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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttatggatttacttgactaagtttcggagaatagagatcccaatatgtttatagcatagtgaattgttcttaaaattgaatgaagttttgttgttgtagGTGTAAGTGGAAGTTCAAAGCAGAGTAGAAGTGAAAAGAAGAGTAGGAAGGCGATGTTGAAGCTCGGTATGAAACCTGTCACTGGTGTTAGTCGAGTAAC

Basic information

species Arabidopsis thaliana
transcript AT3G49470.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G49470.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA04G40550.1 (Glycine max), 3'ss of exon 2
tttatggatttacttgactaagtttcggagaatagagatcccaatatgttta-----tagcatagtgaa-ttgttcttaaaattga---atgaagttttgttgttgtagGTGTAAGTGGAAGTTCAAAGCAGAGTAGAAGTGAAAAGAAGAGTAGGAAGGCGATGTTGAAGCTCGGTATGAAACCTGTCACTGGTGTTAGTCGAGTAAC
        ||| |        | | | |  | |      | | || |||||      |    |  |||  |||||| |||| | |    ||     ||||   ||  |||||    ||   ||||||||||||| |||||||| ||||||||  | || || ||||||||||| ||  |||||||||| |||||||||||| | || ||
--------tttgccctctgttgctgcagccatttctatgctctatttgtttggcttgttatctgttgaccttgttcataaattcgttttatttgactttgagatt-cagGTGGTGCTGAGGGTTCAAAGCAGAGCAGAAGTGAGAAGAAGAGCCGAAAAGCAATGTTGAAGCTGGGACTGAAACCTGTTACTGGTGTTAGTAGGGTCAC

upper sequence: AT3G49470.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA06G14250.1 (Glycine max), 3'ss of exon 2
tttatggatttacttgactaagtttcggagaatagagatcccaatatgtttatagcatagtgaattgttcttaaaattgaatgaagttttgttgttgtagGTGTAAGTGGAAGTTCAAAGCAGAGTAGAAGTGAAAAGAAGAGTAGGAAGGCGATGTTGAAGCTCGGTATGAAACCTGTCACTGGTGTTAGTCGAGTAAC
||      | |   ||      | ||   |                ||||    |   |     |||||| |||| | |  |           | || |||||    ||   ||||||||||||| |||||||| ||||||||| | || || ||||||||||| ||  | ||||||||||| ||||||||| | || ||
ttgccctctgtttctgctgccatatctatgctctatttatttggcttgttatctgttgatcttcttgttcataaattcgttttgttggactgagatgcagGTGGTGCTGAGGGTTCAAAGCAGAGCAGAAGTGAGAAGAAGAGTCGAAAAGCAATGTTGAAGCTGGGACTAAAACCTGTCACCGGTGTTAGTAGGGTCAC

upper sequence: AT3G49470.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv16s0098g00830.t01 (Vitis vinifera), 3'ss of exon 2
tttatggatttacttgactaagtttcggaga-atagagatcccaatatgtttatagcatagtgaattgttcttaaaattgaatgaagttttgttgt----tgtagGTGTAAGTGGAAGTTCAAAGCAGAGTAGAAGTGAAAAGAAGAGTAGGAAGGCGATGTTGAAGCTCGGTATGAAACCTGTCACTGGTGTTAGTCGAGTAAC
    || ||  | ||  |||| | | |   | |||    |   ||||| |  ||  ||  |   ||||| ||| || || |    ||||  |   |    || ||||| || ||   | ||||||||||| |||||||| ||||||||  | ||||| |||||||||||||| |||||||| || ||||||||| |  | || ||
---ctgtatccaattatctaattcttgtttacatactctttttaatat-tcaattacaatgaagattgtccttgaattt-atctcagttgggaaatgaggtgcagGTGCAAATGAGGGCTCAAAGCAGAGCAGAAGTGAGAAGAAGAGCCGCAAGGCAATGTTGAAGCTCGGCATGAAACCCGTTACTGGTGTTGGAAGGGTCAC

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|124880723|gb|EH959625.1|EH959625
EST:     GGAAGACGACGATGCTCAAG                         GTGTAAGTGGAAGTTCAAAGCAGAGTAGAAGTGAGAAGAAGAGTAGGAAGG
genomic: GGAAGACGACGATGCTCAAGgtgcttttga ... gttgttgtagGTGTAAGTGGAAGTTCAAAGCAGAGTAGAAGTGAAAAGAAGAGTAGGAAGG
EST: gi|125090069|gb|EL148201.1|EL148201
EST:     AGAGGAAGACGACAATGCTCAAG                         GTGTAAGTGGAAGTTCAAAGCAGAGTAGAAGTGAAAAGAAGAGTAGG
genomic: AGAGGAAGACGACGATGCTCAAGgtgcttttga ... gttgttgtagGTGTAAGTGGAAGTTCAAAGCAGAGTAGAAGTGAAAAGAAGAGTAGG
EST: gi|164096101|gb|EL984840.1|EL984840
EST:     GATGATGACGAAGAAGAGGAAGACGACGATGCTCAAG                         GTGTAAGTGGAAGTTCAAAGCAGAGTAGAAGTGAAAAGA-GAGTAGGAAGG
genomic: GATGATGACGAAGAAGAGGAAGACGACGATGCTCAAGgtgcttttga ... gttgttgtagGTGTAAGTGGAAGTTCAAAGCAGAGTAGAAGTGAAAAGAAGAGTAGGAAGG
EST: gi|164161914|gb|EL976701.1|EL976701
EST:     GATGATGACGAAGAAGAGGAAGACGACGATGCTCAAG                         GTGTAAGTGGAAGTTCAAAGCAGAGTAGAAGTGAAAAGAAGAGTAGGAAGG
genomic: GATGATGACGAAGAAGAGGAAGACGACGATGCTCAAGgtgcttttga ... gttgttgtagGTGTAAGTGGAAGTTCAAAGCAGAGTAGAAGTGAAAAGAAGAGTAGGAAGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgtttatagcatagtgaattgttcttaaaattgaatgaagttttgttgttgtagGTGTAAGTGGAAGTTCAAAGCAGAGTAGAAGTGAAAAGAAGAGTAGGAAGGCGATGTTGAAGCTCGGTATGAAACCTGTCACTGGTGTTAGTCGAGTAAC
                                         ttttgtt  CT-rich tract
                 aattgttcttaaaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttatggatttacttgactaagtttcggagaatagagatcccaatatgtttatagcatagtgaattgttcttaaaattgaatgaagttttgttgttgtagGTGTAAGTGGAAGTTCAAAGCAGAGTAGAAGTGAAAAGAAGAGTAGGAAGGCGATGTTGAAGCTCGGTATGAAACCTGTCACTGGTGTTAGTCGAGTAAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC
- - - - - - - - - - - - - - - aatagaga
- - - - - - - - - - - - - - - - - - - -cccaata