<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 MDP31957

Description Pre-mRNA-processing protein 40B
SequenceMANNHQYPGIQPFQHPNASSIDLPRGFAPPMNFQFLPTIQAPQSEQVARLSSQNFQCVGRGGTVLSIGYPPQSYAPQLLQSMHHSHERPSQLNQVQVQHVPLGPPTLISQPNVSIASGTSLHQPYVQTPDIGMPGFGGPRALFSYPSATSYEGSRVPPQVTGPSIHSQAQQRASIIHTSAESSIMNPTFEQPKAAFLKPLPSQKALTDWVEHTSADGRKYFFNKRTKKSTWEKPVELMTLFERADARTDWKEHSSPDGRKYYYNKITKQSTWTMPEEMKIVREQAEIASVQGPHAEGIIDASEVLTRSDTASTAAPTGLPSQTSTSEGVEKLTLTSDLKQPASVPGSSSPVENVDRVQMSADETSQLCDTSETDGLSVPVTETSAATLVEKDEISVGNSGDSDDMSTKNANQGSGSGPKESQKPMVESEKVESQTEEKQIHQESFSFNNKLEAVDVFKSLLKSAKVGSDWTWEQAMREIINDKRYGALRTLGERKQAFNEFLLQTKRAAEEERLARQKKLYEDFKRMLEECVELTPSTRWSKTVTMFEDDERFKALEREKDRRNIFEDHVSELKEKGRVKALEDRKRNIIEYKRFLESCNFIKPNSQWRKVQDRLEVDERCSRLEKIDQLEIFQEYLRDLEREEEEKKKIQKEELKKVERKHRDEFHGLLDEHIATGELTAKTIWRDYLMKVKDLPVYSAIASNSSGATPKDLFEDAVEDLKKRDHELKSQIKDVLKLRKVNLSAGSTFDEFKVSISEDIGFPLIPDVRLKLVFDDLLERAKEKEEKEARKQTRQTEKLVDMLRSFKDITASSSWEELKHLVEGSEKCSTIGDESFRKRCFEDYVSLLKEQSNRIKQNKKVPEDVREEHDKGRDKYGREKDRVRERDSDDHHKKGAAGKYNHDMNEPHGKERRRSGRDSHNRHRERHTSVKENDTDHFKESHKAGGGHKKSRHQRGWVSEAEVEGKEKRRRKEEAREHTKEEELEDGECGRY
Length992
PositionUnknown
OrganismArabidopsis thaliana (Mouse-ear cress)
KingdomViridiplantae
LineageEukaryota> Viridiplantae> Streptophyta> Embryophyta> Tracheophyta> Spermatophyta> Magnoliopsida> eudicotyledons> Gunneridae> Pentapetalae> rosids> malvids> Brassicales> Brassicaceae> Camelineae> Arabidopsis.
Aromaticity0.07
Grand average of hydropathy-1.013
Instability index48.49
Isoelectric point6.46
Molecular weight113567.42
Publications
PubMed=10907853
PubMed=27862469
PubMed=17272265
PubMed=19467629
PubMed=22021418

Function

Annotated function Binds the phosphorylated C-terminal domain (CTD) of the largest subunit of RNA polymerase II and functions as a scaffold for RNA processing machineries (PubMed:10907853). May be involved in pre- mRNA splicing (Probable). 
GO - Cellular Component
nucleus	GO:0005634	IDA:TAIR
U1 snRNP	GO:0005685	IBA:GO_Central
U2-type prespliceosome	GO:0071004	IBA:GO_Central

GO - Biological Function
RNA binding	GO:0003723	IBA:GO_Central

GO - Biological Process
mRNA cis splicing, via spliceosome	GO:0045292	IEA:InterPro
mRNA splicing, via spliceosome	GO:0000398	IBA:GO_Central









Interaction





Binary Interactions











Repeat regions





Repeats

>MDP31957
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             3|     161.72|      39|      39|     207|     245|       1
---------------------------------------------------------------------------
  196-  236 (70.74/41.03)	FLKPLPSQKalTDWVEHTSADGRKYFFNKRTKKSTWEKPVE
  237-  277 (69.95/40.49)	LMTLFERADarTDWKEHSSPDGRKYYYNKITKQSTWTMPEE
  457-  474 (21.03/ 7.16)	FKSLLKSAKvgSDW....................TWEQ...
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             6|     425.00|      63|      65|     514|     576|       2
---------------------------------------------------------------------------
  514-  576 (103.12/56.69)	LAR.QK........KLYEDFKRMLE.ECV...ELTPSTRWSKTVTMFEDDERFKALEREKD...R...RNIFEDHVSEL....KEK
  582-  647 (80.27/42.57)	LED.RK........RNIIEYKRFLE.SCN...FIKPNSQWRKVQDRLEVDERCSRLEK.ID...Q...LEIFQEYLRDLereeEEK
  648-  722 (60.44/30.31)	KKI.QKeelkkverKHRDEFHGLLD.EHIatgELTAKTIWRDYLMKVKDLPVYSAIASNSSgatP...KDLFEDAVEDL....K..
  724-  784 (61.59/31.03)	..R.DH........ELKSQIKDVLKlRKV...NLSAGSTFDEFKVSISEDIGF.PLIPDVR...L...KLVFDDLLERA....KEK
  788-  851 (84.76/45.35)	EARkQT........RQTEKLVDMLR.SFK...DITASSSWEELKHLVEGSEKCSTIGDESF...R...KRCFEDYVSLL....KEQ
  855-  891 (34.82/14.49)	IKQ.NK........KVPEDVR...........E.............EHDKGRDK.YGREKD...RvreRD.SDDH...........
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             3|     154.40|      32|      33|     100|     131|       3
---------------------------------------------------------------------------
   58-   92 (46.56/26.11)	VGRGGTVLsIGYPPQSYAPQllQSMHHSHERPSQL
  100-  131 (56.18/33.01)	VPLGPPTL.ISQPNVSIASG..TSLHQPYVQTPDI
  136-  165 (51.66/29.77)	FG.GPRAL.FSYPSATSYEG..SRV.PPQVTGPSI
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             3|     117.58|      28|      28|     324|     351|       4
---------------------------------------------------------------------------
  307-  334 (42.47/25.71)	RSDTASTAAPTGLPSQT...STSEGVEKLTL
  335-  359 (39.86/23.66)	TSDLKQPASVPGSSSPV...E...NVDRVQM
  364-  394 (35.25/20.04)	TSQLCDTSETDGLSVPVtetSAATLVEKDEI
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|     128.32|      38|      39|     902|     940|       5
---------------------------------------------------------------------------
  902-  940 (66.05/45.38)	HDMNEPHGKERRRSGRDSHNR..HRERHTSvKENDTDHFKE
  942-  981 (62.27/38.13)	HKAGGGHKKSRHQRGWVSEAEveGKEKRRR.KEEAREHTKE
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      42.56|      11|      27|       4|      14|       7
---------------------------------------------------------------------------
    4-   14 (24.28/16.36)	NHQY.PGIQPFQ
   32-   43 (18.28/10.46)	NFQFlPTIQAPQ
---------------------------------------------------------------------------




































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 MDP31957 with Med35 domain of Kingdom Viridiplantae
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