Was this page helpful?

Sequence 204 Gene Prediction 204h Evidence

     

    Summary

    This predicted protein (204h) matched to  MA3 domain which is part of the  Pre-mRNA-splicing factor.

    The FGENESH predicted protein is longer than the combination of the two predicted by Genemark. One out of that two protein from Genemark do no have any match and the other one matches to the similar results of FGENESH predicted protein, just with higher e-value and shorter matched area. In this case, I think the FGENESH  model is better for this prediction.

    This result has been further confirmed through Maize EST database in NCBI.

    Combind with the MIF4G domain found in protein 204i ,I would like to name it pre-mRNA-splicing factor because this is a two domains (MIF4G and MA3) containing area and the major function of these two domains is the meditation of ribosomes binding during the initiation of eukaryotic translation.

    FGENESH predicted protein

    >FGENESH:   3   3 exon (s) 149005  - 151894   265 aa, chain -

    MEIRDRTETNLVNLRRTIYLTIMSSVDFEEAGHKLMKIKLEPGQEMELCIMLLECCSQER

    TYLRYYGLLGQRFCMINKVYQENFEKCFVQQYSMIHRLETNKLRNVAKFFAHLLGTDALP

    WHVLAYIRLTEEDTTSSSRIFIKILFQELSEHLGIRLLNERLNDPNMQGSFESIFPKDHP

    KNTRFSINFFTSIGLGGITESLREYLKNMPRLIMQQQKPESSESDSSGSESGSESSSSGS

    SSEPESESSPDERDRRRSNKRRKRT

    Blastp results

     

     204h-F-blastp_NBCI.JPG

    Matched to a lot of proteins e-value from e-58 to e-130. I check several of them from different species include Sorghum, rice (indica & Japonica), Vitis vinifera and Arabidopsis lyrata subsp. Lyrata , I found all these genes contain the MIF4G and MA3 domain. Most of the genes have been named ‘pre-mRNA-splicing factor’. Some others have different name such as GenBank: AAX94836.1 named ‘Major Facilitator Superfamily’. However, this gene also contain the MIF4G domain and the MA3 domain beside the MFS domain. Another example is XP_002530492.1, this gene named ‘cell cycle control protein’, however, it only contain two domain: MIF4G and MA3.
     

    The function of  MIF4G & MA3 domain

    MIF4G domain

    MIF4G is named after Middle domain of eukaryotic initiation factor 4G (eIF4G). Also occurs in NMD2p and CBP80. The domain is rich in alpha-helices and may contain multiple alpha-helical repeats. In eIF4G, this domain binds eIF4A, eIF3, RNA and DNA.

    MIF4G domain.png

    MA3 domain

    Domain in DAP-5, eIF4G, MA-3 and other proteins. Highly alpha-helical. May contain repeats and/or regions similar to MIF4G domains. 

    MA3 domain.png

    Reference

    Mol Cell Biol.1996 Dec;16(12):6870-8.

    Functional dissection of eukaryotic initiation factor 4F: the 4A subunit and the central domain of the 4G subunit are sufficient to mediate internal entry of 43S preinitiation complexes.

    Pestova TV, Shatsky IN, Hellen CU.

    Department of Microbiology and Immunology, Morse Institute for Molecular Genetics, State University of New York Health Science Center at Brooklyn, 11203, USA.

    Abstract

    Eukaryotic translation is initiated following binding of ribosomes either to the capped 5' end of an mRNA or to an internal ribosomal entry site (IRES) within its 5' nontranslated region. These processes are both mediated by eukaryotic initiation factor 4F (eIF4F), which consists of eIF4A (helicase), eIF4E (cap-binding protein), and eIF4G subunits. Here we present a functional analysis of eIF4F which defines the subunits and subunit domains necessary for its function in initiation mediated by the prototypical IRES element of encephalomyocarditis virus. In an initiation reaction reconstituted in vitro from purified translation components and lacking eIF4A and -4F, IRES-mediated initiation did not require the cap-binding protein eIF4E but was absolutely dependent on eIF4A and the central third of eIF4G. This central domain of eIF4G bound strongly and specifically to a structural element within the encephalomyocarditis virus IRES upstream of the initiation codon in an ATP-independent manner and with the same specificity as eIF4F. The carboxy-terminal third of eIF4G did not bind to the IRES. The central domain of eIF4G was itself UV cross-linked to the IRES and strongly stimulated UV cross-linking of eIF4A to the IRES in conjunction with either eIF4B or with the carboxy-terminal third of eIF4G.

     

    GeneMark Proteins

    >seq204 1600001-2000000 Xiaoqing Yu 09-16-2010_7|GeneMark.hmm|gene 7|154_aa

    MEKEGGDKMMAGSMARQLTEEDTTSSSRIFIKILFQELSEHLGIRLLNERLNDPNMQGSF

    ESIFPKDHPKNTRFSINFFTSIGLGGITESLREYLKNMPRLIMQQQKPESSESDSSGSES

    GSESSSSGSSSEPESESSPDERDRRRSNKRRKRT

    This one matches to the similar results of FGENESH predicted protein, just with higher e-value and shorter matched area for its short of its length. In this case, decided to use F model.

    >seq204 1600001-2000000 Xiaoqing Yu 09-16-2010_8|GeneMark.hmm|gene 8|67_aa

    MTLSIVPTILPSTAAVRDLDADAMYLEKNHATAALACLGATSATEERAIRAAGARTWGTA

    AAEDGAN

    No good match

     

    Expression confirmation

    Genome DNA unmasked blast maize EST, Input area149005   to 151894  
    28 hits found, all of that e-value <e-47
    The exon distribution is similar to FGENEFH prediction which can give additional evidence that this prediction fairly good.

    204h_F_prediction exon distribution.JPG

    204h_Expression confirmation_Blast Maize EST.JPG

    Was this page helpful?
    Tag page (Edit tags)
    • No tags
    You must login to post a comment.