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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTGTATTGGCCCAAACTTCTTATACACAAGATAAAGCAACGCTTGACCAAAATGACACAGATGAGGATACGTATGAGGAAACTTGCTTTGAAGACAAGgtttgaaatcaaattctcatgtgcattttgttttatcatgacaaaccatacctaatttatccataagaagcttgtgctccagatgctcttaatttgtttg...

Basic information

species Glycine max
transcript GLYMA06G43930.1
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA06G43930.1 (Glycine max), 5'ss of exon 4
lower sequence: AT1G23280.1 (Arabidopsis thaliana), 5'ss of exon 4
TTGTATTGGCCCAAACTTCTTATACACAAGATAAAGCAACGCTTGACCAAAATGACACAGATGAGGATACGTATGAGGAAACTTGCTTTGAAGACAAGgtttgaaa----tcaaattctcat--gtgcattttgttttatcat--gacaaac-catacctaatt-tatccataagaagcttgtgctccagatgctcttaattt-gtttg----
||||| ||||||||  |  |    || ||| | || ||| |  |||| |||||||| |||||| | || |||||||||||||||||| |||| ||||||| |        ||   || |  |  ||| | |||| | | |  |  ||   ||   |  |||||| | | | |     | ||        | | || ||  ||| |  |     
TTGTACTGGCCCAAGTTGTTGCAGCATAAGGTTAAACAAAGACTGACTAAAATGACTCAGATGCGTATTCGTATGAGGAAACTTGCTCTGAAAACAAGgtcttgtcctcttctggtttttgtttgtggagtttggtatcttgtttgatttacatgtgtctaattcttttcttgttctgattaattatttggtacttttgtttttgaataacag
















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|193552745|gb|FK506996.1|FK506996
EST:     AAAATGACACAGATGAGGATACGTATGAGGAAACTTGCTTTGAAGACAAG                         GGAGAAAATAATGACAACTCCAAGGAAAGAGAAA
genomic: AAAATGACACAGATGAGGATACGTATGAGGAAACTTGCTTTGAAGACAAGgtttgaaatc ... tgttgtacagGGAGAAAATAATGACAACTCCAAGGAAAGAGAAA
EST: gi|193623854|gb|FK575582.1|FK575582
EST:     AAATGACACAGATGAGGATACGTATGAGGAAACTTGCTTTTGAAGACAAG                         GGAGAAAATAATGACAACTCCAAGGAAAGAGAAA
genomic: AAATGACACAGATGAGGATACGTATGAGGAAACTTGCTTT-GAAGACAAGgtttgaaatc ... tgttgtacagGGAGAAAATAATGACAACTCCAAGGAAAGAGAAA
EST: gi|193675302|gb|FK618658.1|FK618658
EST:     AAAATGACACAGATGAGGATACGTATGAGGAAACTTGCTTTGAAGACAAG                         GGAGAAAATAATGACAACTACCAA
genomic: AAAATGACACAGATGAGGATACGTATGAGGAAACTTGCTTTGAAGACAAGgtttgaaatc ... tgttgtacagGGAGAAAATAATGACAACT-CCAA
EST: gi|254345742|gb|GR859389.1|GR859389
EST:     AAAATGACACAGATGAGGATACGTATGAGGAAACTTGCTTTGAAGACAAG                         GGAGAAAATAATGACAACTCC
genomic: AAAATGACACAGATGAGGATACGTATGAGGAAACTTGCTTTGAAGACAAGgtttgaaatc ... tgttgtacagGGAGAAAATAATGACAACTCC
EST: gi|21889376|gb|BQ742589.1|BQ742589
EST:     AAAATGACACAGATGAGGATACGTATGAGGAAACTTGCTTTGAAGACAAG                         GGAGAAAATAATGACAACTC
genomic: AAAATGACACAGATGAGGATACGTATGAGGAAACTTGCTTTGAAGACAAGgtttgaaatc ... tgttgtacagGGAGAAAATAATGACAACTC
EST: gi|18690832|gb|BM519680.1|BM519680
EST:     AAATGACACAGATGAGGATACGTATGAGGAAACTTGCTTTGAAGAACA-G                         GGAGAAAATAATGACAACTCCAAGGA
genomic: AAATGACACAGATGAGGATACGTATGAGGAAACTTGCTTTGAAGA-CAAGgtttgaaatc ... tgttgtacagGGAGAAAATAATGACAACTCCAAGGA
EST: gi|208101229|gb|GD898588.1|GD898588
EST:     AAAATGACACAGATGAGGATACGTATGAGGAAACTTGCTTTGAAGACAAG                         GGAGAAA-TAAATGACAACTCCAAGG
genomic: AAAATGACACAGATGAGGATACGTATGAGGAAACTTGCTTTGAAGACAAGgtttgaaatc ... tgttgtacagGGAGAAAATAA-TGACAACTCCAAGG
EST: gi|208229960|gb|GE023371.1|GE023371
EST:     AAAATGACACAGATGAGGATACGTATGAGGAAACTTGCTTTGAAGACAAG                         GGAGAAAATAATGACAACTCCAAGG
genomic: AAAATGACACAGATGAGGATACGTATGAGGAAACTTGCTTTGAAGACAAGgtttgaaatc ... tgttgtacagGGAGAAAATAATGACAACTCCAAGG
EST: gi|6502229|gb|AW203602.1|AW203602
EST:     AAAATGACACAGATGAGGATACGTATGAGGAAACTTGCTTTGAAGACAAG                         GGAGAAAATTATGANCA-CTNCAAGGAAAGAGAAAAAGAGAGAG
genomic: AAAATGACACAGATGAGGATACGTATGAGGAAACTTGCTTTGAAGACAAGgtttgaaatc ... tgttgtacagGGAGAAAATAATGA-CAACTCCAAGGAAAGAGAAAAAGAGAGAG
EST: gi|193639236|gb|FK586457.1|FK586457
EST:     AAAATGACACAGATGAGGATACGTATGAGGAAACTTGCTTTGAAGACAAG                         GGAGAAAATAATGACAACTCCAAGGAAAGAGAAA
genomic: AAAATGACACAGATGAGGATACGTATGAGGAAACTTGCTTTGAAGACAAGgtttgaaatc ... tgttgtacagGGAGAAAATAATGACAACTCCAAGGAAAGAGAAA
EST: gi|208208147|gb|GE005506.1|GE005506
EST:     AAAATGACACAGATGCGGATACGTATGAGGAAACTTGCTTTGAAGACAAG                         GGAGAAAATAATGACAACTCC
genomic: AAAATGACACAGATGAGGATACGTATGAGGAAACTTGCTTTGAAGACAAGgtttgaaatc ... tgttgtacagGGAGAAAATAATGACAACTCC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTGTATTGGCCCAAACTTCTTATACACAAGATAAAGCAACGCTTGACCAAAATGACACAGATGAGGATACGTATGAGGAAACTTGCTTTGAAGACAAGgtttgaaatcaaattctcatgtgcattttgttttatcatgacaaaccatacctaatttatccataagaagcttgtgctccagatgctcttaatttgtttg

- - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA