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Gene 7-4

    Table of contents
    1. 1. Synopsis
      1. 1.1. Predicted protein models

    Synopsis

    Based on EST evidence, Neither the Genemark nor FGENESH prediction is completely correct.  EST evidence suggests a continuous transcript from 71953 - ca. 82440 on the negative strand.  In plants, LEUNIG is usually present as two homologs, referred to as LEUNIG (LUG) and LEUNIG-homolog (LUG).  The genes have at least partial functional overlap based on knockout analysis (Sitarman et al., 2008). The gene model prsented below is an end to end match with other plant Leunig genes.

    LEUNIG is a transcriptional co-repressor that lacks a DNA interaction domain.  Interaction specificity is usually provided by an adaptor protein such as SEUSS (SEU).  The LUG/SEUSS complex appears act similarly to the yeast  Tup1/Ssn6 complex, and is believed to be a repressor of AGAMOUS (AG) (Liu & Meyerowitz, 1995).  Lug/luh mutants also show defects in leaf growth and polarity (Stahle et al., 2009), and possibly act in conjunction with YAB proteins.

     

    Sitaraman J, Bui M, Liu Z. LEUNIG_HOMOLOG and LEUNIG perform partially
    redundant functions during Arabidopsis embryo and floral development. Plant
    Physiol. 2008 Jun;147(2):672-81.
    
    Stahle MI, Kuehlich J, Staron L, von Arnim AG, Golz JF. YABBYs and the
    transcriptional corepressors LEUNIG and LEUNIG_HOMOLOG maintain leaf polarity and
    meristem activity in Arabidopsis. Plant Cell. 2009 Oct;21(10):3105-18.
    Liu Z, Meyerowitz EM. LEUNIG regulates AGAMOUS expression in Arabidopsis
    flowers. Development. 1995 Apr;121(4):975-91

     

    Gene Model

                              GU    FU   EST
    71953 72256   UTR        +++          18
    72257 72400   exon 18    +++   -++    18          
    72736 72942   exon 17    -++   +++     7     
    73430 73549   exon 16    -++   +++    18    
    73650 73814   exon 15    +++   +++    23, intron between 14 and 15 retained in two cases, creates stop codons   
    73902 74051   exon 14    ++-   +++    25           
    74136 74245   exon 13          +++    10, skipped in 4 cases, not multiple of 3, changes frame
    74629 74746   exon 12    +++   +++    13, skipped in 3 cases, not multiple of 3, changes frame        
    74853 75083   exon 11          +++    22 
    75647 75844   exon 10    ++-   +++    16   
    77217 77513   exon 9     +++   +++    16        
    77905 77954   exon 8     +++   +++    11, skipped along with exon 7 in 1 case
    78111 78186   exon 7     +++   +++     8   
    78290 78380   exon 6     -+-   -+-     8
    79113 79287                    ---     0     
    79556 79641   exon 5           +++    11
    79739 80149   exon 4           +++    18    
    80684 80793   exon 3     +++   +++     8, skipped in 1 case, not multiple of 3, changes frame    
    80917 81014   exon 2     ++-   +++    11
    82020 82051   exon 1           +++     3
    82052 82688   UTR              +++     3, up to 82440
    

    GU and FU indicate Genemark and FGENESH predictions respectively, using unmasked sequences.  The symbols indicate whether the left boudary of the exon is correct (+), the predicted exon overlaps a true exon (+), and whether the right boundaryn is correct (+).  The values in the EST column indicate the number of supporting ESTs for the exon.

    Final Protein Sequence

    MSQTNWEADKMLDVYIYDYFMKRNLQATAKAFQAEGKVSSDPVAIDAPGGFLFEWWSVFW
    DIFIARTNEKHSDVAASYIETQLMKAREQQHQQQQQIPQQRQQQPQHIQMQQMLLQRAVQ
    QQQQQQQQQQQQQQQQQQQQQQQQPQQQQQQQLQQQQLQQQRRDGSHLLNGSANGISGNN
    PLMRQNQSTANVMATKMYEERLKVPSERDSLEEASLKQRYGENAGQLLDSNEASLLKAAS
    SAQSSGQILHGTVGGLSGTLQQVQARSPQLPGPAQASIKTEINPILTPRAAGPEGSFIGA
    QGSNQAGNNLTLKGWPLTGLEQLRSGILQQKSFIHNQQQLQQQIQMLTPQQQQQLMLHAQ
    QNMSSPTSSDVDNRRLRMMLNRNAVLGRDGQTNSGSDIIPNIGSPSQSGGDIDMLIKKLA
    QQQQLLQQQSNSQQLPQQHQLQQPAVSSQQSQSSNQHLQQEKPGIGSMPADGGIPNSFGG
    AEQTAKKRKKPGSSSGRANSSGTANTAGPSPSSAPSTPSTHTPGDVMSVPQLQQNGGSAK
    PMVMFGSDGTGSLTSPANPLDDVDRLLEDGSLDDNVESFLSQDDMDPRDNLGRCMDASKG
    FGFSEVAKARASTAKVVCCHFSADGKLLATGGHDKKVTLWCTDSLNPKSYLEEHSFLITD
    VRFSPSMSRLATSSFDKTVRVWDADNTDYSLRTFTGHSATVMSLDFHPNKEDMICSCDSD
    GEVRSWSINNGSCLTCVKVFKGGATQMRFQPRKGKYLAAASDKAIYILDGETQHACRSPL
    QGHNKNIQSLCWDSAGEYLASVSEDSVRIWSFSSGREGEFVHELNRSGNQFHSCVFHPTY
    QSLLVIGCYESLELWDIREKNTMTFNNAHDGLVAALASSSATGKVASVSHDRTLKLWK

     

    genemark-4m model

    7-4m_blastp.jpg

    Typical alignment to Leunig like portion

    ref|XP_002458130.1|  hypothetical protein SORBIDRAFT_03g027390 [Sorghum bicolor]
            gb|EES03250.1|  hypothetical protein SORBIDRAFT_03g027390 [Sorghum bicolor]
            Length=716
     
     GENE ID: 8082520 SORBIDRAFT_03g027390 | hypothetical protein [Sorghum bicolor]
    (10 or fewer PubMed links)
     
     Score =   426 bits (1095),  Expect = 4e-134, Method: Compositional matrix adjust.
     Identities = 290/527 (55%), Positives = 330/527 (63%), Gaps = 131/527 (25%)
    Query  394  IKTEINPILTPRAAGPEGSFIGAQGSNQAGNNLTLKGWPLTGLEQLRSGILQQKSFIHNQ  453
                I+TEINP+LTPRAAG EGS IG QGSNQAGNNLTLKGWPLTGL+  RSGILQQK F+ + 
    Sbjct  198  IRTEINPVLTPRAAGTEGSLIGLQGSNQAGNNLTLKGWPLTGLDHFRSGILQQKPFMQSP  257
    
    Query  454  QQLQQQIQMLTPQQQQQLMLHAQQNMSSPTSSDVDNRRLRMML-NRNAVLGRDGQTNSGS  512
                QQ  QQ+Q LTPQQQQQL+LHAQQN+SS  S+DVD RRLRM+L NRN VLG+DGQTNSG 
    >Sbjct  258  QQ-FQQLQFLTPQQQQQLLLHAQQNLSSSMSNDVDTRRLRMLLNNRNVVLGQDGQTNSGG  316
    
    Query  513  DIIPNIGSPSQSGG---DIDMLIKQSQSSNQHLQQEKP-GIGSMPADGGIPNSFGG--AE  566
                DIIPNIGSP QSGG   DID+LIK   SS       KP GI  +         F     +
    Sbjct  317  DIIPNIGSPGQSGGSRNDIDILIKLDFSS-------KPIGIYMLIQTFSFKVPFNTLLCQ  369
    
    Query  567  QD--------DVDRLLEDGSLDDNVESFLSQDDMDPRDNLGRCMDASK------------  606
                QD        DVDRLLEDGSLD+NVESFLSQDDMDPR+ +G  MD+SK            
    Sbjct  370  QDNKNPQLQGDVDRLLEDGSLDENVESFLSQDDMDPRETMGHSMDSSKGLGFTEVAKARA  429
    
    Query  607  -------------------------------DSLNPKSYLEEHSFLITDVRFSPSMSRLA  635                                           D L                                                  KS LEEHS LITDVRFSP M+RLA
    Sbjct  430  STNKVVCCHFSLDGKLLATGGHDKKVVLWFTDVLKRKSALEEHSLLITDVRFSPGMTRLA  489
    
    Query  636  TSSFDKTVRT------DYSLRTFTGHSATVMSLDFHPNKEDMICSCDSDGEVRSWSINNG  689
                TSSFDKTVR       DYSLRTFTGHSA+VMSLDFHPNKED+ICSCDSDGEVR WSINNG
    Sbjct  490  TSSFDKTVRVWDADNPDYSLRTFTGHSASVMSLDFHPNKEDIICSCDSDGEVRCWSINNG  549
    
    Query  690  SCLTCVKVFKGGATQMRFQPRKGK--------------------------GTIRIFNRFV  723
                SC+TCV+VF GGATQ+RFQPR+GK                          G I+I     
    Sbjct  550  SCVTCVRVFNGGATQLRFQPRQGKYLAAASEKGISILDAETLQVCRTPLQGHIQIIQSVC  609
    
    Query  724  ----GILLANISLLSVKTRS-----------------EYGHSVL------------DVKS  750
                    G  LA++S  SV+  S                    HS +              +S
    Sbjct  610  WDAAGNYLASVSEDSVRVWSFTSGNDIECIHELNCSGNKFHSCVFHPSYPNLLIIGCYES  669
    
    Query  751  LELWDIREKNTMTFNNAHDGLVAALASSSATGKVASVSHDRTLKLWK  797
                LELWD+REKNT+T +NAH+G+VAALA+SSA+G VASVSHD+ +KLWK
    Sbjct  670  LELWDLREKNTVTISNAHEGMVAALAASSASGLVASVSHDQLVKLWK  716
    

    Score =   126 bits (316),  Expect = 5e-27, Method: Compositional matrix adjust.
    Identities = 61/82 (74%), Positives = 66/82 (80%), Gaps = 3/82 (4%)

    Query  298  KRPDIFVVNSF-GSGFQATAKAFQAEGKVSSDPVAIDAPGGFLFEWWSVFWDIFIARTNE  356
                K  D+++ + F     QATAKAFQAEGKVSSDPVAIDAPGGFLFEWWSVFWDIFIARTNE
    Sbjct  10   KMLDVYIYDYFVKRNLQATAKAFQAEGKVSSDPVAIDAPGGFLFEWWSVFWDIFIARTNE  69
    
    Query  357  KHSDVAASYIEALCNKFRPGAL  378
                KHSDVAASYIE     F+P  L
    Sbjct  70   KHSDVAASYIER--TFFKPCGL  89
    

    Predicted protein models


    >FGENESH:[mRNA]  14  21 exon (s)  69041  -  82051  3333 bp, chain -
    ATGTCGCAAACTAACTGGGAGGCGGACAAGATGCTGGATGTATACATATATGATTATTTT
    ATGAAGAGAAATTTGCAGGCAACTGCAAAGGCCTTCCAAGCAGAGGGAAAGGTCTCTTCG
    GATCCAGTTGCAATTGACGCACCTGGTGGATTTCTTTTCGAGTGGTGGTCGGTTTTTTGG
    GATATATTCATAGCAAGAACTAATGAGAAGCATTCAGATGTTGCAGCCTCATATATTGAG
    GTACAAATGAGCACATTATTCCAGACTCAGCTCATGAAAGCCAGGGAGCAACAACATCAA
    CAGCAGCAACAGATCCCTCAACAGAGGCAGCAGCAGCCACAGCATATACAAATGCAACAA
    ATGCTGTTGCAAAGAGCTGTGCAGCAGCAGCAGCAGCAGCAGCAACAACAACAACAACAA
    CAACAACAACAACAACAACAACAACAACAACAACAACCTCAGCAGCAGCAGCAGCAGCAG
    CTGCAACAGCAACAGCTGCAACAGCAGCGTAGAGATGGTTCTCATCTTCTCAATGGTTCT
    GCAAATGGAATTTCTGGAAACAATCCTTTAATGCGGCAAAACCAAAGTACTGCAAATGTT
    ATGGCAACAAAAATGTACGAGGAAAGGTTAAAGGTACCTTCCGAGAGAGACTCTTTGGAA
    GAGGCATCATTGAAGCAAAGGTACGGAGAGAATGCTGGGCAACTACTTGATTCAAATGAA
    GCATCATTGTTGAAAGCAGCTTCAAGCGCGCAATCCTCAGGGCGTCTCCTAGGCGACGCC
    CTAGGCGTCCAGGCGCTCACAAACTCTGGATGTCCACCATCACCATGCAGAATGAGACAC
    GGAGGAAGGGAGGAGGGAGAGGAAGATGAGGGAAAGCGTTCCAATGTTGATTTCGCGGGG
    AGAGTGGGTGTCGATCTGGATGGGGAAGTGGTGGTGGCACTCTGCAACAAGTTCAGGCCA
    GGAGCCCTCAACTTCCTGGTCCTGCTCAGGCTAGTCTTTTTTGGTACCCTGGGTATCAAG
    ACAGAGATTAATCCCATTCTGACCCCCAGAGCTGCAGGCCCAGAAGGGTCATTTATAGGT
    GCTCAAGGATCTAATCAAGCTGGGAACAATTTGACTCTGAAAGGATGGCCACTCACGGGA
    CTTGAGCAACTTAGGTCAGGAATTCTTCAGCAGAAGTCGTTTATACATAATCAACAGCAA
    TTGCAGCAGCAAATCCAGATGCTGACTCCACAGCAGCAGCAGCAGCTTATGCTGCATGCT
    CAGCAAAATATGTCTTCACCAACATCTAGTGATGTCGACAACAGAAGATTGAGGATGATG
    CTAAATAGAAATGCTGTTCTTGGCCGGGATGGGCAGACAAACAGTGGTAGTGATATTATT
    CCAAATATTGGCTCTCCTAGTCAAAGTGGTGGCGATATAGATATGCTTATAAAGAAGAAA
    CTTGCTCAGCAGCAGCAACTATTACAACAGCAAAGCAATAGCCAACAGCTCCCACAGCAA
    CATCAGCTTCAGCAACCTGCTGTCTCTAGCCAGCAATCTCAAAGTTCAAATCAACATCTT
    CAACAAGAAAAGCCAGGAATTGGAAGTATGCCTGCTGATGGGGGCATACCAAATTCATTT
    GGGGGAGCTGAACAGACAGCAAAGAAGAGAAAGAAGCCAGGCTCATCCTCTGGTAGAGCT
    AATAGTTCAGGCACAGCCAATACTGCTGGTCCCTCTCCAAGTTCTGCACCATCGACACCT
    TCCACTCATACACCAGGAGACGTGATGTCTGTGCCACAGCTGCAGCAGAATGGCGGTTCA
    GCTAAACCCATGGTAATGTTTGGCTCTGACGGAACTGGGAGCTTGACATCTCCAGCAAAC
    CCATTGGATGATGTTGACCGCTTGCTAGAAGATGGCTCATTGGATGATAATGTTGAATCT
    TTTCTATCACAGGATGACATGGATCCTAGGGACAACTTGGGGCGATGCATGGATGCTAGT
    AAAGGGTTTGGTTTTTCTGAGGTTGCCAAAGCACGCGCAAGCACAGCCAAAGTTGTCTGT
    TGCCACTTCTCAGCTGATGGTAAACTGCTTGCTACTGGTGGTCATGATAAAAAGGTCACT
    TTGTGGTGTACAGATTCTCTGAACCCTAAATCTTATCTGGAAGAGCACTCGTTTCTTATC
    ACTGATGTTAGATTTAGCCCAAGCATGTCACGCCTTGCTACATCCTCCTTTGACAAAACT
    GTGCGGGTTTGGGATGCAGATAATACTGACTATTCACTACGAACTTTCACGGGCCATTCA
    GCAACTGTTATGTCACTTGATTTTCATCCAAATAAAGAGGATATGATATGCTCCTGTGAT
    AGTGATGGGGAAGTGCGCAGCTGGAGCATAAATAATGGTAGCTGTTTGACATGTGTTAAG
    GTGTTTAAGGGAGGTGCTACTCAGATGAGATTTCAACCTCGTAAGGGAAAGTATCTAGCA
    GCGGCCTCAGATAAAGCTATCTACATACTTGATGGGGAGACACAACATGCTTGTAGAAGT
    CCCTTGCAGGGGCACAATAAGAATATTCAATCGCTTTGTTGGGATTCTGCTGGCGAATAT
    CTCGCTTCTGTCAGTGAAGACTCGGTCAGAATATGGTCATTCAGTTCTGGACGTGAAGGT
    GAATTTGTGCATGAATTGAATCGCAGCGGAAATCAATTCCACTCGTGTGTTTTCCACCCA
    ACTTATCAGTCATTGCTAGTGATTGGTTGTTACGAGTCTTTGGAACTTTGGGACATAAGG
    GAGAAGAACACCATGACCTTCAACAATGCGCATGACGGTTTGGTTGCAGCCCTGGCATCA
    TCCAGTGCTACAGGGAAGGTTGCCTCAAACAACCCTAGAGTCGCCGGCATTGGCGACGAC
    CATGAGGTCCCCCTATTTGAAGATGGACAGCGCCGTGCAGCCGCTCTGGACCGTGTCCAA
    GCGGCGGCTGCGCCGGAGCTTACCGAACACAGCGACACATGCAGTCACGTAGTACTGCTT
    CCAGAGGTCGAACTGGCAGTCGCCAAGCTTCTTTTCGTCGTCGATGAGCGACGCCAACGC
    GAGCGCCTCCTGCCAGTGGTGTTTGTTCGGGGTTTCCAAGCACTTTATGAAGTTAAGCCA
    AAAGGAGCAAAAGAGACTTTGATTAAGAAAGGAGAAGATGGACTGGTCTGCGGTCTGGTG
    CGGCGGTGCCACCCACCGGACAGTCCTATGTGCATCGGACAGTCCAATGCACGGTCCGAC
    CAAGGGGCAGCTCTCGGGAAATTTCAGCCAGTGTTGGCTATAAATCACCGGACAGTCCGC
    GCGGAGCGCCGGACAGTCCGGTGTGCCAGCTAG
    >FGENESH:  14  21 exon (s)  69041  -  82051  1110 aa, chain -
    MSQTNWEADKMLDVYIYDYFMKRNLQATAKAFQAEGKVSSDPVAIDAPGGFLFEWWSVFW
    DIFIARTNEKHSDVAASYIEVQMSTLFQTQLMKAREQQHQQQQQIPQQRQQQPQHIQMQQ
    MLLQRAVQQQQQQQQQQQQQQQQQQQQQQQQQPQQQQQQQLQQQQLQQQRRDGSHLLNGS
    ANGISGNNPLMRQNQSTANVMATKMYEERLKVPSERDSLEEASLKQRYGENAGQLLDSNE
    ASLLKAASSAQSSGRLLGDALGVQALTNSGCPPSPCRMRHGGREEGEEDEGKRSNVDFAG
    RVGVDLDGEVVVALCNKFRPGALNFLVLLRLVFFGTLGIKTEINPILTPRAAGPEGSFIG
    AQGSNQAGNNLTLKGWPLTGLEQLRSGILQQKSFIHNQQQLQQQIQMLTPQQQQQLMLHA
    QQNMSSPTSSDVDNRRLRMMLNRNAVLGRDGQTNSGSDIIPNIGSPSQSGGDIDMLIKKK
    LAQQQQLLQQQSNSQQLPQQHQLQQPAVSSQQSQSSNQHLQQEKPGIGSMPADGGIPNSF
    GGAEQTAKKRKKPGSSSGRANSSGTANTAGPSPSSAPSTPSTHTPGDVMSVPQLQQNGGS
    AKPMVMFGSDGTGSLTSPANPLDDVDRLLEDGSLDDNVESFLSQDDMDPRDNLGRCMDAS
    KGFGFSEVAKARASTAKVVCCHFSADGKLLATGGHDKKVTLWCTDSLNPKSYLEEHSFLI
    TDVRFSPSMSRLATSSFDKTVRVWDADNTDYSLRTFTGHSATVMSLDFHPNKEDMICSCD
    SDGEVRSWSINNGSCLTCVKVFKGGATQMRFQPRKGKYLAAASDKAIYILDGETQHACRS
    PLQGHNKNIQSLCWDSAGEYLASVSEDSVRIWSFSSGREGEFVHELNRSGNQFHSCVFHP
    TYQSLLVIGCYESLELWDIREKNTMTFNNAHDGLVAALASSSATGKVASNNPRVAGIGDD
    HEVPLFEDGQRRAAALDRVQAAAAPELTEHSDTCSHVVLLPEVELAVAKLLFVVDERRQR
    ERLLPVVFVRGFQALYEVKPKGAKETLIKKGEDGLVCGLVRRCHPPDSPMCIGQSNARSD
    QGAALGKFQPVLAINHRTVRAERRTVRCAS
    

     

    >Sat Oct 20 07:36:42 EDT 2012_10|GeneMark.hmm|gene 10|624_aa
    MEMATAKAFQAEGKVSSDPVAIDAPGGFLFEWWSVFWDIFIARTNEKHSDVAASYIETQL
    MKAREQQHQQQQQIPQQRQQQPQHIQMQQMLLQRAVQQQQQQQQQQQQQQQQQQQQQQQQ
    QPQQQQQQQLQQQQLQQQRRDGSHLLNGSANGISGNNPLMRQNQSTANVMATKMYEERLK
    VPSERDSLEEASLKALCNKFRPGALNFLVLLRLVFFGTLGIKTEINPILTPRAAGPEGSF
    IGAQGSNQAGNNLTLKGWPLTGLEQLRSGILQQKSFIHNQQQLQQQIQMLTPQQQQQLML
    HAQQNMSSPTSSDVDNRRLRMMLNRNAVLGRDGQTNSGSDIIPNIGSPSQSGGDIDMLIK
    QSQSSNQHLQQEKPGIGSMPADGGIPNSFGGAEQDDVDRLLEDGSLDDNVESFLSQDDMD
    PRDNLGRCMDASKDSLNPKSYLEEHSFLITDVRFSPSMSRLATSSFDKTVRTDYSLRTFT
    GHSATVMSLDFHPNKEDMICSCDSDGEVRSWSINNGSCLTCVKVFKGGATQMRFQPRKGK
    GTIRIFNRFVGILLANISLLSVKTRSEYGHSVLDVKSLELWDIREKNTMTFNNAHDGLVA
    ALASSSATGKVASVSHDRTLKLWK
    
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    Files 3

    FileSizeDateAttached by 
     7-4_est.xlsx
    detailed EST analysis for region 69000-83000
    229.89 kB17:57, 4 Nov 2012gribskovActions
     7-4_model.docx
    detailed gene model, yellow indicates EST, red indicates blastx
    61.3 kB17:56, 4 Nov 2012gribskovActions
     7-4m_blastp.jpg
    genemark-4m model
    52.13 kB12:02, 19 Oct 2012gribskovActions
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