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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgaggccacatatttgatttacctgactagaaatttaactacgtactgaattttttgtttgacaacttatagGAAATGTTTACGAATTTGGGTGAGCTCTTATGTACGATCACTGGATTCGACTCTTTCTCATTGCAACCTAATGCCGGTGCTGCTGGCGAGTACGCCGGGC

Basic information

species Arabidopsis thaliana
transcript AT2G26080.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT2G26080.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA14G10820.1 (Glycine max), 3'ss of exon 5
------------------------------------------gtgaggccacatatttgat-ttacctgactagaaatttaac---tacgtactgaattttttgtttga------caact----tat-agGAAATGTTTACGAATTTGGGTGAGCTCTTATGTACGATCACTGGATTCGACTCTTTCTCATTGCAACCTAATGCCGGTGCTGCTGGCGAGTACGCCGGGC
                                             |   || | || |  | ||   || ||  || | |       | ||  ||  || ||||| | |      ||| |    ||| |||||||||| |  ||||||||||| || || || || |||||||| |||||||| ||||| |||||||| ||||| ||||||||||| || || || || |
gtaattccgggtttaaataatcttacaacaataaagattcaaagaaattcatagatatactgttctgtgcctgaaagtatgggatagaagttgtgttttctttgtctaaaacaagcaaatctggtatcagGAAATGTTCAACAATTTGGGTGAACTGTTGTGCACCATCACTGGGTTCGACTCCTTCTCTTTGCAACCAAATGCTGGTGCTGCTGGAGAATATGCTGGAC

upper sequence: AT2G26080.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA17G34690.1 (Glycine max), 3'ss of exon 5
------------------------------------------gtgaggccacatatttgat---ttacctgactagaaatttaact---acgtactgaattttttgtttgacaactta----------tagGAAATGTTTACGAATTTGGGTGAGCTCTTATGTACGATCACTGGATTCGACTCTTTCTCATTGCAACCTAATGCCGGTGCTGCTGGCGAGTACGCCGGGC
                                             |   ||||||| |      || | || ||  |||| |       | ||  ||  || ||||| | |  | | |           |||||||||| |  ||||||||||| || || || || |||||||| || ||||| ||||| |||||||| ||||| ||||||||||| || || ||||| |
gtaattctatgtttaaataatcttacaacaattatgactcaaagaaattcacatatatatactgttgcgtgcctgaaaatatgggatagaagtcgtgttttctttgtctaaacaatcaaatctggtatcagGAAATGTTCAATAATTTGGGTGAACTGTTGTGCACCATCACTGGGTTTGACTCCTTCTCCTTGCAACCAAATGCTGGTGCTGCTGGAGAATATGCCGGAC

upper sequence: AT2G26080.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA06G05470.1 (Glycine max), 3'ss of exon 6
----------------gtgaggccacatatttgatttacctgactagaaatt---taactacgtactgaattttttgtttgacaactta----tagGAAATGTTTACGAATTTGGGTGAGCTCTTATGTACGATCACTGGATTCGACTCTTTCTCATTGCAACCTAATGCCGGTGCTGCTGGCGAGTACGCCGGGC
                 | |    | |  ||   ||||       | | ||    ||| |   |  ||   | |      |  ||  |      |||||||||||   ||||||||| | || || ||||| ||||| || || ||||| ||||| |||||||||||||| ||||||||||| || || || || |
gtatgtacaaggctgaataaaattaaa-gttctttttatacaggaaaatatgggataaatgttttttggtgtctaaacaagcaaatctggtaccagGAAATGTTTGAAAATTTGGGTAAACTGTTGTGTACAATCACCGGGTTTGACTCCTTCTCTTTGCAACCTAATGCTGGTGCTGCTGGAGAATATGCTGGAC

upper sequence: AT2G26080.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA04G05420.2 (Glycine max), 3'ss of exon 5
----gtgaggccacatatttgatttacctgact---agaaatttaactacgtactgaatttttt-----gtttga-----caact----tat-agGAAATGTTTACGAATTTGGGTGAGCTCTTATGTACGATCACTGGATTCGACTCTTTCTCATTGCAACCTAATGCCGGTGCTGCTGGCGAGTACGCCGGGC
    ||        | |||| ||  |  || ||   | | |   || |  |   | ||| ||||     || | |     ||| |    ||| ||||||||||    ||||||||| |  |  | ||||| |||||||| || || || ||||| |||||||||||||| |||||||| || || || || || |
gtatgtacatggctaaatttaataaaagtgccttttatacaggaaaatgtgggataaatattttttggtgtctaaacaagcaaatctggtatcagGAAATGTTCGAAAATTTGGGTAAATTGCTGTGTACAATCACTGGGTTTGATTCCTTCTCTTTGCAACCTAATGCTGGTGCTGCCGGAGAATATGCTGGAC

upper sequence: AT2G26080.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv11s0016g02280.t01 (Vitis vinifera), 3'ss of exon 6
----------------------------gtgaggccacatatttgatttacctgactagaaatttaactacgtactgaattttttgtttgacaacttatagGAAATGTTTACGAATTTGGGTGAGCTCTTATGTACGATCACTGGATTCGACTCTTTCTCATTGCAACCTAATGCCGGTGCTGCTGGCGAGTACGCCGGGC
                             |    ||||||||  || | | |  |    | | ||    ||  | | | |  |   |||      |  ||||| ||||| |   |||||||||| || || ||||| ||||||||||||||||| |||||  ||||||||||||| |||||||| || ||||| || ||||
gtaacttaaatttcttgaaattctgattctatatccacatataagagtaatccaaggtcagactt---cacccattcactcataaattttcattttcttagGAGATGTTCAATGATTTGGGTGAACTATTGTGTACCATCACTGGATTCGACTCGTTCTCTCTGCAACCTAATGCTGGTGCTGCAGGGGAGTATGCTGGGC

upper sequence: AT2G26080.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv04s0008g01300.t01 (Vitis vinifera), 3'ss of exon 5
------------------------gtgaggccacatatttgatttacctgactagaaatttaacta-cgtactga-attttttgtt------tgacaacttat------agGAAATGTTTACGAATTTGGGTGAGCTCTTATGTACGATCACTGGATTCGACTCTTTCTCATTGCAACCTAATGCCGGTGCTGCTGGCGAGTACGCCGGGC
                          || |  |||| ||||   |  ||  || | |  ||||||| |  | ||| ||| |||| |      | |  | || |      |||||||||| |  || |||||||| || |||||||| ||||||||||| |||||||||||||||||||| ||||| |||||| |||||||||| || || |
gtagttaccaacattttctttacctggaagttacatgtttgtgctgtctttcttgca--ttaactagcaaattgacattgtttgctgttgaattatgattttttttgctagGAAATGTTCAATAACTTGGGTGAACTATTATGTACCATCACTGGATTTGACTCTTTCTCATTGCAACCCAATGCTGGTGCTTCTGGCGAGTATGCTGGCC

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|116425822|gb|EG468414.1|EG468414
EST:     CACCAACATGCACCCTTTTTGCTCCTGTTGAACAAGCCCAAGGTTATCAG                         GAAATGTTTACGAATTTGGGTGAGCTCTTATGTACGATCACTGGATTCGAC
genomic: CACCAACATGCACCCTTTT-GCTCCTGTTGAACAAGCCCAAGGTTATCAGgtgaggccac ... caacttatagGAAATGTTTACGAATTTGGGTGAGCTCTTATGTACGATCACTGGATTCGAC
EST: gi|47829567|gb|CK119251.1|CK119251
EST:     TCACCAACATGCACCCTTTTGCTCCTGTTGAACAAGCCCAAGGTTATCAG                         GAAATGTTTACGAATTTGGGTGAGCTCTTATGTACGATCACTGGATTCGAC
genomic: TCACCAACATGCACCCTTTTGCTCCTGTTGAACAAGCCCAAGGTTATCAGgtgaggccac ... caacttatagGAAATGTTTACGAATTTGGGTGAGCTCTTATGTACGATCACTGGATTCGAC
EST: gi|47831551|gb|CK121235.1|CK121235
EST:     TCACCAACATGCACCCTTTTGCTCCTGTTGAACAAGCCCAAGGTTATCAG                         GAAATGTTTACGAATTTGGGTGAGCTCTTATGTACGATCACTGGATTCGAC
genomic: TCACCAACATGCACCCTTTTGCTCCTGTTGAACAAGCCCAAGGTTATCAGgtgaggccac ... caacttatagGAAATGTTTACGAATTTGGGTGAGCTCTTATGTACGATCACTGGATTCGAC
EST: gi|47830981|gb|CK120665.1|CK120665
EST:     TCACCAACATGCACCCTTTTGCTCCTGTTGAACAAGCCCAAGGTTATCAG                         GAAATGTTTACGAATTTGGGTGAGCTCTTATGTACGATCACTGGATTCGAC
genomic: TCACCAACATGCACCCTTTTGCTCCTGTTGAACAAGCCCAAGGTTATCAGgtgaggccac ... caacttatagGAAATGTTTACGAATTTGGGTGAGCTCTTATGTACGATCACTGGATTCGAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttacctgactagaaatttaactacgtactgaattttttgtttgacaacttatagGAAATGTTTACGAATTTGGGTGAGCTCTTATGTACGATCACTGGATTCGACTCTTTCTCATTGCAACCTAATGCCGGTGCTGCTGGCGAGTACGCCGGGC
          tagaaatttaacta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgaggccacatatttgatttacctgactagaaatttaactacgtactgaattttttgtttgacaacttatagGAAATGTTTACGAATTTGGGTGAGCTCTTATGTACGATCACTGGATTCGACTCTTTCTCATTGCAACCTAATGCCGGTGCTGCTGGCGAGTACGCCGGGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT