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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatactaaatgcatatttacagcttggtatgtccatgaaaaatggtgctaaaaatggtttttccttcttaaaattaatgagatatttttgacagGGAGGAAACAAGAACTGAGAGACAGGAAGAAAGCTCATGAGATTTATTTACAAGTGAAATCTGAGGTAGAGAGATGTATTGCTTATTTAAAGGTGAAAAG

Basic information

species Glycine max
transcript GLYMA19G27200.1
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA19G27200.1 (Glycine max), 3'ss of exon 12
lower sequence: Vv14s0068g01430.t01 (Vitis vinifera), 3'ss of exon 13
gtatactaaatgcatatttacagcttggtatgtccatgaaaaatggtgctaaaaat---ggtttttccttcttaaaattaatgagatatttttgac--agGGAGGAAACAAGAACTGAGAGACAGGAAGAAAGCTCATGAGATTTATTTACAAGTGAAATCTGAGGTAGAGAGATGTATTGCTTATTTAAAGGTGAAAAG
|  |    ||  | |  |      ||  | | |  |       |  |  |  || |    || |  |||   | | |  |||      ||| ||    ||||||||| || ||||| ||||| | | | || ||||||||  | |||||||| || ||||||||||| ||||| ||  ||||||||||||||| ||||||
gcttgaataacacttcctagggaatttctgtctttaatttttttttttttccaattcttagtgtaccctgaatgacaagaatctccattttgtggtgaagGGAGGAAGCAGGAACTAAGAGAAAAGGAAAAGGCTCATGAATTGTATTTACATGTCAAATCTGAGGTTGAGAGTTGCCTTGCTTATTTAAAGGAGAAAAG
















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|254319092|gb|GR828820.1|GR828820
EST:     AGTTCCTGGTCGGTTCTACTATTATTTTGGAAAACCATTGGAAATGGAAG                         GGAGGAAACAAGAACTGAGAGACAGGAAGAAAGCTCATGAGATTTATTTAC
genomic: AGTTCCTGGTCGGTTCTACTATTATTTTGGAAAACCATTGGAAATGGAAGgtatactaaa ... tttttgacagGGAGGAAACAAGAACTGAGAGACAGGAAGAAAGCTCATGAGATTTATTTAC
EST: gi|214005477|gb|DB989167.1|DB989167
EST:     AGTTCCTGGTCGGTTCTACTATTATTTTGGAAAACCATTGGAAATGGAAG                         GGAGGAAACAAGAACTGAGAGACAGGAAGAAAGCTCATGAGATTTATTTAC
genomic: AGTTCCTGGTCGGTTCTACTATTATTTTGGAAAACCATTGGAAATGGAAGgtatactaaa ... tttttgacagGGAGGAAACAAGAACTGAGAGACAGGAAGAAAGCTCATGAGATTTATTTAC
EST: gi|151398463|gb|EV268334.1|EV268334
EST:     CTACTATTATTTTGGAAAACCATTGGAAATGGAAG                         GGAGGAAACAAGAACTGAGAGACAGGAAGAAAGCTCATGAGATTTATTTAC
genomic: CTACTATTATTTTGGAAAACCATTGGAAATGGAAGgtatactaaa ... tttttgacagGGAGGAAACAAGAACTGAGAGACAGGAAGAAAGCTCATGAGATTTATTTAC
EST: gi|209709678|gb|BW657207.1|BW657207
EST:     AGTTCCTGGTCGGTTCTACTATTATTTTGGAAAACCATTGGAAATGGAAG                         GGAGGAAACAAGAACTGAGAGACAGGAAGAAAGCTCATGAGATTTATTTAC
genomic: AGTTCCTGGTCGGTTCTACTATTATTTTGGAAAACCATTGGAAATGGAAGgtatactaaa ... tttttgacagGGAGGAAACAAGAACTGAGAGACAGGAAGAAAGCTCATGAGATTTATTTAC
EST: gi|58014697|gb|CX701439.1|CX701439
EST:     GGTCGGTTCTACTATTATTTTGGAAAACCATTGGAAATGGAAG                         GGAGGAAACAAGAACTGAGAGACAGGAAGAAAGCTCATGAGATTTATTTAC
genomic: GGTCGGTTCTACTATTATTTTGGAAAACCATTGGAAATGGAAGgtatactaaa ... tttttgacagGGAGGAAACAAGAACTGAGAGACAGGAAGAAAGCTCATGAGATTTATTTAC
EST: gi|58017660|gb|CX704402.1|CX704402
EST:     AGTTCCTGGTCGGTTCTACTATTATTTTGGAAAACCATTGGAAATGGAAG                         GGAGGAAACAAGAACTGAGAGACAGGAAGAAAGCTCATGAGATTTATTTAC
genomic: AGTTCCTGGTCGGTTCTACTATTATTTTGGAAAACCATTGGAAATGGAAGgtatactaaa ... tttttgacagGGAGGAAACAAGAACTGAGAGACAGGAAGAAAGCTCATGAGATTTATTTAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaatggtgctaaaaatggtttttccttcttaaaattaatgagatatttttgacagGGAGGAAACAAGAACTGAGAGACAGGAAGAAAGCTCATGAGATTTATTTACAAGTGAAATCTGAGGTAGAGAGATGTATTGCTTATTTAAAGGTGAAAAG
                                           tattttt  CT-rich tract
                         ttcttaaaattaatga  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatactaaatgcatatttacagcttggtatgtccatgaaaaatggtgctaaaaatggtttttccttcttaaaattaatgagatatttttgacagGGAGGAAACAAGAACTGAGAGACAGGAAGAAAGCTCATGAGATTTATTTACAAGTGAAATCTGAGGTAGAGAGATGTATTGCTTATTTAAAGGTGAAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATG