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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GACAAATGATCCCCATGACGCGATTGATCGAATTGTGAGAGgttttttccttgacactttctccttttattgtgtttgaagtgttatgtctgtctttacttttttcttgagcacgcatgcctttttttctagtaaagtagc...

Basic information

species Zea mays
transcript GRMZM5G812553_T02
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G812553_T02 (Zea mays), 5'ss of exon 7
lower sequence: LOC_Os03g03400.2 (Oryza sativa), 5'ss of exon 7
GACAAATGATCCCCATGACGCGATTGATCGAATTGTGAGAGgttttttccttgacactttctccttttattgtgtttgaagtgttatgtctgtctttacttttttcttgagcacgcatgcctttttttcta-gtaaagtagc----
|||||||||||| ||||| |||||||||||||||||||||||||  ||| ||||    |||| ||||||| |||| ||  ||    |   |     |  | |  |  ||  ||  |||  | |  | | |   ||     ||    
GACAAATGATCCTCATGAGGCGATTGATCGAATTGTGAGAGgttccttctttga----ttcttcttttatagtgtgtgctgt-cagtccatactcgtggtctcatagtggtcattcatctcctggtatatgtatatgaatgcacag
















Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|78075654|gb|DV504088.1|DV504088
EST:     GACAAATGATCCCCATGACGCGATTGATCGAATTGTGAGAG                         GAGTAAAATCAAAACTAGACGTAGGCGTGATGGAGGGTCCAAACAGAGAAC
genomic: GACAAATGATCCCCATGACGCGATTGATCGAATTGTGAGAGgttttttcct ... ctttttgcagGAGTAAAATCAAAACTAGACGTAGGCGTGATGGAGGGTCCAAACAGAGAAC
EST: gi|40334416|gb|CK368486.1|CK368486
EST:     GACAAATGATCCCCATGACGCGATTGATCGAATTGTGAGAG                         GAGTAAAATCNAAACTAGACGTAGGCGTGATGGAGGGTCCAAACAGAGAAC
genomic: GACAAATGATCCCCATGACGCGATTGATCGAATTGTGAGAGgttttttcct ... ctttttgcagGAGTAAAATCAAAACTAGACGTAGGCGTGATGGAGGGTCCAAACAGAGAAC
EST: gi|50336722|gb|CO531848.1|CO531848
EST:     GACAAATGATCCCCATGACGCGATTGATCGAATTGTGAGAG                         GAGTAAAATCAAAACTAGACGTAGGCGTGATGGAGGGTCCAAACAGAGAAC
genomic: GACAAATGATCCCCATGACGCGATTGATCGAATTGTGAGAGgttttttcct ... ctttttgcagGAGTAAAATCAAAACTAGACGTAGGCGTGATGGAGGGTCCAAACAGAGAAC
EST: gi|71764065|gb|DR962002.1|DR962002
EST:     GACAAATGATCCCCATGACGCGATTGATCGAATTGTGAGAG                         GAGTAAAATCAAAACTAGACGTAGGCGTGATGGAGGGTCCAAACAGAGAAC
genomic: GACAAATGATCCCCATGACGCGATTGATCGAATTGTGAGAGgttttttcct ... ctttttgcagGAGTAAAATCAAAACTAGACGTAGGCGTGATGGAGGGTCCAAACAGAGAAC
EST: gi|91878207|gb|EB408164.1|EB408164
EST:     GACAAATGATCCCCATGACGCGATTGATCGAATTGTGAGAG                         GAGTAAAATCAAAACTAGACGTAG
genomic: GACAAATGATCCCCATGACGCGATTGATCGAATTGTGAGAGgttttttcct ... ctttttgcagGAGTAAAATCAAAACTAGACGTAG
EST: gi|76285904|gb|DV025472.1|DV025472
EST:     GACAAATGATCCCCATGACGCGATTGATCGAATTGTGAGAG                         GAGTAAAATCAAAACTAGACGTAGGCGTGATGGAGGGTCCAAACAGAGAAC
genomic: GACAAATGATCCCCATGACGCGATTGATCGAATTGTGAGAGgttttttcct ... ctttttgcagGAGTAAAATCAAAACTAGACGTAGGCGTGATGGAGGGTCCAAACAGAGAAC
EST: gi|89759547|gb|DY688342.1|DY688342
EST:     GACAAATGATCCCCATGACGCGATTGATCGAATTGTGAGAG                         GAGTAAAATCAAAACTAGACGTAGGCGTGATGGAGGGTCCAAACAGAGAAC
genomic: GACAAATGATCCCCATGACGCGATTGATCGAATTGTGAGAGgttttttcct ... ctttttgcagGAGTAAAATCAAAACTAGACGTAGGCGTGATGGAGGGTCCAAACAGAGAAC
EST: gi|30307231|gb|CD001904.1|CD001904
EST:     GACAAATGATCCCCATGACGCGATTGATCGAATTGTGAGAG                         GAGTAAAATCAAAACTAGACGTAGGCGTGATGGAGGGTCCAAACAGAGAAC
genomic: GACAAATGATCCCCATGACGCGATTGATCGAATTGTGAGAGgttttttcct ... ctttttgcagGAGTAAAATCAAAACTAGACGTAGGCGTGATGGAGGGTCCAAACAGAGAAC
EST: gi|149080870|gb|EE169951.2|EE169951
EST:     GACAAATGATCCCCATGACGCGATTGATCGAATTGTGAGAG                         GAGTAAAATCAAAACTAGACGTAGGCGTGATGGAGGGTCCAAACAGAGAAC
genomic: GACAAATGATCCCCATGACGCGATTGATCGAATTGTGAGAGgttttttcct ... ctttttgcagGAGTAAAATCAAAACTAGACGTAGGCGTGATGGAGGGTCCAAACAGAGAAC
EST: gi|32867364|gb|CF007046.1|CF007046
EST:     CCCATGACGCGATTGATCGAATTGTGAGAG                         GAGTAAAATCAAAACTAGACGTAGGCGTGATGGAGGGTCCAAACAGAGAAC
genomic: CCCATGACGCGATTGATCGAATTGTGAGAGgttttttcct ... ctttttgcagGAGTAAAATCAAAACTAGACGTAGGCGTGATGGAGGGTCCAAACAGAGAAC
EST: gi|93281461|gb|EB673725.1|EB673725
EST:     GACAAATGATCCCCATGACGCGATTGATCGAATTGTGAGAG                         GAGTAAAATCAAAACTAGACGTAGGCGTGATGGAGGGTCCAAACAGAGAAC
genomic: GACAAATGATCCCCATGACGCGATTGATCGAATTGTGAGAGgttttttcct ... ctttttgcagGAGTAAAATCAAAACTAGACGTAGGCGTGATGGAGGGTCCAAACAGAGAAC
EST: gi|76021472|gb|DT948642.1|DT948642
EST:     GACAAATGATCCCCATGACGCGATTGATCGAATTGTGAGAG                         GAGTAAAATCAAAACTAGACGTAGGCGTGATGGAGGGTCCAAACAGAGAAC
genomic: GACAAATGATCCCCATGACGCGATTGATCGAATTGTGAGAGgttttttcct ... ctttttgcagGAGTAAAATCAAAACTAGACGTAGGCGTGATGGAGGGTCCAAACAGAGAAC
EST: gi|148976019|gb|EE025878.2|EE025878
EST:     GACAAATGATCCCCCATGACGCGATTGATCGAATTGTGAGAG                         GAGTAAAATCAAAACTAGACGTAGGCGTGATGGAGGGTCCAAACAGAGAAC
genomic: GACAAATGATCCCC-ATGACGCGATTGATCGAATTGTGAGAGgttttttcct ... ctttttgcagGAGTAAAATCAAAACTAGACGTAGGCGTGATGGAGGGTCCAAACAGAGAAC
EST: gi|50322460|gb|CO517586.1|CO517586
EST:     GACAAATGATCCCCATGACGCGATTGATCGAATTGTGAGAG                         GAGTAAAATCAAAACTAGACGTAGGCGTGATGGAGGGTCCAAACAGAGAAC
genomic: GACAAATGATCCCCATGACGCGATTGATCGAATTGTGAGAGgttttttcct ... ctttttgcagGAGTAAAATCAAAACTAGACGTAGGCGTGATGGAGGGTCCAAACAGAGAAC
EST: gi|32933409|gb|CF038221.1|CF038221
EST:     GGACGAATGATCCCCATGACGCGATTGATCGAATTGTGAGAG                         GAGTAAAATCAAAACTAGACGTAGGCGTGATGGAGGGTCCAAACAGAGAAC
genomic: GGACAAATGATCCCCATGACGCGATTGATCGAATTGTGAGAGgttttttcct ... ctttttgcagGAGTAAAATCAAAACTAGACGTAGGCGTGATGGAGGGTCCAAACAGAGAAC
EST: gi|78105461|gb|DV523879.1|DV523879
EST:     GACAAATGATCCCCATGACGCGATTGATCGAATTGTGAGAG                         GAGTAAAATCAAAACTAGACGTAGGCGTGATGGAGGGTCCAAACAGAGAAC
genomic: GACAAATGATCCCCATGACGCGATTGATCGAATTGTGAGAGgttttttcct ... ctttttgcagGAGTAAAATCAAAACTAGACGTAGGCGTGATGGAGGGTCCAAACAGAGAAC
EST: gi|50334433|gb|CO529559.1|CO529559
EST:     GACAAATGATCCCCATGACGCGATTGATCGAATTGTGAGAG                         GAGTAAAATCAAAACTAGACGTAGGCGTGATGGAGGGTCCAAACAGAGAAC
genomic: GACAAATGATCCCCATGACGCGATTGATCGAATTGTGAGAGgttttttcct ... ctttttgcagGAGTAAAATCAAAACTAGACGTAGGCGTGATGGAGGGTCCAAACAGAGAAC
EST: gi|71774560|gb|DR972438.1|DR972438
EST:     GACAAATGATCCCCATGACGCGATTGATCGAATTGTGAGAG                         GAGTAAAATCAAAACTAGACGTAGGCGTGATGGAGGGTCCAAACAGAGAAC
genomic: GACAAATGATCCCCATGACGCGATTGATCGAATTGTGAGAGgttttttcct ... ctttttgcagGAGTAAAATCAAAACTAGACGTAGGCGTGATGGAGGGTCCAAACAGAGAAC
EST: gi|91051589|gb|EB162007.1|EB162007
EST:     GACAAATGATCCCCATGACGCGATTGATCGAATTGTGAGAG                         GAGTAAAATCAAAACTAGACGTAGGCGTGATGGAGGGTCCAAACAGAGAAC
genomic: GACAAATGATCCCCATGACGCGATTGATCGAATTGTGAGAGgttttttcct ... ctttttgcagGAGTAAAATCAAAACTAGACGTAGGCGTGATGGAGGGTCCAAACAGAGAAC
EST: gi|78085115|gb|DV513508.1|DV513508
EST:     GACAAATGATCCCCCATGACGCGATTGATCGAATTGTGAGAG                         GAGTAAAATCAAAACTAGACGTAGGCGTGATGGAGGGTCCAAACAGAGAAC
genomic: GACAAATGATCCCC-ATGACGCGATTGATCGAATTGTGAGAGgttttttcct ... ctttttgcagGAGTAAAATCAAAACTAGACGTAGGCGTGATGGAGGGTCCAAACAGAGAAC
EST: gi|78078210|gb|DV506625.1|DV506625
EST:     GACAAATGATCCCCATGACGCGATTGATCGAATTGTGAGAG                         GAGTAAAATCAAAACTAGACGTAGGCGTGATGGAGGGTCCAAACAGAGAAC
genomic: GACAAATGATCCCCATGACGCGATTGATCGAATTGTGAGAGgttttttcct ... ctttttgcagGAGTAAAATCAAAACTAGACGTAGGCGTGATGGAGGGTCCAAACAGAGAAC
EST: gi|91878508|gb|EB408465.1|EB408465
EST:     GACAAATGATCCCCATGACGCGATTGATCGAATTGTGAGAG                         GAGTAAAATCAAAACTAGACGTAGGCGTGATGGA
genomic: GACAAATGATCCCCATGACGCGATTGATCGAATTGTGAGAGgttttttcct ... ctttttgcagGAGTAAAATCAAAACTAGACGTAGGCGTGATGGA
EST: gi|78105462|gb|DV523880.1|DV523880
EST:     GACAAATGATCCCCATGACGCGATTGATCGAATTGTGAGAG                         GAGTAAAATCAAAACTAGACGTAGGCGTGATGGAGGGTCCAAACAGAGAAC
genomic: GACAAATGATCCCCATGACGCGATTGATCGAATTGTGAGAGgttttttcct ... ctttttgcagGAGTAAAATCAAAACTAGACGTAGGCGTGATGGAGGGTCCAAACAGAGAAC
EST: gi|71436209|gb|DR817259.1|DR817259
EST:     GACAAATGATCCCCATGACGCGATTGATCGAATTG--AG--                         ---TAAAATCAAAACTAGACGTAGGCGTGATGGAGGGTCCAAACAGAGAAC
genomic: GACAAATGATCCCCATGACGCGATTGATCGAATTGTGAGAGgttttttcct ... ctttttgcagGAGTAAAATCAAAACTAGACGTAGGCGTGATGGAGGGTCCAAACAGAGAAC
EST: gi|67022745|gb|CO451494.1|CO451494
EST:     GACAAATGATCCCCATGACGCGATTGATCGAATTGTGAGAG                         GAGTAAAATCAAAACTAGACGTAGGCGTGATGGAGGGTCCAAACAGAGAAC
genomic: GACAAATGATCCCCATGACGCGATTGATCGAATTGTGAGAGgttttttcct ... ctttttgcagGAGTAAAATCAAAACTAGACGTAGGCGTGATGGAGGGTCCAAACAGAGAAC
EST: gi|78121934|gb|DV540318.1|DV540318
EST:     GACAAATGATCCCCATGACGCGATTGATCGAATTGTGAGAG                         GAGTAAAATCAAAACTAGACGTAGGCGTGATGGAGGGTCCAAACAGAGAAC
genomic: GACAAATGATCCCCATGACGCGATTGATCGAATTGTGAGAGgttttttcct ... ctttttgcagGAGTAAAATCAAAACTAGACGTAGGCGTGATGGAGGGTCCAAACAGAGAAC
EST: gi|78113487|gb|DV531878.1|DV531878
EST:     GACAAATGATCCCCATGACGCGATTGATCGAATTGTGAGAG                         GAGTAAAATCAAAACTAGACGTAGGCGTGATGGAGGGTCCAAACAGAGAAC
genomic: GACAAATGATCCCCATGACGCGATTGATCGAATTGTGAGAGgttttttcct ... ctttttgcagGAGTAAAATCAAAACTAGACGTAGGCGTGATGGAGGGTCCAAACAGAGAAC
EST: gi|76285903|gb|DV025471.1|DV025471
EST:     ATTTGGCTGGACAAATGATCCCCATGACGCGATTGATCGAATTGTGAGAG                         GAGTAAAATCAAAACTAGACGTAGGCGTGATGGAGGGTCCAAACAGAGAAC
genomic: ATTTGGCTGGACAAATGATCCCCATGACGCGATTGATCGAATTGTGAGAGgttttttcct ... ctttttgcagGAGTAAAATCAAAACTAGACGTAGGCGTGATGGAGGGTCCAAACAGAGAAC
EST: gi|211469689|gb|FK976086.1|FK976086
EST:     GACAAATGATCCCCATGACGCGATTGATCGAATTGTGAGAG                         GAGTAAAATCAAAACTAGACGTAGGCGTGATGGAGGGTCCAAACAGAGAAC
genomic: GACAAATGATCCCCATGACGCGATTGATCGAATTGTGAGAGgttttttcct ... ctttttgcagGAGTAAAATCAAAACTAGACGTAGGCGTGATGGAGGGTCCAAACAGAGAAC
EST: gi|40335239|gb|CK369309.1|CK369309
EST:     GACAAATGATCCCCATGACGCGATTGATCGAATTGTGAGAG                         GAGTAAAATCAAAACTAGACGTAGGCGTGATGGAGGGTCCAAACAGAGAAC
genomic: GACAAATGATCCCCATGACGCGATTGATCGAATTGTGAGAGgttttttcct ... ctttttgcagGAGTAAAATCAAAACTAGACGTAGGCGTGATGGAGGGTCCAAACAGAGAAC
EST: gi|78121935|gb|DV540319.1|DV540319
EST:     GACAAATGATCCCCATGACGCGATTGATCGAATTGTGAGAG                         GAGTAAAATCAAAACTAGACGTAGGCGTGATGGAGGGTCCAAACAGAGAAC
genomic: GACAAATGATCCCCATGACGCGATTGATCGAATTGTGAGAGgttttttcct ... ctttttgcagGAGTAAAATCAAAACTAGACGTAGGCGTGATGGAGGGTCCAAACAGAGAAC
EST: gi|71298751|gb|DR785364.1|DR785364
EST:     GACAAATGATCCCCATGACGCGATTGATCGAATTGTGAGAG                         GAGTAAAATCAAAACTAGACGTAGGCGTGATGGAGGGTCCAAACAGAGAAC
genomic: GACAAATGATCCCCATGACGCGATTGATCGAATTGTGAGAGgttttttcct ... ctttttgcagGAGTAAAATCAAAACTAGACGTAGGCGTGATGGAGGGTCCAAACAGAGAAC
EST: gi|8102673|gb|AW927320.1|AW927320
EST:     GACAAATGATCCCCATGACGCGATTGATCGAATTGTGAGAG                         GAGTAAAATCAAAACTAGACATAGGCGTGATGGAGGGTCCAAACAGAGAAC
genomic: GACAAATGATCCCCATGACGCGATTGATCGAATTGTGAGAGgttttttcct ... ctttttgcagGAGTAAAATCAAAACTAGACGTAGGCGTGATGGAGGGTCCAAACAGAGAAC
EST: gi|71436272|gb|DR817322.1|DR817322
EST:     GACAAATGATCCCCATGACGCGATTGATCGAATTGTGAGAG                         GAGTAAAATCAAAACTAGACGTAGGCGTGATGGAGGGTCCAAACAGAGAAC
genomic: GACAAATGATCCCCATGACGCGATTGATCGAATTGTGAGAGgttttttcct ... ctttttgcagGAGTAAAATCAAAACTAGACGTAGGCGTGATGGAGGGTCCAAACAGAGAAC
EST: gi|32867365|gb|CF007047.1|CF007047
EST:     GACAAATGATCCCCATGACGCGATTGATCGAATTGTGAGAG                         GAGTAAAATCAAAACTAGACGTAGGCGTGATGGAGGGTCCAAACAGAGAAC
genomic: GACAAATGATCCCCATGACGCGATTGATCGAATTGTGAGAGgttttttcct ... ctttttgcagGAGTAAAATCAAAACTAGACGTAGGCGTGATGGAGGGTCCAAACAGAGAAC
EST: gi|30087080|gb|CB885288.1|CB885288
EST:     GACAAATGATCCCCATGACGCGATTGATCGAATTGTGAGAG                         GAGTAAAATCAAAACTAGACGTA
genomic: GACAAATGATCCCCATGACGCGATTGATCGAATTGTGAGAGgttttttcct ... ctttttgcagGAGTAAAATCAAAACTAGACGTA
EST: gi|31406361|gb|CD485093.1|CD485093
EST:     GACAAATGATCCCCATGACGCGATTGATCGAATTGTGAGAG                         GAGTAAAATCAAAACTAGACGTA
genomic: GACAAATGATCCCCATGACGCGATTGATCGAATTGTGAGAGgttttttcct ... ctttttgcagGAGTAAAATCAAAACTAGACGTA

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 4 RNA-Seq libraries.


Block sizes: 41 (upstream exon), 48 (downstream exon)
Score: 158

GACAAATGATCCCCATGACGCGATTGATCGAATTGTGAGAGgttttttcct ... ctttttgcagGAGTAAAATCAAAACTAGACGTAGGCGTGATGGAGGGTCCAAACAGAGAACCACACTTCTTTGTTAATGTTGCTGATATCCATTT


Block sizes: 41 (upstream exon), 49 (downstream exon)
Score: 121

GACAAATGATCCCCATGACGCGATTGATCGAATTGTGAGAGgttttttcct ... ctttttgcagGAGTAAAATCAAAACTAGACGTAGGCGTGATGGAGGGTCCAAACAGAGAACCACACTTCTTTGTTAATGTTGCTGATATCCATTT


Block sizes: 41 (upstream exon), 49 (downstream exon)
Score: 98

GACAAATGATCCCCATGACGCGATTGATCGAATTGTGAGAGgttttttcct ... ctttttgcagGAGTAAAATCAAAACTAGACGTAGGCGTGATGGAGGGTCCAAACAGAGAACCACACTTCTTTGTTAATGTTGCTGATATCCATTT


Block sizes: 41 (upstream exon), 48 (downstream exon)
Score: 156

GACAAATGATCCCCATGACGCGATTGATCGAATTGTGAGAGgttttttcct ... ctttttgcagGAGTAAAATCAAAACTAGACGTAGGCGTGATGGAGGGTCCAAACAGAGAACCACACTTCTTTGTTAATGTTGCTGATATCCATTT