFVRIGKWFVKPYEKDEKPVNKSEHLSCAFTFFLHGESNVCTSVEINQHQPIYHLTEEHLTLAQQASTPFQVILSPFGLNGTLTGQSFKMSDPPTQKLIEEWNQFYPISPSAKQTVSEDKPEDMDWEDDSLASVEVLVGGVRMVYPACLVLVPQSDIPVVTPVGSSQCTAVYSGGYQVPAMQREPAMSLVTLTPPTSPEEVHTVDSHSAQKWLKMPSSSDVFSVDRTNHHGGKVPRRLASQVVERVWQECNINRAQNKRKFSATTNCTGEEEVPEKVGAWDFVEPSQRSYCVCSRHKSVKQRAGGAQGLTQSMGQPSQPPTKHKTGGEKVDKGEKQQKRPQTPFHHRNLTSDETSMETEAAVGQRLNLRGQDGGRFRSANVTTIPKAPQLQSGRISTGPSEQVNSPQPPPLSPHPCDRGEESGEGMRNPSTPNNQHFYQPPLEPCLIGVKGGGEDAGGLVCLNQHFHSTHPHPHSGTSALTEPPEPTVYVSAAVNLEDDSSLTPWRLYNLPRRKEAEVPTPVLPIDRLRDEILPQELVSVTELMSTSKYTLKVSEERVQRYRARRNQYLSAAITDGEHEHEVDPYAFEEGDDKFVFSSKKDKSGGEREPGNKHKSEDGGAGPSDDAQGAVGHNRMASTSLIHETDLVVSINDLDNLFNSDEDDLAPGSKRLERTDEKGTKGLTSKEPKASTLDHVSCISSAELHQMYPTPPSLEQHIMGYSPMNMCSKEYGSMEPNTGMTMLDGISTLGGHFKIEVEESFCSPKPSEVKDFSFVYKPEQCQPFVGCSMFAPLKTLPSQCLPPIKTPEDCTYRPSWTMGREMLNPVPVMTFLHKDSNIPSVGSTMDQDYSQTYTPQTQAPFVSNSAPPSNSGAGILPSPATPRFAPTPRTPRTPRTPRGPSSVQGSLKYENSDLYSPASTPSTCRPLNSVEPATVPSIPEAHSLYVTLILSESVMNLFKDCNFDSCCICVCNMNLKGADVGVYLSDPISEAQEPCSCGFSAVVNRRYGNGSGLFLEDELDIIGRGTDVSREVEKRFEQLRLSGVGRGDRVPDELILLLQDQCTNPFSAIVTLEHDGVKRGPSGVPVPPCVRVEERDYCSDCYMALKHGREFMDSMSGDKVDEVLVKSTCLHQWAKENTVDMSALCSQDVLRVLMSLQPVLQDAIQKKRTVRSWGVQGPLTWQQFHKMAGRGSYGTDESPEPLPIPTFLVGYEYDFLVLSPFALPYWEKLLLDPFGSQRDIGYLVVCPDNEALLSGAKSFFRDLTSVYESCRLGQHRPISRGYPDGIVLVGGSEAQSLADKPVSDWFLKAASGNSDAFTKLKLYAQVCRHNLAPYLASQPLDSSLLTQPCPPPTSNQPSSTQQPSSASSAASHQGSSSIPTSSSGAGSANASASLHSHSASSGQPASTLSSAKPSSFPPFGSMGSQGSQNGQLGQQAGAQNTGSSGDTSNTQTQGSTEPLESTLEREKVGVPTDGESHAVTYPPAIVLYIVDPFSYEEADGCSGQLDSSVWTLSLLRCYLEMLQSLPPHIQNSISVQIVPCQYLLQPVRGEHCHIYAQHLKSLAFSAFTQCRRPLPFSTNVKSLTGFGPGLAIDTALRSPERPERLRLYTPPFILAPVKDKQTELGETFGEASQKYNVLFVAYCLSHDQRWLLATCTDLYGELLETCIINIDVPNRARRKKGSGRLLGLQKLWEWCLGLVQMTSLPWRVVIGRLGRIGHGELKDWSILLSRRSLQSLSRRLKEMCRMCGISASDTPSILSVCLVAMEPQGSFVIMPDSVSTGSVFGRSTTLNMQTSQLSTPQDTSCTHILVFPTSAFVQITSSSYTNIDTNIDILNGTNDAIGIFDLLDPENELVDPDIINISPPTSPVHSPGSHYHHGGDGSKGPNTNHMPSLEEVPNLLQQPLALGYFVSTAKAGPLPDWFWSACPHAQNQCPLFLKASLHLHVSSVQSDELLHSKHSHPLDSNQTSDVLRYVLEQYNALSWLTCDPATQDRRSCLPLHFVVLNQMYNFIKNML
Length2148
PositionMiddle
OrganismOryzias latipes (Japanese rice fish) (Japanese killifish)
KingdomMetazoa
LineageEukaryota> Metazoa> Chordata> Craniata> Vertebrata> Euteleostomi> Actinopterygii> Neopterygii> Teleostei> Neoteleostei> Acanthomorphata> Ovalentaria> Atherinomorphae> Beloniformes> Adrianichthyidae> Oryziinae> Oryzias.
Aromaticity0.07
Grand average of hydropathy-0.420
Instability index53.73
Isoelectric point5.68
Molecular weight236337.59
Publications
PubMed=17554307

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	IBA:GO_Central

GO - Biological Function
transcription coregulator activity	GO:0003712	IBA:GO_Central

GO - Biological Process
regulation of transcription by RNA polymerase II	GO:0006357	IBA:GO_Central









Interaction





Binary Interactions











Repeat regions





Repeats

>MDP22258
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             3|     129.19|      27|      28|     526|     553|       1
---------------------------------------------------------------------------
  527-  553 (52.67/21.16)	GRISTGPSEQVNS..P.QPPPLSPHPCDRG
  557-  579 (34.17/11.98)	GEGMRNPSTPNNQ..HfYQPPL..EPC...
 2012- 2040 (42.35/14.38)	GDGSKGPNTNHMPslE.EVPNLLQQPLALG
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             3|     113.43|      25|      30|     899|     925|       2
---------------------------------------------------------------------------
  899-  925 (45.31/32.63)	PSEVkdFSFVYKPEQC..QP..FVGCSM.......FAP
  930-  958 (37.11/19.93)	PSQC..LPPIKTPEDCtyRPswTMGREM.......LNP
  960-  988 (31.00/15.26)	PV....MTFLHK.DSN..IP..SVGSTMdqdysqtYTP
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      41.65|      11|      21|    1458|    1476|       3
---------------------------------------------------------------------------
 1458- 1472 (16.53/21.22)	QVCrhnlAPYLASQP
 1480- 1490 (25.12/ 7.07)	QPC....PPPTSNQP
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             3|      77.05|      17|      21|    1357|    1373|       6
---------------------------------------------------------------------------
 1357- 1373 (31.96/17.75)	PY......WEKLLLDPFGSQRDI
 1374- 1396 (20.85/ 8.85)	GYlvvcpdNEALLSGAKSFFRDL
 1398- 1411 (24.24/11.56)	SV......YESCRL...GQHRPI
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      99.79|      29|      30|    1007|    1036|       7
---------------------------------------------------------------------------
 1007- 1036 (51.44/30.28)	GILPSPATPRFAP..TPRTPRtPRTPRGPSSV
 1038- 1068 (48.35/24.11)	GSLKYENSDLYSPasTPSTCR.PLNSVEPATV
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             3|     110.30|      31|      32|    1114|    1145|       8
---------------------------------------------------------------------------
 1115- 1145 (58.16/36.95)	VYLSDPISEAQEPCSCG....FSAVVNRRY......G..NG.SG
 1146- 1180 (28.35/ 9.94)	LFLEDELD......IIGrgtdVSREVEKRFeqlrlsG..VG.RG
 1188- 1216 (23.79/ 9.53)	......ILLLQDQCTNP....FSAIVTLEH.....dGvkRGpSG
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      52.86|      15|      25|     828|     842|       9
---------------------------------------------------------------------------
  828-  842 (29.39/17.45)	HVSCIS.....SAELHQMYP
  850-  869 (23.47/12.39)	HIMGYSpmnmcSKEYGSMEP
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|     130.72|      44|    1199|     134|     213|      10
---------------------------------------------------------------------------
  134-  213 (58.52/99.78)	RSFVRIG..KW..FVK.....PYEKDEKPvnksEHLSCAfTFFLHGESNVctsveinqhqpiyhlteehltlaqqastpfqVILSPFGL
 1304- 1356 (72.20/42.63)	RSWGVQGplTWqqFHKmagrgSYGTDESP....EPLPIP.TFLVGYEYDF...............................LVLSPFAL
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      66.40|      21|    1199|     643|     677|      11
---------------------------------------------------------------------------
  616-  641 (29.59/21.32)	EPPEPTVYVSaavNLEDDssLTPWRL
  651-  671 (36.81/20.85)	EVPTPVLPID...RLRDE..ILPQEL
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      95.10|      26|     190|    1790|    1815|      12
---------------------------------------------------------------------------
 1790- 1815 (46.20/26.36)	DLYGELLETCIINIDVPNRARRKKGS
 1981- 2006 (48.91/28.37)	DPENELVDPDIINISPPTSPVHSPGS
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      55.74|      17|      23|    1498|    1514|      13
---------------------------------------------------------------------------
 1498- 1514 (30.50/14.98)	SASSAA...SHQGSSSIPTS
 1520- 1539 (25.24/11.11)	SANASAslhSHSASSGQPAS
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      65.96|      21|     394|    1217|    1247|      14
---------------------------------------------------------------------------
 1217- 1247 (31.76/46.18)	VPVPPCV........RVEERDYCSdcymalkhGRefMDS
 1612- 1640 (34.19/20.16)	VTYPPAIvlyivdpfSYEEADGCS........GQ..LDS
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      62.31|      20|      26|     441|     462|      15
---------------------------------------------------------------------------
  441-  462 (29.84/22.41)	QGLTQsMGQPsQPPTKHK..TGGE
  466-  487 (32.47/15.33)	KGEKQ.QKRP.QTPFHHRnlTSDE
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      41.57|      13|      26|     401|     413|      18
---------------------------------------------------------------------------
  401-  413 (22.96/14.71)	CTGEEEVPEKV.GA
  427-  440 (18.61/10.29)	CSRHKSVKQRAgGA
---------------------------------------------------------------------------




































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 MDP22258 with Med13 domain of Kingdom Metazoa
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