Human pre-mRNA 3'-end processing machinery database

Sequences of human proteins were taken from UniProt.

Molecular weights and theoretical isoelectric points were calculated by Isoelectric Point Calculator.

Protein disorder was predicted using GeneSilico MetaDisorder.

Secondary structure is taken from GeneSilico Fold Recognition metaserver. It is arithmetic consensus based on predictions of psipred, prof, jnet, sable, proteus, sspro4, psspred, spineX, raptorxss, SPARROW, *SPARROW, HMMSTR, porter, spine, nnssp, pssfinder, sspal, ssp, sspred, netsurfp, soprano. For more details simply see secondary structure raw output. Three letter alphabet is used: H - for α helix, E - for β sheet and '-' for others.

Low complexity were calculated by SEG.

Domains are taken from PFAM.

Domains boundaries are predicted by DomainSVM.

Models:
Templates are based on predictions from GeneSilico Fold Recognition metaserver. It allows to automatic search for remote homology by using PSI-BLAST, COMA, PRC, COMPASS, CSBLAST, HHSEARCH, HHBLITS, FFAS, MGenThreader, Phyre, Sp3 and PCONS.
Next, based on alignments to known structures from PDB two kind of models are build. Crude models are simple models based on coordinates taken from template. More advanced models are build by MODELLER program.

Predictions, models and other type of data are available as flat files in download section.

WWW:

General review papers:

Mandel CR, Bai Y, Tong L et al. et al. Protein factors in pre-mRNA 3"-end processing. Cell Mol Life Sci 2008 65(7-8):1099-122, doi: 10.1007/s00018-007-7474-3, PMID: 18158581.
Millevoi S, Vagner S. Molecular mechanisms of eukaryotic pre-mRNA 3" end processing regulation. Nucleic Acids Res 2010 38(9):2757-74, doi: 10.1093/nar/gkp1176, PMID: 20044349.
Danckwardt S, Hentze MW, Kulozik AE et al. et al. 3" end mRNA processing: molecular mechanisms and implications for health and disease. EMBO J 2008 27(3):482-98, doi: 10.1038/sj.emboj.7601932, PMID: 18256699.
Chan S, Choi EA, Shi Y et al. et al. Pre-mRNA 3"-end processing complex assembly and function. Wiley Interdiscip Rev RNA 2011 2(3):321-35, doi: 10.1002/wrna.54, PMID: 21957020.
Yang Q, Doublie S. Structural biology of poly(A) site definition. Wiley Interdiscip Rev RNA 2011 2(5):732-47, doi: 10.1002/wrna.88, PMID: 21823232.
Shi Y, Di Giammartino DC, Taylor D et al. et al. Molecular architecture of the human pre-mRNA 3" processing complex. Mol Cell 2009 33(3):365-76, doi: 10.1016/j.molcel.2008.12.028, PMID: 19217410.

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Contact: Lukasz Kozlowski

This work was supported by Polish Ministry of Science and Higher Education (grant NN301 190139).