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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaattcccctaaaccaaaaccggtttattttacctaaaccggatttatcaaatcttaaccggttttaatttgttttcttttcagGGGACCGGGAATTGCAGTGTTGGTTTTGTCATGGGTCATAACACTATACACATTATGGCAAATGGTGGAAATGCATGAAATGGTTCCTGGAAAGCGTTTT

Basic information

species Arabidopsis thaliana
transcript AT5G40780.2
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G40780.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA19G24520.1 (Glycine max), 3'ss of exon 1
---gtaaattcccctaaaccaaa------accggtttattttacctaaaccggatt-tatcaaatcttaaccggttttaat----ttgttttcttttcagGGGACCGGGAATTGCAGTGTTGGTTTTGTCATGGGTCATAACACTATACACATTATGGCAAATGGTGGAAATGCATGAAATGGTTCCTGGAAAGCGTTTT
    ||||   |  || |  | |      |   |||| | |||   |||    | | ||  |    ||      ||| |       | |  | | |||||||| || ||  |  | ||| | ||  |||||||| |||| ||  | |||||  ||||||||||||| || ||||||||||||||||||||||| ||||||
tagataaacaacattatagtatatatactatgcgtttttgttatggaaagaaaaatgtactatgcgttttttaatttgagaatcactatgctttcttcagGGGTCCCGGTGTAACTGTGCTAGTCCTGTCATGGATCATTACCTTGTACACCCTATGGCAAATGGTAGAGATGCATGAAATGGTTCCTGGAAAACGTTTT

upper sequence: AT5G40780.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA16G06750.1 (Glycine max), 3'ss of exon 1
-------------gtaaattcccctaaaccaaaaccggtttattttacctaaaccggatttatcaaatcttaacc--ggttttaatttgttttcttttcagGGGACCGGGAATTGCAGTGTTGGTTTTGTCATGGGTCATAACACTATACACATTATGGCAAATGGTGGAAATGCATGAAATGGTTCCTGGAAAGCGTTTT
               | |       |||   ||||   ||| |  ||  || ||   | |   |   | ||||     |  | | | |||||| |||||||||| || ||  |  | ||  |  |  |||||||| |||| || || |||||  ||||||||||||| || |||||||||||||| |||||||| ||||||
cttccatgacctcaaagaaataaaaaaagataaacaactttttagtatatatactatactatgcgttttttaatttgagaatcactatgtttt-ttttcagGGGTCCTGGTGTAACTGTACTAATCCTGTCATGGATCATCACCCTGTACACTCTATGGCAAATGGTTGAGATGCATGAAATGGTACCTGGAAAACGTTTT

upper sequence: AT5G40780.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA19G22590.1 (Glycine max), 3'ss of exon 2
---gta-aattcccctaaaccaaaac-cggtttattttacctaaaccggattta--tcaaatcttaaccggtttta--att----tgttttctttt-cagGGGACCGGGAATTGCAGTGTTGGTTTTGTCATGGGTCATAACACTATACACATTATGGCAAATGGTGGAAATGCATGAAATGGTTCCTGGAAAGCGTTTT
   ||| |||  |   ||||     | |||||  | | || |        ||||    || | ||    | ||| |  |||    |||  |||| | |||||| || ||  |  |  |  |  |  | |||||| |||| || || |||||| ||||||||||||| || ||||||||||||||||| ||||| || |||
atggtataatgtcatgaaacttcggcacggttagtgtaacttgctttttttttaaactaagtgtttgttgatttgagaattacaatgtcctcttatacagGGGTCCAGGTGTAACTATACTTATCCTCTCATGGATCATCACCCTGTACACACTATGGCAAATGGTTGAGATGCATGAAATGGTTCCAGGAAAACGGTTT

upper sequence: AT5G40780.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv14s0171g00400.t01 (Vitis vinifera), 3'ss of exon 2
---------gtaaattcccctaaaccaaaaccggtttatttt----acctaaaccggatttatcaaatcttaaccggttttaatttgttttcttttcagGGGACCGGGAATTGCAGTGTTGGTTTTGTCATGGGTCATAACACTATACACATTATGGCAAATGGTGGAAATGCATGAAATGGTTCCTGGAAAGCGTTTT
          |   |      ||   | |   |  ||||| |      || |  |   || || ||   | |||       || |  |  |||||||||||| || ||  | |   |  ||||  | |||||| |||| || || |||||| ||||||||||||| || ||||| || ||||||||||| ||  | |||
gtatgtcttttgtgtctttacaagagatagttgccttattatttatgtctgattccatttgattaaggttgaacataaaaaaaatattgatcttttcagGGGTCCTGGTGTGGTGATAATGGTGCTATCATGGATCATTACTCTTTACACACTATGGCAAATGGTTGAGATGCACGAGATGGTTCCTGGGAAAAGGTTT

upper sequence: AT5G40780.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: EFJ10950 (Selaginella moellendorffii), 3'ss of exon 2
---------gtaaattcccctaaaccaaaaccggtttattttacctaaaccggatttatcaaatctt--aaccggttttaa----tttgttttcttttcagGGGACCGGGAATTGCAGTGTTGGTTTTGTCATGGGTCATAACACTATACACATTATGGCAAATGGTGGAAATGCATGAAATGGTTCCTGGAAAGCGTTTT
         ||   |  |||  || |    | | |  || ||    | |   | |||  ||| | ||  || |   |||||    ||| ||||| || ||||||||||||  |    ||  | ||  |||| ||||| || ||||| |||||  | |||||||||||||||||||| |||||||| || || ||| | |||
accctagtcgtgtgtcgcccgcaatcctc-cagctccatgttcttgacaaatggttttccaacttttccaagcaactttaaagatttttttttcgttccagGGGACCGGGGGTCCTTGTTCTTGTACTGTCGTGGGTGATCACACTCTACACGCTGTGGCAAATGGTGGAAATGCACGAAATGGTCCCGGGGAAGAGATTT

upper sequence: AT5G40780.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: EFJ25874 (Selaginella moellendorffii), 3'ss of exon 2
--------gtaaattcccctaaaccaaaaccggtttattttacctaaaccggatttatcaaatctt--aaccggttttaa---tttgttttct-tttcagGGGACCGGGAATTGCAGTGTTGGTTTTGTCATGGGTCATAACACTATACACATTATGGCAAATGGTGGAAATGCATGAAATGGTTCCTGGAAAGCGTTTT
           ||| | |   |||    || |    || ||    | |     |||  ||| | ||  || |   |||||   ||||||||   || ||||||||| ||  |    ||  | ||  | || ||||| || ||||| |||||  | |||||||||||||||||||| |||||||| || || ||| | |||
gtgtcacccgcaatcctcaagaactttcacagccccatgttcttgacaaatcgttttccaacttttccaagcaactttaaagatttgtttttcgttccagGGGACCAGGGGTCCTGGTTCTTGTACTCTCGTGGGTGATCACACTCTACACGCTGTGGCAAATGGTGGAAATGCACGAAATGGTCCCGGGGAAGAGATTT

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|125104895|gb|EL158831.1|EL158831
EST:     GTCGGTGCCGGAGTTCTTGGACTCCCTTACGCCATGTCTCAGCTCGGATG                         GGGGACCGGGAATTGCAGTGTTGGTTTTGTCATG
genomic: GTCGGTGCCGGAGTTCTTGGACTCCCTTACGCCATGTCTCAGCTCGGATGgtaaattccc ... ttcttttcagGGG-ACCGGGAATTGCAGTGTTGGTTTTGTCATG
EST: gi|116442688|gb|EG485280.1|EG485280
EST:     GTCGGTGCCGGAGTTCTTGGACTCCCTTACGCCATGTCTCAGCTCGGATG                         GGGACCGGGAATTGCAGTGTTGGTTTTGTCATGGGTCATAACACTATACAC
genomic: GTCGGTGCCGGAGTTCTTGGACTCCCTTACGCCATGTCTCAGCTCGGATGgtaaattccc ... ttcttttcagGGGACCGGGAATTGCAGTGTTGGTTTTGTCATGGGTCATAACACTATACAC
EST: gi|124775457|gb|EH865586.1|EH865586
EST:     GTCGGTGCCGGAGTTCTTGGACTCCCTTACGCCATGTCTCAGCTCGGATG                         GGGACCGGGAATTG
genomic: GTCGGTGCCGGAGTTCTTGGACTCCCTTACGCCATGTCTCAGCTCGGATGgtaaattccc ... ttcttttcagGGGACCGGGAATTG
EST: gi|125232575|gb|EL246660.1|EL246660
EST:     GTCGGTGCCGGAGTTCTTGGACTCCCTTACGCCATGTCTCAGCTCGGATG                         GGGACCGGGAATTGCAGTGTTGGT
genomic: GTCGGTGCCGGAGTTCTTGGACTCCCTTACGCCATGTCTCAGCTCGGATGgtaaattccc ... ttcttttcagGGGACCGGGAATTGCAGTGTTGGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttacctaaaccggatttatcaaatcttaaccggttttaatttgttttcttttcagGGGACCGGGAATTGCAGTGTTGGTTTTGTCATGGGTCATAACACTATACACATTATGGCAAATGGTGGAAATGCATGAAATGGTTCCTGGAAAGCGTTTT
                                       tttgttttcttttc  CT-rich tract
                                 ttttaatttgttttct  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaattcccctaaaccaaaaccggtttattttacctaaaccggatttatcaaatcttaaccggttttaatttgttttcttttcagGGGACCGGGAATTGCAGTGTTGGTTTTGTCATGGGTCATAACACTATACACATTATGGCAAATGGTGGAAATGCATGAAATGGTTCCTGGAAAGCGTTTT

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