<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 MDP04102

Description Mediator of RNA polymerase II transcription subunit 16
SequenceMIHILDTEHPWEVHSVSSGHSEAITCLEWDQSGSRLLSADADGQIKCWSMADHLANSWESSVGSQVEGDPIVALSWLHNGVKLALHVEKSGASSFGEKFSRVKFSPSLTLFGGKPMEGWIAVTVSGLVTVSLLKPSGQVLTSTESLCRLRGRVALADIAFTGGGNIVVAAADGSSASPVKFYKVCVSVVSEKCRIDTEILPSLFMRCTTDPNRKDRFPAITHLKFLARDMSEQVLLCASSQTSSLVECWSLRKEGLPVNNIFQQISPVVGDKQPMILKWRILSATNDLDRVSAVALPKLPISLTNTDLKVASDTQFYPGLGLALAFQDGSVHMVHRLSLQTMAVFYSSAPRSLDEPALKRPRTTGPAVHFKAMQLSWTSLALVGIDNHGKLSMLRISPSLGHALEPKLALQHLLFLLEYCMVTGYDWWDILLHVQPGMVQSLVERLHEEYTRQKPALQQVLSTRILAMKASLCKLSPCTMARVCDYHTKLFLMAITSTLKSLLRPHFLNTPDKSPGDRLAEICAKITDVDIDKVMINLKTEEFVLDMNTLQALQQLLQWVGDFVLYLLVSLPNQGAEHSSGLPDSASHGPVLKSHVSPDFTKGSALRPGHSFLRDGASLGMLRELMVVIRIWGLLKPSCLPVYTATSDTQDSMSLLFRLLTKLWICCRDEGPASEPDEGLVDECCLLPSQLLVPSLDWLPASDGLVSRLQPKQPLRLRFGRAPTLPSSTSILQLDGLTRAPGQPKIDHLRRLHLGAYPTEECKACTRCGCVTMLKSPNKTTAVKQWEQRWIKNCLCGGLWRRVPLSCS
Length808
PositionTail
OrganismRattus norvegicus (Rat)
KingdomMetazoa
LineageEukaryota> Metazoa> Chordata> Craniata> Vertebrata> Euteleostomi> Mammalia> Eutheria> Euarchontoglires> Glires> Rodentia> Myomorpha> Muroidea> Muridae> Murinae> Rattus.
Aromaticity0.06
Grand average of hydropathy0.017
Instability index49.05
Isoelectric point8.39
Molecular weight88975.39
Publications
PubMed=15057822

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

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

GO - Biological Process
positive regulation of transcription initiation from RNA polymerase II promoter	GO:0060261	ISO:RGD
positive regulation of transcription, DNA-templated	GO:0045893	ISO:RGD









Interaction





Binary Interactions











Repeat regions





Repeats

>MDP04102
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|     103.86|      31|      36|     688|     723|       1
---------------------------------------------------------------------------
  688-  723 (54.16/36.70)	PSQLLVPSLDWLPASDGlvsrlQPK.QPL.RLRFGRAP
  726-  758 (49.69/24.88)	PSSTSILQLDGLTRAPG.....QPKiDHLrRLHLGAYP
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      97.79|      31|      36|      60|      95|       2
---------------------------------------------------------------------------
   17-   50 (49.04/23.20)	SSGHSEAITCLEWDQSGSRL.LSADADGQIkcwSM
   64-   95 (48.75/23.57)	SQVEGDPIVALSWLHNGVKLaLHVEKSGAS...SF
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      83.16|      24|      36|     107|     130|       3
---------------------------------------------------------------------------
  107-  130 (42.17/25.46)	SLTLFGGKPMEGWIAVTVSGLVTV
  145-  168 (40.99/24.56)	SLCRLRGRVALADIAFTGGGNIVV
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             3|     200.65|      54|      96|     354|     408|       4
---------------------------------------------------------------------------
  354-  408 (89.00/57.44)	DEPALKRPRTTgPAVHFKA..MQ..LSWTSLALV.GIDNHGKLSMLRISPSLGHALEPKL
  410-  442 (26.68/10.44)	.....................LQhlLFLLEYCMVtGYDWWDIL..LHVQPGMVQSL....
  453-  507 (84.97/50.23)	QKPALQQVLST.RILAMKAslCK..LSPCTMARV..CDYHTKLFLMAITSTLKSLLRPHF
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      84.76|      28|      31|     602|     632|       6
---------------------------------------------------------------------------
  602-  632 (41.67/32.16)	KGSALrPGHSFLRDGA.SLGMLRELMVviRIW
  636-  664 (43.09/23.15)	KPSCL.PVYTATSDTQdSMSLLFRLLT..KLW
---------------------------------------------------------------------------




































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 MDP04102 with Med16 domain of Kingdom Metazoa
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