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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttttgatattttctgtatttatggtataaagacttcagcttttgatatatatgtgattaatattgtaacaatttgatcgcacagTCTCGGGCTCATCCCCGTGAAATAATGACGGAAGTCCTGAAAGCCCTGCAAGATTTGAATGTATGTTGGAAGAAGATAGGGCACTACAACATGAAGTGCA

Basic information

species Arabidopsis thaliana
transcript AT3G01090.2
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G01090.2 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: LOC_Os05g45420.3 (Oryza sativa), 3'ss of exon 9
--gttttgatatt-ttctgtatttatggtataaagacttcagcttttgatatatatg-tgattaatattgtaacaatttgatcgcacagTCTCGGGCTCATCCCCGTGAAATAATGACGGAAGTCCTGAAAGCCCTGCAAGATTTGAATGTATGTTGGAAGAAGATAGGGCACTACAACATGAAGTGCA
   || || | ||  | |    || |  | ||   |||| |  | ||   |  |||  | ||| || ||||    ||||  |   ||||||||| || ||||| || |||||||| || ||||| || ||||| ||||||||  | ||||| || ||||||||||| || || || |||||||| ||||
gttttatgctgttactataaggttcttatttattcactttatttattataagttatcctaattcat-ttgtctgtatttattta-acagTCTCGAGCACATCCACGAGAAATAATAACTGAAGTTCTTAAAGCTCTGCAAGAGCTAAATGTTTGCTGGAAGAAGATTGGACATTATAACATGAAATGCA

upper sequence: AT3G01090.2 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GRMZM2G180704_T01 (Zea mays), 3'ss of exon 9
gttttgatattttctgtatttatggtataaagacttcagcttttgatatatatgtgatt-aatattgtaacaatttgatcgcacagTCTCGGGCTCATCCCCGTGAAATAATGACGGAAGTCCTGAAAGCCCTGCAAGATTTGAATGTATGTTGGAAGAAGATAGGGCACTACAACATGAAGTGCA
    | || |  | | || | |   |  |     ||    ||||  |   | | | ||| ||||||       ||||       ||||||| || |||||    ||||||||| | ||||| |||||||| |||||||| || ||||| |  ||||| |||||||| ||||| |||||||||||||
---gtaatctaatttctagtaacc-tccaccattttattattttattgcttttctcattcaatatttctttgttttgtgt---tagTCTCGAGCACATCCAAAAGAAATAATGTCTGAAGTGCTGAAAGCTCTGCAAGAATTAAATGTTTACTGGAAAAAGATAGGTCACTATAACATGAAGTGCA

upper sequence: AT3G01090.2 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GRMZM2G077278_T01 (Zea mays), 3'ss of exon 9
---gttttgatattttctgtat-ttatggtataaagacttcagcttttgatatatatgt-gattaatattgtaacaatttgatcgcacagTCTCGGGCTCATCCCCGTGAAATAATGACGGAAGTCCTGAAAGCCCTGCAAGATTTGAATGTATGTTGGAAGAAGATAGGGCACTACAACATGAAGTGCA
    ||||  | ||   |  || ||||| | |      ||||    ||  |    ||   |||| || |      ||||   ||  ||||||||| || ||||| || |||||||| |  ||||| || ||||| ||||||||  ||||||| |  ||||| ||||| || |||||||||||||| ||||
gtaattttcttgttaagtacatcttatgatgtg----tttcatgaattattccgaattccgattcatttatctgtaatt--gtctaacagTCTCGAGCACATCCACGAGAAATAATAAGTGAAGTGCTTAAAGCTCTGCAAGAACTGAATGTTTACTGGAAAAAGATTGGACACTACAACATGAAATGCA

upper sequence: AT3G01090.2 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA08G26180.1 (Glycine max), 3'ss of exon 9
--------gttttgatattttctgtatttatggtataaagacttcagcttttgata---tatatgtgatta---atattgtaacaatttgatcgc-acagTCTCGGGCTCATCCCCGTGAAATAATGACGGAAGTCCTGAAAGCCCTGCAAGATTTGAATGTATGTTGGAAGAAGATAGGGCACTACAACATGAAGTGCA
        ||||  || |||    || ||    |   || | ||    |||||||    | |  ||  |||   |  || |    |||   | |  ||||||||| || ||||| |||||||||||||| || ||||| |||||  ||||||| || ||||| |||||||||||||| || ||||||||||||||||| |
taacggctgtttgaatttttgtaatagttgccatcagaaaaattgtagttttgatgtcttgttggtagttatatactttttgttcattatcttgtgacagTCTCGAGCCCATCCTCGTGAAATAATGACTGAGGTCCTTAAAGCTTTGCAAGAATTAAATGTTTGTTGGAAGAAGATTGGTCACTACAACATGAAGTGTA

upper sequence: AT3G01090.2 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA18G49770.1 (Glycine max), 3'ss of exon 10
--------gttttgatattttctgtatttatgg----tataaagacttcagcttt--tgatatatatgtgattaatattgtaacaatttgatcgc-acagTCTCGGGCTCATCCCCGTGAAATAATGACGGAAGTCCTGAAAGCCCTGCAAGATTTGAATGTATGTTGGAAGAAGATAGGGCACTACAACATGAAGTGCA
            || |  ||| |||| |  |||     | ||| | |  ||  ||  ||   | |  ||  ||| |    |     ||   | |  ||||||||| || ||||| |||||||||||||| || || || |||||  ||||||| || ||||| |||||||||||||| || ||||||||||||||||| |
atatctaaaagctgtttgtttttgtaatagtggccatcagaaaaattgtagtcttgatgtcttgttggtagttacttactttttgtttatcttgtgacagTCTCGAGCCCATCCTCGTGAAATAATGACTGAGGTTCTTAAAGCTTTGCAAGAATTAAATGTTTGTTGGAAGAAGATTGGTCACTACAACATGAAGTGTA

upper sequence: AT3G01090.2 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA13G05700.1 (Glycine max), 3'ss of exon 9
---------gttttgatattttctgtatttatggtataaagacttcagcttttgat-atatatgtgattaatattgtaacaatttgatcgc-----acagTCTCGGGCTCATCCCCGTGAAATAATGACGGAAGTCCTGAAAGCCCTGCAAGATTTGAATGTATGTTGGAAGAAGATAGGGCACTACAACATGAAGTGCA
         ||| | | |  |  || | || || | ||   | ||      ||  |  |   || | |   | |||      |||| |  |     | ||||||| || || || |||||||||||||| || ||||| ||||| || ||||| || ||||| |||||||||||||| || ||||| |||||||||||||
ttattaatggttatcagaaatattgaagttctgatgtacttattttgatggttacttgtgactgaggtctttgttggttatgtttgttaacttgtgatagTCTCGAGCCCAACCACGTGAAATAATGACTGAGGTCCTTAAAGCTCTACAAGAATTAAATGTTTGTTGGAAGAAGATTGGACACTATAACATGAAGTGCA

upper sequence: AT3G01090.2 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: Vv14s0108g01230.t01 (Vitis vinifera), 3'ss of exon 9
--------------gttttgatattttctgtatttatggtataaagacttcagcttttgatatatatgtgattaatattgtaacaatttgatcgc-acagTCTCGGGCTCATCCCCGTGAAATAATGACGGAAGTCCTGAAAGCCCTGCAAGATTTGAATGTATGTTGGAAGAAGATAGGGCACTACAACATGAAGTGCA
                |||   || |||| |  ||||    || |   ||  |||| | | | |    | || | |||  |  ||| |   |    ||||||||| || || ||  |  | |||||||| ||||| || ||||| || |||||  ||||||| |||||||| ||||| ||||| ||||||||||| ||||
gctcatcaaaatattatttacaatcttctttgattatatcttatactgttttgcttataagaaaagaataatgattatcttttcaactaacttttgacagTCTCGAGCCCAGCCTAGACAGATAATGACTGAAGTTCTCAAAGCTCTACAAGAACTGAATGTGTGTTGGAAAAAGATTGGGCATTACAACATGAAATGCA

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|164002416|gb|ES046108.1|ES046108
EST:     GCTTGAGATCTCAATACCCTGTTGAGAGAAAATGGGCTCTTGGACTTCAG                         TCTCGGGCTCATCCCCGTGAAATAATGACGGAAGTCCTGAAAG
genomic: GCTTGAGATCTCAATACCCTGTTGAGAGAAAATGGGCTCTTGGACTTCAGgttttgatat ... gatcgcacagTCTCGGGCTCATCCCCGTGAAATAATGACGGAAGTCCTGAAAG
EST: gi|124787153|gb|EH876832.1|EH876832
EST:     GGCTCTTGGACTTCAG                         TCTCGGGCTCATCCCCGTGAAATAATGACGGAAGTCCTGAAAGCCCTGCAA
genomic: GGCTCTTGGACTTCAGgttttgatat ... gatcgcacagTCTCGGGCTCATCCCCGTGAAATAATGACGGAAGTCCTGAAAGCCCTGCAA
EST: gi|124889038|gb|EH967940.1|EH967940
EST:     CTCTTGGACTTCAG                         TCTCGGGCTCATCCCCGTGAAATAATGACGGAAGTCCTGAAAGCCCTGCAA
genomic: CTCTTGGACTTCAGgttttgatat ... gatcgcacagTCTCGGGCTCATCCCCGTGAAATAATGACGGAAGTCCTGAAAGCCCTGCAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agacttcagcttttgatatatatgtgattaatattgtaacaatttgatcgcacagTCTCGGGCTCATCCCCGTGAAATAATGACGGAAGTCCTGAAAGCCCTGCAAGATTTGAATGTATGTTGGAAGAAGATAGGGCACTACAACATGAAGTGCA
          ttttgatatatatgtg  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttttgatattttctgtatttatggtataaagacttcagcttttgatatatatgtgattaatattgtaacaatttgatcgcacagTCTCGGGCTCATCCCCGTGAAATAATGACGGAAGTCCTGAAAGCCCTGCAAGATTTGAATGTATGTTGGAAGAAGATAGGGCACTACAACATGAAGTGCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG