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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...attagttccatgcaatgttttcttatttcgagtattcatttctagcacacaggagagtgtgtttaaacttaaacatttaacttgaccttaatctttgtagGCTGTTAGTCGGGAAATCCGGAAGATTTTGACTGAAAGGGCTGCTAACTTCAATATTGCCCTTGATGATGTGTCAATTACTAGTCTGACTTTTGGCAAGG

Basic information

species Glycine max
transcript GLYMA09G30410.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA09G30410.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv19s0085g00730.t01 (Vitis vinifera), 3'ss of exon 5
attagttccatgcaatgttttcttatttcgagtattcatttctagcacacaggagagtgtgtttaa-acttaaacatttaacttgaccttaa--tctttgtagGCTGTTAGTCGGGAAATCCGGAAGATTTTGACTGAAAGGGCTGCTAACTTCAATATTGCCCTTGATGATGTGTCAATTACTAGTCTGACTTTTGGCAAGG
  || ||        | |  |  |  |   || ||   ||  ||| |   | || |   | || || |  | ||  | | |     || ||   ||||| ||| |||||||| ||||||| || ||| | ||||| |||||||| || || ||||| ||||| || ||||||||||| ||||| || || |||||||| | ||
--tattttagcatggtataataattgtggaaggataggttgttaggat-tacgataaaattttaaatatatcaagttctgagcaatccatatgttctttatagACTGTTAGTAGGGAAATACGTAAGTTATTGACAGAAAGGGCAGCCAATTTCAACATTGCTCTGGATGATGTGTCCATTACAAGCCTTACTTTTGGGAGGG

upper sequence: GLYMA09G30410.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv15s0048g02350.t01 (Vitis vinifera), 3'ss of exon 5
attagttccatgcaatgttttcttatttcgagtattcatttctagcacacaggagagtgtgtttaaacttaaacatttaacttgacct---taatctttgtagGCTGTTAGTCGGGAAATCCGGAAGATTTTGACTGAAAGGGCTGCTAACTTCAATATTGCCCTTGATGATGTGTCAATTACTAGTCTGACTTTTGGCAAGG
  || ||        |||  |     |   || ||   ||  ||| |   ||   |     |||||| |      ||       |  |   |  ||||| |||||||||||  ||||||| || ||||| ||||| |||||||| || || ||||| || || || ||||||||||| || || || || |||||||| ||||
--tattttagcttggtgtaataactgtggaagaataggttgttaggat-tagataaaaaattttaaattactgagttctgagcaatttgtatgttctttatagGCTGTTAGCAGGGAAATACGTAAGATATTGACAGAAAGGGCAGCCAATTTCAACATCGCTCTGGATGATGTGTCCATCACAAGCCTTACTTTTGGGAAGG
















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|254318422|gb|GR832590.1|GR832590
EST:     TGCCCAGTACAATGCCAGCCAGCTTATTACTCAGCGAGAG                         GCTGTTAGTCGGGAAATCCGGAAGATTTTGACTGAAAGGGCTGCTAACTTC
genomic: TGCCCAGTACAATGCCAGCCAGCTTATTACTCAGCGAGAGgtaaggagca ... atctttgtagGCTGTTAGTCGGGAAATCCGGAAGATTTTGACTGAAAGGGCTGCTAACTTC
EST: gi|58019484|gb|CX706226.1|CX706226
EST:     AAGCCGTGGTTGCCCAGTACAATGCCAGCCAGCTTATTACTCAGCGAGAG                         GCTGTTAGTCGGGAAATCCGGAAGATTTTGACTGAAAGGGCTGCTAACTTC
genomic: AAGCCGTGGTTGCCCAGTACAATGCCAGCCAGCTTATTACTCAGCGAGAGgtaaggagca ... atctttgtagGCTGTTAGTCGGGAAATCCGGAAGATTTTGACTGAAAGGGCTGCTAACTTC
EST: gi|192298739|gb|FG988605.1|FG988605
EST:     AAGCCGTGGTTGCCCAGTACAATGCCAGCCAGCTTATTACTCAGCGAGAG                         GCTGTTAGTCGGGAAATCCGGAAGATTTTGACTGAAAGGGCTGCTAACTTC
genomic: AAGCCGTGGTTGCCCAGTACAATGCCAGCCAGCTTATTACTCAGCGAGAGgtaaggagca ... atctttgtagGCTGTTAGTCGGGAAATCCGGAAGATTTTGACTGAAAGGGCTGCTAACTTC
EST: gi|5753706|gb|AI960993.1|AI960993
EST:     AAGCCGTGGTTGCCCAGTACAATGCCAGCCAGCTTATTACTCAGCGAGAG                         GCTGTTAGTCGGGAAATCCGGAAGATTTTGACTGAAAGGGCTGCTAACTTC
genomic: AAGCCGTGGTTGCCCAGTACAATGCCAGCCAGCTTATTACTCAGCGAGAGgtaaggagca ... atctttgtagGCTGTTAGTCGGGAAATCCGGAAGATTTTGACTGAAAGGGCTGCTAACTTC
EST: gi|26059988|gb|CA802902.1|CA802902
EST:     AAGCCGTGGTTGCCCAGTACAATGCCAGCCAGCTTATTACTCAGCGAGAG                         GCTGTTAGTCGGGAAATCCGGAAGATTTTGACTGAAAGGGCTGCTAACTTC
genomic: AAGCCGTGGTTGCCCAGTACAATGCCAGCCAGCTTATTACTCAGCGAGAGgtaaggagca ... atctttgtagGCTGTTAGTCGGGAAATCCGGAAGATTTTGACTGAAAGGGCTGCTAACTTC
EST: gi|33388681|gb|CA851888.1|CA851888
EST:     AAGCCGTGGTTGCCCAGTACAATGCCAGCCAGCTTATTACTCAGCGAGAG                         GCTGTTAGTCGGGAAATCCGGAAGATTTTGACTGAAAGGGCTGCTAACTTC
genomic: AAGCCGTGGTTGCCCAGTACAATGCCAGCCAGCTTATTACTCAGCGAGAGgtaaggagca ... atctttgtagGCTGTTAGTCGGGAAATCCGGAAGATTTTGACTGAAAGGGCTGCTAACTTC
EST: gi|13562892|gb|BG551112.1|BG551112
EST:     AAGCCGTGGTTGCCCAGTACAATGCCAGCCAGCTTATTACTCAGCGAGAG                         GCTGTTAGTCGGGAAATCCGGAAGATTCTAACTGAAAGGGCTGCTAACTTC
genomic: AAGCCGTGGTTGCCCAGTACAATGCCAGCCAGCTTATTACTCAGCGAGAGgtaaggagca ... atctttgtagGCTGTTAGTCGGGAAATCCGGAAGATTTTGACTGAAAGGGCTGCTAACTTC
EST: gi|13563054|gb|BG551274.1|BG551274
EST:     AAGCCGTGGTTGCCCAGTACAATGCCAGCCAGCTTATTACTCAGCGAGAG                         GCTGTTAGTCGGGAAATCCGGAAGATTCTAACTGAAAGGGCTGCTAACTTC
genomic: AAGCCGTGGTTGCCCAGTACAATGCCAGCCAGCTTATTACTCAGCGAGAGgtaaggagca ... atctttgtagGCTGTTAGTCGGGAAATCCGGAAGATTTTGACTGAAAGGGCTGCTAACTTC
EST: gi|13563055|gb|BG551275.1|BG551275
EST:     AAGCCGTGGTTGCCCAGTACAATGCCAGCCAGCTTATTACTCAGCGAGAG                         GCTGTTAGTCGGGAAATCCGGAAGATTCTAACTGAAAGGGCTGCTAACTTC
genomic: AAGCCGTGGTTGCCCAGTACAATGCCAGCCAGCTTATTACTCAGCGAGAGgtaaggagca ... atctttgtagGCTGTTAGTCGGGAAATCCGGAAGATTTTGACTGAAAGGGCTGCTAACTTC
EST: gi|151410209|gb|EV280024.1|EV280024
EST:     AAGCCGTGGTTGCCCAGTACAATGCCAGCCAGCTTATTACTCAGCGAGAG                         GCTGTTAGTCGGGAAATCCGGAAGATTTTGACTGAAAGGGCTGCTAACTTC
genomic: AAGCCGTGGTTGCCCAGTACAATGCCAGCCAGCTTATTACTCAGCGAGAGgtaaggagca ... atctttgtagGCTGTTAGTCGGGAAATCCGGAAGATTTTGACTGAAAGGGCTGCTAACTTC
EST: gi|151411498|gb|EV281309.1|EV281309
EST:     AAGCCGTGGTTGCCCAGTACAATGCCAGCCAGCTTATTACTCAGCGAGAG                         GCTGTTAGTCGGGAAATCCGGAAGATTTTGACTGAAAGGGCTGCTAACTTC
genomic: AAGCCGTGGTTGCCCAGTACAATGCCAGCCAGCTTATTACTCAGCGAGAGgtaaggagca ... atctttgtagGCTGTTAGTCGGGAAATCCGGAAGATTTTGACTGAAAGGGCTGCTAACTTC
EST: gi|192325059|gb|FK016170.1|FK016170
EST:     AAGCCGTGGTTGCCTAGTACAATGCCAGCCAGCTTATTACTCAGCGAGAG                         GCTGTTAGTCGGGAAATCCGGAAGATTTTGACTGAAAGGGCTGCTAACTTC
genomic: AAGCCGTGGTTGCCCAGTACAATGCCAGCCAGCTTATTACTCAGCGAGAGgtaaggagca ... atctttgtagGCTGTTAGTCGGGAAATCCGGAAGATTTTGACTGAAAGGGCTGCTAACTTC
EST: gi|254318421|gb|GR832589.1|GR832589
EST:     AAGCCGTGGTTGCCCAGTACAATGCCAGCCAGCTTATTACTCAGCGAGAG                         GCTGTTAGTCGGGAAATCCGGAAGATTTTGACTGAAAGGGCTGCTAACTTC
genomic: AAGCCGTGGTTGCCCAGTACAATGCCAGCCAGCTTATTACTCAGCGAGAGgtaaggagca ... atctttgtagGCTGTTAGTCGGGAAATCCGGAAGATTTTGACTGAAAGGGCTGCTAACTTC
EST: gi|298166390|gb|HO010969.1|HO010969
EST:     AAGCCGTGGTTGCCCAGTACAATGCCAGCCAGCTTATTACTCAGCGAGAG                         GCTGTTAGTCGGGAAATCCGGAAGATTTTGACTGAAAGGGCTGCTAACTTC
genomic: AAGCCGTGGTTGCCCAGTACAATGCCAGCCAGCTTATTACTCAGCGAGAGgtaaggagca ... atctttgtagGCTGTTAGTCGGGAAATCCGGAAGATTTTGACTGAAAGGGCTGCTAACTTC
EST: gi|57574895|gb|CX547870.1|CX547870
EST:     AAGCCGTGGTTGCCCAGTACAATGCCAGCCAGCTTATTACTCAGCGAGAG                         GCTGTTAGTCGGGAAATCCGGAAGATTTTGACTGAAAGGGCTGCTAACTTC
genomic: AAGCCGTGGTTGCCCAGTACAATGCCAGCCAGCTTATTACTCAGCGAGAGgtaaggagca ... atctttgtagGCTGTTAGTCGGGAAATCCGGAAGATTTTGACTGAAAGGGCTGCTAACTTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cacacaggagagtgtgtttaaacttaaacatttaacttgaccttaatctttgtagGCTGTTAGTCGGGAAATCCGGAAGATTTTGACTGAAAGGGCTGCTAACTTCAATATTGCCCTTGATGATGTGTCAATTACTAGTCTGACTTTTGGCAAGG
                                              tctttgt  CT-rich tract
                tttaaacttaaacatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
attagttccatgcaatgttttcttatttcgagtattcatttctagcacacaggagagtgtgtttaaacttaaacatttaacttgaccttaatctttgtagGCTGTTAGTCGGGAAATCCGGAAGATTTTGACTGAAAGGGCTGCTAACTTCAATATTGCCCTTGATGATGTGTCAATTACTAGTCTGACTTTTGGCAAGG

- - - -ccatgca
- - - - - - - - - - - - - - - - - - - - - - -cacacag
- - - - - - - - - - - - - - - - - - - - - - - - - - - gagtgtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cttgacc