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Sequence 204 Gene Prediction 204c Evidence

     

    FGENESH Prediction

    >FGENESH:   1  11 exon (s)  32419  -  43858   685 aa, chain -
    MAPPRTLLRRRALNAQRGRMAPGFWYMIWNLHGEASSSVNHGNYDDAEVIEEPNEDDDIS
    GLLRDLAAGLDDKGDFEDNISIIGCCDELAAIEKLFSEKLLTQYFCNIFNMPITYVNRYL
    MRLKGSVHTKSHCEGSIMEWSMFTECLTFCARYLHGETQLNHQVRYEYDEDCTTTPFFHT
    IGQGLAGKCLVNLDHKTWLQAHRYVLFNYDNITPYLDDKMTFAASMLTICPQLVIEIKEI
    SIAYSMNPFMSGLGCIRDIDGYFVDPKNLKKIYKRIHNTSDVATEGHNLRARPQKNCVEN
    GNEQINEDLGCESIGDFLCDNEDSRNIAEKKRKGRGITRLDEIFARKPSMPKIKVELNKY
    GQPIGDNCRRFSSALGCHVRRKLSVGCSDWRLVDPQKKYEVWEDMMTRSEIAKECRSKVG
    NHHTSGNKSFACSAHELANKLRRSPRRDEVYIKTHTRKNGVPSRHAEPIINKLKAIVEAH
    PELKQRTIQEGDAFAAACGEKEPRGRVCALGLGPTPQDVGTPGLKCYTPTRLQMEGLAHK
    KAKCEKVALQQRITELEQQMQEERVARELQDMELISHNGSNSRQTGSRRYEEHDVEAHHD
    AQFVEDEDCAENHINHHCDDGEQHHQNGPVGAAPTVQHHQSSPVGAAPTVQRHQSSHVGA
    APTVQRHQNNHVRAAQQFNTIKIVL

    BlastP result

    204c_directly_blastp.jpg

    conserved dormain of transposase_24

    This dormain start from 400aa to 516aa of FGENESH perdicted protein sequence

    conserved dormain of transposase_24.jpg

    Further analysis of the blast results

    First match

    First match is a Sorghum putative protein. However, it contains a trasposase domain and belongs to super family. The following is its sequence:


    >gi|242042521:514-641 hypothetical protein SORBIDRAFT_01g049735 [Sorghum bicolor]
    NDDDWNFLKNHWSSPESEAQTEIAKANRAKLSIHHTTGSKSFACNGHELAIKLGRPPRRDELYIKTHTRK
    NGIASRNAEPVINKLKAIIEAQPELTERTIQEGDAFAVACGKKEPKRRVRVLGLGPTP

    Blastp result using Sorghum putative protein as query
    The result indicate this active part is do a transposase_24 family

    First match blastp result.jpg

    Second match

    The second match is another Sorghum hypothetical protein SORBIDRAFT_07g004115 [Sorghum bicolor]
    This match also contain s transpontase 24 domain in the range of 232aa -358aa

    Third match

    The third match is a putative Rice protein which also contain a Transposase_24 domain in the range of 255aa - 382aa 

    Splicing and exons distribution

    Splicing and exons distribution Confirmed through using the Genome DNA sequence (32243-44869 masked) blastn in NCBI. After comparison to FGENESH prediction result, we can see the exons distritution are very similar.


       204c_Genome_32243-44869_masked_blastn_result.jpg

    204c_FGENESH_prediction_with_conserved dormain.jpg

     

    Expression confirmation

    Genome DNA unmasked blast maize EST
    Using sequence 204_32243-44869 maize EST in NCBI using high similarity
    Found more than 50 hits e-value = 0
    Good match and FGENESH predicted protein lost four exons or UTR in area around 7827-8469, 8570-9100, 9872-10533, 10662-11259, corresponding to genome region: 40070-40712, 40813-41343, 42115-42776, 42905-43502

    204c_Expression confirmation_blast EST.JPG
     

    Conclusion

     

    Based on the evidence about, I have relatively strong evidence to draw a conclusion that this should be a Transposase_24 domain containing gene.
     

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