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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaaaacaaataaacattactgcctttaatctttcttgttgtgattggtttgtctcactgggttcttgattgattgtgtgatattaaacaaaacagGTACAACTTGAAGAAACTGACTTACGAAGAGAGGAAGAACAAGTTGATCGAGAGAGTGAAGGCATTAAACGGAGCAGGTGGTGATGATGATGATGAGGAT

Basic information

species Arabidopsis thaliana
transcript AT5G39740.2
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G39740.2 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA07G06580.1 (Glycine max), 3'ss of exon 8
--------------------------------------------------------------------------------------gtaaaaacaaataaacattactgcctttaatcttt--cttgttgtgattggt-ttgtctcactgg-----gttcttgattgattgtgtgatattaaacaaaacagGTACAACTTGAAGAAACTGACTTACGAAGAGAGGAAGAACAAGTTGATCGAGAGAGTGAAGGCATTAAACGGAGCAGGTGGTGATGATGATGATGAGGAT
                                                                                      |    | |   |     | |||      ||| ||    | ||     ||||| ||  || | |||     |||| |||  |  | ||   |           |||||||||||||||||| |||||||| || |||||||||   |||||||| |   | |||  | |  | |||   || | || | | ||||| ||||| || 
gtaaaaatgagttttgacttgaactagaataatactagattcttgatttccagcagtgattttcagctatttatgtgctatattgggcgtgaccgtttttgtttgacttttagaaattttggattggtaacttttggtatttactgattggagaatgttcctgagagtatctgctctgcctctttctgcagGTACAACTTGAAGAAGCTGACTTATGAGGAGAGGAAGGCTAAGTTGATTGCACGTGTGGCGTCTCTCAACTCTGCTGCTGATAACGATGAAGATGATGAG
















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|125085339|gb|EL145213.1|EL145213
EST:     AAAACCGAGAAATCTGCTCCCAAGGAACACAAGAG                         GTACAACTTGAAGAAACTGACTTACGAAGAGAGGAAGAACAAGTTGATCGA
genomic: AAAACCGAGAAATCTGCTCCCAAGGAACACAAGAGgtaaaaacaa ... aacaaaacagGTACAACTTGAAGAAACTGACTTACGAAGAGAGGAAGAACAAGTTGATCGA
EST: gi|164162357|gb|ES018583.1|ES018583
EST:     AAGAAAACCGAGAAATCTGCTCCCAAGGAACACAAGAG                         GTACAACTTGAAGAAACTGACTTACGAAGAGAGGAAGAACAAGTTGATCGA
genomic: AAGAAAACCGAGAAATCTGCTCCCAAGGAACACAAGAGgtaaaaacaa ... aacaaaacagGTACAACTTGAAGAAACTGACTTACGAAGAGAGGAAGAACAAGTTGATCGA
EST: gi|164219353|gb|ES039589.1|ES039589
EST:     GAACCCAACCATAAGAAAACCGAGAAATCTGCTCCCAAGGAACACAAGAG                         GTACAACTTGAAGAAACTGACTTACGAAGAGAGGAAGAACAAGTTGATCGA
genomic: GAACCCAACCATAAGAAAACCGAGAAATCTGCTCCCAAGGAACACAAGAGgtaaaaacaa ... aacaaaacagGTACAACTTGAAGAAACTGACTTACGAAGAGAGGAAGAACAAGTTGATCGA
EST: gi|164109740|gb|ES138490.1|ES138490
EST:     GAAAACCGAGAAATCTGCTCCCAAGGAACACAAGAG                         GTACAACTTGAAGAAACTGACTTACGAAGAGAGGAAGAACAAGTTGATCGA
genomic: GAAAACCGAGAAATCTGCTCCCAAGGAACACAAGAGgtaaaaacaa ... aacaaaacagGTACAACTTGAAGAAACTGACTTACGAAGAGAGGAAGAACAAGTTGATCGA
EST: gi|163983469|gb|ES037915.1|ES037915
EST:     GAACCCAACCATAAGAAAACCGAGAAATCTGCTCCCAAGGAACACAAGAG                         GTACAACTTGAAGAAACTAGACTTACGAAGAGAGGAAGAACAAGTTGATCG
genomic: GAACCCAACCATAAGAAAACCGAGAAATCTGCTCCCAAGGAACACAAGAGgtaaaaacaa ... aacaaaacagGTACAACTTGAAGAAACT-GACTTACGAAGAGAGGAAGAACAAGTTGATCG
EST: gi|164208569|gb|ES192142.1|ES192142
EST:     AACCCAACCATAAGAAAACCGAGAAAATCTGCTCCCAAGGAACACAAGAG                         GTACAACTTGAAGAAACTGACTTACGAAGAGAGGAAGAACAAGTTGATCGA
genomic: AACCCAACCATAAGAAAACCGAG-AAATCTGCTCCCAAGGAACACAAGAGgtaaaaacaa ... aacaaaacagGTACAACTTGAAGAAACTGACTTACGAAGAGAGGAAGAACAAGTTGATCGA
EST: gi|125075202|gb|EL138856.1|EL138856
EST:     GAACCCAACCATAAGAAAACCGAGAAATCTGCTCCCAAGGAACACAAGAG                         GTACAACTTGAAGAAACTGACTTACGAAGAGAGGAAGAACAAGTTGAT
genomic: GAACCCAACCATAAGAAAACCGAGAAATCTGCTCCCAAGGAACACAAGAGgtaaaaacaa ... aacaaaacagGTACAACTTGAAGAAACTGACTTACGAAGAGAGGAAGAACAAGTTGAT
EST: gi|125176355|gb|EL195724.1|EL195724
EST:     GAACCCAACCATAAGAAAACCGAGAAATCTGCTCCCAAGGAACACAAGAG                         GTACAACTTGAAGAAACTGACTTACGAAGAGAGGAAGAACAAGTTGA
genomic: GAACCCAACCATAAGAAAACCGAGAAATCTGCTCCCAAGGAACACAAGAGgtaaaaacaa ... aacaaaacagGTACAACTTGAAGAAACTGACTTACGAAGAGAGGAAGAACAAGTTGA
EST: gi|164119042|gb|ES158592.1|ES158592
EST:     ATCTGCTCCCAAGGAACACAAGAG                         GTACAACTTGAAGAAACTGACTTACGAAGAGAGGAAGAACAAGTTGATCGA
genomic: ATCTGCTCCCAAGGAACACAAGAGgtaaaaacaa ... aacaaaacagGTACAACTTGAAGAAACTGACTTACGAAGAGAGGAAGAACAAGTTGATCGA
EST: gi|164169412|gb|ES130838.1|ES130838
EST:     GAACCCAACCATAAGAAAACCGAGAAATCTGCTCCCAAGGAACACAAGAG                         GTACAACTTGAAGAAACTGACTTACGAAGAGAGGAAGAACAAGTTGATCGA
genomic: GAACCCAACCATAAGAAAACCGAGAAATCTGCTCCCAAGGAACACAAGAGgtaaaaacaa ... aacaaaacagGTACAACTTGAAGAAACTGACTTACGAAGAGAGGAAGAACAAGTTGATCGA
EST: gi|124844766|gb|EH929203.1|EH929203
EST:     GAACCCAACCATAAGAAAACCGAGAAATCTGCTCCCAAGGAACACAAGAG                         GTACAACTTGAAGAAACTGACTTACGAAGAGAGGAAGAACA
genomic: GAACCCAACCATAAGAAAACCGAGAAATCTGCTCCCAAGGAACACAAGAGgtaaaaacaa ... aacaaaacagGTACAACTTGAAGAAACTGACTTACGAAGAGAGGAAGAACA
EST: gi|164234072|gb|ES158820.1|ES158820
EST:     GAACCCAACCATAAGAAAACCGAGAAATCTGCTCCCAAGGAACACAAGAG                         GTACAACTTGAAGAAACTGACTTACGAAGAGAGGAAGAACAAGTTGATCGA
genomic: GAACCCAACCATAAGAAAACCGAGAAATCTGCTCCCAAGGAACACAAGAGgtaaaaacaa ... aacaaaacagGTACAACTTGAAGAAACTGACTTACGAAGAGAGGAAGAACAAGTTGATCGA
EST: gi|125237949|gb|EL252034.1|EL252034
EST:     TCTGCTCCCAAGGAACACAAGAG                         GTACAACTTGAAGAAACTGACTTACGAAGAGAGGAAGAACAAGTTGATCGA
genomic: TCTGCTCCCAAGGAACACAAGAGgtaaaaacaa ... aacaaaacagGTACAACTTGAAGAAACTGACTTACGAAGAGAGGAAGAACAAGTTGATCGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgattggtttgtctcactgggttcttgattgattgtgtgatattaaacaaaacagGTACAACTTGAAGAAACTGACTTACGAAGAGAGGAAGAACAAGTTGATCGAGAGAGTGAAGGCATTAAACGGAGCAGGTGGTGATGATGATGATGAGGAT
                                     tgatattaaacaaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaaaacaaataaacattactgcctttaatctttcttgttgtgattggtttgtctcactgggttcttgattgattgtgtgatattaaacaaaacagGTACAACTTGAAGAAACTGACTTACGAAGAGAGGAAGAACAAGTTGATCGAGAGAGTGAAGGCATTAAACGGAGCAGGTGGTGATGATGATGATGAGGAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAT