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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aaaacaaaatatgattttggttgatttatttgagctttaaactcagggtagtactagtacctatgattagttagtttgactctttgaattgtcttttcagGCCCTTTTTGCCAAAGGGTGTTGCTGACACTGGAGGAAAAACATCTACCTTATGACCCCAAGTTGGTGGATTTGACCAACAAGCCAGAATG

Basic information

species Glycine max
transcript GLYMA11G33700.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA11G33700.2 (Glycine max), 3'ss of exon 1
lower sequence: AT5G16710.1 (Arabidopsis thaliana), 3'ss of exon 1
aaaacaaaatatgattttggttgatttatttgagctttaaactcagggtagtactagtacctatgattagttagtttgactctttgaattgtcttttc---agGCCCTTTTTGCCAAAGGGTGTTGCTGACACTGGAGGAAAAACATCTACCTTATGACCCCAAGTTGGTGGATTTGACCAACAAGCCAGAATG
  || ||  ||  |   | | |  | | |||| |      |||  |  | | | || ||  | |  | ||| |||| || | | || ||  | || |    ||||||||||||||||| |||||| |||||| ||||||| ||  || | |||||||||   ||  ||||||||||||  ||||| ||||||||
ttaataagctaacacgattgcttctatgtttgtggcgagtact-ggttttgaagta-tattttttctcagtgagtt-gattatatgcataattttgttgatagGCCCTTTTTGCCAAAAGGTGTTACTGACAATGGAGGAGAAGAATGTTCCTTATGACATGAAAATGGTGGATTTGAGTAACAAACCAGAATG

upper sequence: GLYMA11G33700.2 (Glycine max), 3'ss of exon 1
lower sequence: Vv14s0006g00630.t01 (Vitis vinifera), 3'ss of exon 1
aaaacaaaatatgattttggttgatttatttgagctttaaactcagggtagtactagtacctatgattagttagtt--tgactctt-tgaattgtcttttcagGCCCTTTTTGCCAAAGGGTGTTGCTGACACTGGAGGAAAAACATCTACCTTATGACCCCAAGTTGGTGGATTTGACCAACAAGCCAGAATG
       | | |  ||  | |  |||||| |||         ||||| |||  |   ||  ||  |  | |||  |  ||| | || || | |||||||| ||| || || |  |||||| |  ||||||| || |||||||||||||| ||||||||    |||||||| |||||||| ||||||||||||||
-cccttcacttttgttaggatgaatttatgtgaaaaagtggttcaggttagagcctata--taaaaaaaattaactgttgattgttctggaatgtctttttagGTCCCTTCTCACAAAGGATTCTGCTGACTCTCGAGGAAAAACATCTCCCTTATGAAATGAAGTTGGTAGATTTGACTAACAAGCCAGAATG
















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|192296135|gb|FG989495.1|FG989495
EST:     CGAAATCGCCGTTAAAGCTTCCGTCACCACACCCAACAGGCTCGGCGACT                         GCCCTTTTTGCCAAAGGGTGTTGCTGACACTGGAGGAAAAACATCTACCTT
genomic: CGAAATCGCCGTTAAAGCTTCCGTCACCACACCCAACAGGCTCGGCGACTgtaacatctt ... gtcttttcagGCCCTTTTTGCCAAAGGGTGTTGCTGACACTGGAGGAAAAACATCTACCTT
EST: gi|209722386|gb|BW665859.1|BW665859
EST:     CGAAATCGCCGTTAAAGCTTCCGTCACCACACCCAACAGGCTCGGCGACT                         GCCCTTTTTGCCAAAGGGTGTTGCTGACACTGGAGGAAAAACATCTACCTT
genomic: CGAAATCGCCGTTAAAGCTTCCGTCACCACACCCAACAGGCTCGGCGACTgtaacatctt ... gtcttttcagGCCCTTTTTGCCAAAGGGTGTTGCTGACACTGGAGGAAAAACATCTACCTT
EST: gi|213609040|gb|DB957428.1|DB957428
EST:     CGAAATCGCCGTTAAAGCTTCCGTCACCACACCCAACAGGCTCGGCGACT                         GCCCTTTTTGCCAAAGGGTGTTGCTGACACTGGAGGAAAAACATCTACCTT
genomic: CGAAATCGCCGTTAAAGCTTCCGTCACCACACCCAACAGGCTCGGCGACTgtaacatctt ... gtcttttcagGCCCTTTTTGCCAAAGGGTGTTGCTGACACTGGAGGAAAAACATCTACCTT
EST: gi|7147501|gb|AW509423.1|AW509423
EST:     CGAAATCGCCGTTAAAGCTTCCGTCACCACACCCAACAGGCTCGGCGACT                         GCCCTTTTTGCCAAAGGGTGTTGCTGACACTGGAGGAAAAACATCTACCTT
genomic: CGAAATCGCCGTTAAAGCTTCCGTCACCACACCCAACAGGCTCGGCGACTgtaacatctt ... gtcttttcagGCCCTTTTTGCCAAAGGGTGTTGCTGACACTGGAGGAAAAACATCTACCTT
EST: gi|209708272|gb|BW678644.1|BW678644
EST:     CGAAATCGCCGTTAAAGCTTCCGTCACCACACCCAACAGGCTCGGCGACT                         GCCCTTTTTGCCAAAGGGTGTTGCTGACACTGGAGGAAAAACATCTACCTT
genomic: CGAAATCGCCGTTAAAGCTTCCGTCACCACACCCAACAGGCTCGGCGACTgtaacatctt ... gtcttttcagGCCCTTTTTGCCAAAGGGTGTTGCTGACACTGGAGGAAAAACATCTACCTT
EST: gi|151403447|gb|EV273257.1|EV273257
EST:     CGAAATCGCCGTTAAAGCTTCCGTCACCACACCCAACAGGCTCGGCGACT                         GCCCTTTTTGCCAAAGGGTGTTGCTGACACTGGAGGAAAAACATCTACCTT
genomic: CGAAATCGCCGTTAAAGCTTCCGTCACCACACCCAACAGGCTCGGCGACTgtaacatctt ... gtcttttcagGCCCTTTTTGCCAAAGGGTGTTGCTGACACTGGAGGAAAAACATCTACCTT
EST: gi|192299879|gb|FG990087.1|FG990087
EST:     CGAAATCGCCGTTAAAGCTTCCGTCACCACACCCAACAGGCTCGGCGACT                         GCCCTTTTTGCCAAAGGGTGTTGCTGACACTGGAGGAAAAACATCTACCTT
genomic: CGAAATCGCCGTTAAAGCTTCCGTCACCACACCCAACAGGCTCGGCGACTgtaacatctt ... gtcttttcagGCCCTTTTTGCCAAAGGGTGTTGCTGACACTGGAGGAAAAACATCTACCTT
EST: gi|13789768|gb|BG652359.1|BG652359
EST:     CGAAATCGCCGTTAAAGCTTCCGTCACCACACCCAACAGGCTCGGCGACT                         GCCCTTTTTGCCAAAGGGTGTTGCTGACACTGGAGGAAAAACATCTACCTT
genomic: CGAAATCGCCGTTAAAGCTTCCGTCACCACACCCAACAGGCTCGGCGACTgtaacatctt ... gtcttttcagGCCCTTTTTGCCAAAGGGTGTTGCTGACACTGGAGGAAAAACATCTACCTT
EST: gi|14011917|gb|BG726839.1|BG726839
EST:     CGAAATCGCCGTTAAAGCTTCCGTCACCACACCCAACAGGCTCGGCGACT                         GCCCTTTTTGCCAAAGGGTGTTGCTGACACTGGAGGAAAAACATCTACCTT
genomic: CGAAATCGCCGTTAAAGCTTCCGTCACCACACCCAACAGGCTCGGCGACTgtaacatctt ... gtcttttcagGCCCTTTTTGCCAAAGGGTGTTGCTGACACTGGAGGAAAAACATCTACCTT
EST: gi|298165886|gb|HO008857.1|HO008857
EST:     CGAAATCGCCGTTAAAGCTTCCGTCACCACACCCAACAGGCTCGGCGACT                         GCCCTTTTTGCCAAAGGGTGTTGCTGACACTGGAGGAAAAACATCTACCTT
genomic: CGAAATCGCCGTTAAAGCTTCCGTCACCACACCCAACAGGCTCGGCGACTgtaacatctt ... gtcttttcagGCCCTTTTTGCCAAAGGGTGTTGCTGACACTGGAGGAAAAACATCTACCTT
EST: gi|12691145|gb|BG157481.1|BG157481
EST:     CGAAATCGCCGTTAAAGCTTCCGTCACCACACCCAACAGGCTCGGCGACT                         GCCCTTTTTGCCAAAGGGTGTTGCTGACACTGGAGGAAAAACATCTACCTT
genomic: CGAAATCGCCGTTAAAGCTTCCGTCACCACACCCAACAGGCTCGGCGACTgtaacatctt ... gtcttttcagGCCCTTTTTGCCAAAGGGTGTTGCTGACACTGGAGGAAAAACATCTACCTT
EST: gi|209705734|gb|BW661402.1|BW661402
EST:     CGAAATCGCCGTTAAAGCTTCCGTCACCACACCCAACAGGCTCGGCGACT                         GCCCTTTTTGCCAAAGGGTGTTGCTGACACTGGAGGAAAAACATCTACCTT
genomic: CGAAATCGCCGTTAAAGCTTCCGTCACCACACCCAACAGGCTCGGCGACTgtaacatctt ... gtcttttcagGCCCTTTTTGCCAAAGGGTGTTGCTGACACTGGAGGAAAAACATCTACCTT
EST: gi|11688459|gb|BF596135.1|BF596135
EST:     GAAATCGCCGTTAAAGCTTCCGTCACCACACCCAACAGGCCTCGGCGACT                         GCCCTTTTTGCCAAAGGGTGTTGCTGACACTGGAGGAAAAACATCTACCTT
genomic: GAAATCGCCGTTAAAGCTTCCGTCACCACACCCAACAGG-CTCGGCGACTgtaacatctt ... gtcttttcagGCCCTTTTTGCCAAAGGGTGTTGCTGACACTGGAGGAAAAACATCTACCTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gggtagtactagtacctatgattagttagtttgactctttgaattgtcttttcagGCCCTTTTTGCCAAAGGGTGTTGCTGACACTGGAGGAAAAACATCTACCTTATGACCCCAAGTTGGTGGATTTGACCAACAAGCCAGAATG
                            gtttgac  putative branch site (score: 4)
                                           ttgtcttttc  putative PPT
                tatgatta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aaaacaaaatatgattttggttgatttatttgagctttaaactcagggtagtactagtacctatgattagttagtttgactctttgaattgtcttttcagGCCCTTTTTGCCAAAGGGTGTTGCTGACACTGGAGGAAAAACATCTACCTTATGACCCCAAGTTGGTGGATTTGACCAACAAGCCAGAATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA