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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATGTGGTTCATCCCCTGAAGGTCTCTCTGGAGGATCTTTACCTCGGAACTTCAAAGAAACTCTCTCTTTCACGAAACGTGTTGTGCTCAAAATGCAATGGgtgtgtgttgcgcaattaggttttgtttgaagggcatacttgttgatcctttttgttaatagggtttttgacattgttgatttgttgtatgtaattgattacttacag

Basic information

species Glycine max
transcript GLYMA13G38790.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA13G38790.1 (Glycine max), 5'ss of exon 3
lower sequence: GRMZM2G028218_T01 (Zea mays), 5'ss of exon 3
ATGTGGTTCATCCCCTGAAGGTCTCTCTGGAGGATCTTTACCTCGGAACTTCAAAGAAACTCTCTCTTTCACGAAACGTGTTGTGCTCAAAATGCAATGGgtgtgtgttgcgcaattaggttttg----tttgaagggcatacttgttgatcctttttgttaatagggtttttgacattgttgatttgttgtatgtaattgattacttacag
||||||||||||| |||||||| |||||||||||| | |||   || || |||||||| |||||||| || || || ||  | ||||| || ||||||||||  ||  |  | |   |           |   ||   |  | ||    ||    ||| |  ||  | || ||   ||   |||||   ||  |||||| |   |       
ATGTGGTTCATCCTCTGAAGGTTTCTCTGGAGGATTTGTACAATGGCACATCAAAGAAGCTCTCTCTGTCCCGCAATGTCCTCTGCTCCAAGTGCAATGGgtaggtcatctgaatccacaacacaaggatgccaaaaactcaattac-aatatgctttctatattagattcttaggatc--tgattgtgtgcttgtaatcgtgcag------
















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|151402572|gb|EV272385.1|EV272385
EST:     TCAAAGAAACTCTCTCTTTCACGGAACGTGTTGTGCTCAAAATGCAATGG                         GAAGGGCTCAAAGTCTGGGGCTTCAATGACCTGTGCTGGTTGCCAGGGTAC
genomic: TCAAAGAAACTCTCTCTTTCACGAAACGTGTTGTGCTCAAAATGCAATGGgtgtgtgttg ... ttacttacagGAAGGGCTCAAAGTCTGGGGCTTCAATGACCTGTGCTGGTTGCCAGGGTAC
EST: gi|207769891|gb|GD742205.1|GD742205
EST:     TCAAAGAAACTCTCTCTTTCACGAAACGTGTTGTGCTCAAAATGCAATGG                         GAAGGGCTCAAAGTCTGGGGCTTCAATGACCTGTGCTGGTTGCCAGGGTAC
genomic: TCAAAGAAACTCTCTCTTTCACGAAACGTGTTGTGCTCAAAATGCAATGGgtgtgtgttg ... ttacttacagGAAGGGCTCAAAGTCTGGGGCTTCAATGACCTGTGCTGGTTGCCAGGGTAC
EST: gi|6072029|gb|AW101476.1|AW101476
EST:     TCAAAGAAACTCTCTCTTTCACGAAACGTGTTGTGCTCAAAATGCAATGG                         GAAGGGCTCAAAGTCTGGGGCTTCAATGACCTGTGCTGGTTGCCAGGGTAC
genomic: TCAAAGAAACTCTCTCTTTCACGAAACGTGTTGTGCTCAAAATGCAATGGgtgtgtgttg ... ttacttacagGAAGGGCTCAAAGTCTGGGGCTTCAATGACCTGTGCTGGTTGCCAGGGTAC
EST: gi|209720721|gb|BW677539.1|BW677539
EST:     TCAAAGAAACTCTCTCTTTCACGAAACGTGTTGTGCTCAAAATGCAATGG                         GAAGGGCTCAAAGTCTGGGGCTTCAATGACCTGTGCTGGTTGCCA
genomic: TCAAAGAAACTCTCTCTTTCACGAAACGTGTTGTGCTCAAAATGCAATGGgtgtgtgttg ... ttacttacagGAAGGGCTCAAAGTCTGGGGCTTCAATGACCTGTGCTGGTTGCCA
EST: gi|193591557|gb|FK545958.1|FK545958
EST:     TCAAAGAAACTCTCTCTTTCACGAAACGTGTTGTGCTCAAAATGCAATGG                         GAAGGGCTCAAAGTCTGGGGCTTCAATGACCTGTGCTGGTTGCCAGGGTAC
genomic: TCAAAGAAACTCTCTCTTTCACGAAACGTGTTGTGCTCAAAATGCAATGGgtgtgtgttg ... ttacttacagGAAGGGCTCAAAGTCTGGGGCTTCAATGACCTGTGCTGGTTGCCAGGGTAC
EST: gi|193443306|gb|FK407414.1|FK407414
EST:     TCAAAGAAACTCTCTCTTTCACGAAACGTGTTGTGCTCAAAATGCAATGG                         GAAGGGCTCAAAGTCTGGGGCTTCAATGACCTGTGCTGGTTG
genomic: TCAAAGAAACTCTCTCTTTCACGAAACGTGTTGTGCTCAAAATGCAATGGgtgtgtgttg ... ttacttacagGAAGGGCTCAAAGTCTGGGGCTTCAATGACCTGTGCTGGTTG
EST: gi|19935305|gb|BQ080335.1|BQ080335
EST:     TCAAAGAAACTCTCTCTTTCACGAAACGTGTTGTGCTCAAAATGCAATGG                         GAAGGGCTCAAAGTCTGGGGCTTCAATG
genomic: TCAAAGAAACTCTCTCTTTCACGAAACGTGTTGTGCTCAAAATGCAATGGgtgtgtgttg ... ttacttacagGAAGGGCTCAAAGTCTGGGGCTTCAATG
EST: gi|209697332|gb|BW655573.1|BW655573
EST:     TCAAAGAAACTCTCTCTTTCACGAAACGTGTTGTGCTCAAAATGCAATGG                         GAAGGGCTCAAAGTCTGGGGC
genomic: TCAAAGAAACTCTCTCTTTCACGAAACGTGTTGTGCTCAAAATGCAATGGgtgtgtgttg ... ttacttacagGAAGGGCTCAAAGTCTGGGGC
EST: gi|6566370|gb|AW234039.1|AW234039
EST:     CTAAGAAACTCTCTCTTTCACGAAACGTGTTGTGGCTCAAA-TGCAATGG                         GAAGGGCCTCAA
genomic: CAAAGAAACTCTCTCTTTCACGAAACGTGTTGTG-CTCAAAATGCAATGGgtgtgtgttg ... ttacttacagGAAGGGC-TCAA
EST: gi|193600247|gb|FK551132.1|FK551132
EST:     TCAAAGAAACTCTCTCTTTCACGAAACGTGTTGTGCTCAAAATGCAATGG                         GAAGGGCTCAAAGTCTGGGGCTTCAATGACCTGTGCTGGTTGCCAGGGTAC
genomic: TCAAAGAAACTCTCTCTTTCACGAAACGTGTTGTGCTCAAAATGCAATGGgtgtgtgttg ... ttacttacagGAAGGGCTCAAAGTCTGGGGCTTCAATGACCTGTGCTGGTTGCCAGGGTAC
EST: gi|209705227|gb|BW673767.1|BW673767
EST:     TCAAAGAAACTCTCTCTTTCACGAAACGTGTTGTGCTCAAAATGCAATGG                         GAAGGGCTCAAAGTCTGGGGCTTNCA-TGACCTGTGCTGGTTGCCAGGGTA
genomic: TCAAAGAAACTCTCTCTTTCACGAAACGTGTTGTGCTCAAAATGCAATGGgtgtgtgttg ... ttacttacagGAAGGGCTCAAAGTCTGGGGCTT-CAATGACCTGTGCTGGTTGCCAGGGTA
EST: gi|213593343|gb|DB966112.1|DB966112
EST:     TCAAAGAAACTCTCTCTTTCACGAAACGTGTTGTGCTCAAAATGCAATGG                         GAAGGGCTCAAAGTCTGGGGCTT
genomic: TCAAAGAAACTCTCTCTTTCACGAAACGTGTTGTGCTCAAAATGCAATGGgtgtgtgttg ... ttacttacagGAAGGGCTCAAAGTCTGGGGCTT
EST: gi|16346351|gb|BI971946.1|BI971946
EST:     TCAAAGAAACTCTCTCTTTCACGAAACGTGTTGTGCTCAAAATGCAATGG                         GAAGGGCTCAAAGTCTGGGGCTTCAATGACCTGTGCTGGTTGCCAGGGTAC
genomic: TCAAAGAAACTCTCTCTTTCACGAAACGTGTTGTGCTCAAAATGCAATGGgtgtgtgttg ... ttacttacagGAAGGGCTCAAAGTCTGGGGCTTCAATGACCTGTGCTGGTTGCCAGGGTAC
EST: gi|193594773|gb|FK546758.1|FK546758
EST:     TCAAAGAAACTCTCTCTTTCACGAAACGTGTTGTGCTCAAAATGCAATGG                         GAAGGGCTCAAAGTCTGGGGCTTCAATGACCTGTGCTGGTTGCCAGGGTAC
genomic: TCAAAGAAACTCTCTCTTTCACGAAACGTGTTGTGCTCAAAATGCAATGGgtgtgtgttg ... ttacttacagGAAGGGCTCAAAGTCTGGGGCTTCAATGACCTGTGCTGGTTGCCAGGGTAC
EST: gi|6567081|gb|AW234708.1|AW234708
EST:     TCAAAGAAACTCTCTCTTTCACGAAACGTGTTGTGCTCAAAATGCAATGG                         GAAGGGCTCAAAGTCTTGGGCTTCAATGACCTGTGCTGGTTGCCATGGTAC
genomic: TCAAAGAAACTCTCTCTTTCACGAAACGTGTTGTGCTCAAAATGCAATGGgtgtgtgttg ... ttacttacagGAAGGGCTCAAAGTCTGGGGCTTCAATGACCTGTGCTGGTTGCCAGGGTAC
EST: gi|298171124|gb|HO016156.1|HO016156
EST:     TCAAAGAAACTCTCTCTTTCACGAAACGTGTTGTGCTCAAAATGCAATGG                         GAAGGGCTCAAAGTCTGGGGCTTCAATGACCTGTGCTGGTTGCCAGGGTAC
genomic: TCAAAGAAACTCTCTCTTTCACGAAACGTGTTGTGCTCAAAATGCAATGGgtgtgtgttg ... ttacttacagGAAGGGCTCAAAGTCTGGGGCTTCAATGACCTGTGCTGGTTGCCAGGGTAC
EST: gi|208144015|gb|GD943718.1|GD943718
EST:     CTCAAAATGCAATGG                         GAAGGGCTCAAAGTCTGGGGCTTCAATGACCTGTGCTGGTTGCCAGGGTAC
genomic: CTCAAAATGCAATGGgtgtgtgttg ... ttacttacagGAAGGGCTCAAAGTCTGGGGCTTCAATGACCTGTGCTGGTTGCCAGGGTAC
EST: gi|193671260|gb|FK607852.1|FK607852
EST:     TCAAAGAAACTCTCTCTTTCACGAAACGTGTTGTGCTCAAAATGCAATGG                         GAAGGGCTCAAAGTCTGGGGCTTCAATGACCTGTGCTGGTTGCCAGGGTAC
genomic: TCAAAGAAACTCTCTCTTTCACGAAACGTGTTGTGCTCAAAATGCAATGGgtgtgtgttg ... ttacttacagGAAGGGCTCAAAGTCTGGGGCTTCAATGACCTGTGCTGGTTGCCAGGGTAC
EST: gi|213610686|gb|DB961161.1|DB961161
EST:     TCAAAGAAACTCTCTCTTTCACGAAACGTGTTGTGCTCAAAATGCAATGG                         GAAGGGCTCAAAGTCTGGGGCTTNCA-TGACCTGTGCTGGTTGCCAGGGTA
genomic: TCAAAGAAACTCTCTCTTTCACGAAACGTGTTGTGCTCAAAATGCAATGGgtgtgtgttg ... ttacttacagGAAGGGCTCAAAGTCTGGGGCTT-CAATGACCTGTGCTGGTTGCCAGGGTA
EST: gi|7925317|gb|AW831404.1|AW831404
EST:     TCAAAGAAACTCTCTCTTTCACGAAACGTGTTGTGCTCAAAATGCAATGG                         GAAGGGCTCAAAGTCTGGGGCTTCAATGACCTGTGCTGGTTGCCAGGGTAC
genomic: TCAAAGAAACTCTCTCTTTCACGAAACGTGTTGTGCTCAAAATGCAATGGgtgtgtgttg ... ttacttacagGAAGGGCTCAAAGTCTGGGGCTTCAATGACCTGTGCTGGTTGCCAGGGTAC
EST: gi|192308577|gb|FK002473.1|FK002473
EST:     TCAAAGAAACTCTCTCTTTCACGAAACGTGTTGTGCTCAAAATGCAATGG                         GAAGGGCTCAAAGTCTGGGGCTTCAATGACCTGTGCTGGTTGCCAGGGTAC
genomic: TCAAAGAAACTCTCTCTTTCACGAAACGTGTTGTGCTCAAAATGCAATGGgtgtgtgttg ... ttacttacagGAAGGGCTCAAAGTCTGGGGCTTCAATGACCTGTGCTGGTTGCCAGGGTAC

Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATGTGGTTCATCCCCTGAAGGTCTCTCTGGAGGATCTTTACCTCGGAACTTCAAAGAAACTCTCTCTTTCACGAAACGTGTTGTGCTCAAAATGCAATGGgtgtgtgttgcgcaattaggttttgtttgaagggcatacttgttgatcctttttgttaatagggtttttgacattgttgatttgttgtatgtaattgattacttacag

- - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA