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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatacttcgggtatttggagttgtataaccacaatattctagatgcaggccctagaatgaaattggaactagtcaatttttatgtgttgtggcttgttacgttcactaatgtgttttatgttttggggtgtgaatgggaaattagGTGGTCAGAAAAGCAGAGTTGCATTTGCGAAGATAACATTCAAGAAACCACACTTGCTATTGCTTGATGAGCCGTCCAATCATCTT

Basic information

species Arabidopsis thaliana
transcript AT1G64550.1
intron # 15
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G64550.1 (Arabidopsis thaliana), 3'ss of exon 15
lower sequence: LOC_Os02g58020.2 (Oryza sativa), 3'ss of exon 15
------------gtatacttcgggtatttggagttgtataaccacaatattctagatgcaggccctagaatgaaattggaactagtcaatttttatgtgttgtggcttgttacgttcactaatgtgttttatgttttgg--ggtgtgaatgggaaattagGTGGTCAGAAAAGCAGAGTTGCATTTGCGAAGATAACATTCAAGAAACCACACTTGCTATTGCTTGATGAGCCGTCCAATCATCTT
             | |  |    || ||  |  |  || |  |   ||||      | |  |    |  |  || |  ||||||  |  ||      || |    ||  |        || |  | | | | ||  ||    | |    |   |    ||||||||||||||| || ||||| ||||| ||||| || |||||||| |||||| |  |  | || |||||||| || || ||||||
gtaatgagagcgttttgatagatgtcttaagcatattaaaggctgcatatggcctttcccagtttcatgagaaattgagaactatcctcttgcccaatgattcatctgctcgtagaatcttaaatttgtca-gtcctgattagagcctttccaatcccagGTGGTCAGAAAAGTAGGGTTGCCTTTGCAAAGATCACCTTCAAGAAGCCACACATTATTCTTCTCGATGAGCCTTCTAACCATCTT

upper sequence: AT1G64550.1 (Arabidopsis thaliana), 3'ss of exon 15
lower sequence: GLYMA20G16170.1 (Glycine max), 3'ss of exon 14
---gtatacttcgggtatttggagttgtataaccacaatattctagatg--caggccctagaatga-aattggaac---tagtcaatttttatgtgttgtggcttgttacgttcactaatgtgttttatgttttggggtg--tgaatgggaaattagGTGGTCAGAAAAGCAGAGTTGCATTTGCGAAGATAACATTCAAGAAACCACACTTGCTATTGCTTGATGAGCCGTCCAATCATCTT
    | |  |    ||      | ||  |||| ||     ||   |||    | |  |    || | |||||| ||     ||   | || |  ||   ||| |   ||  |    || ||  || ||| ||||    |   | |||     | ||||||||||||||||||| ||||| ||||| |||||||| |||||||| |||||| |  ||||||||||||| || ||||||||||| 
gtattgtcttcaaagtcaccataatt-cataaacaattcgttaatgatttttaagaacagcgataataattgggacactcggtgggtgttgagttgcaatggatatatatttctgtta-tgaattatatttttttacttctctaaattctttactagGTGGTCAGAAAAGCAGGGTTGCCTTTGCAAAGATAACTTTCAAGAAGCCACACATAATATTGCTTGATGAACCATCCAATCATCTG

upper sequence: AT1G64550.1 (Arabidopsis thaliana), 3'ss of exon 15
lower sequence: GLYMA13G10530.1 (Glycine max), 3'ss of exon 14
gtatacttcgggtatttggagttgtataaccacaatattctagatgcaggccctagaatgaaat----tggaactagtcaatttttatgtgttgtggcttgttacgttcactaatgtgt-tttatgttttggggtgtg--------------aatgggaaattagGTGGTCAGAAAAGCAGAGTTGCATTTGCGAAGATAACATTCAAGAAACCACACTTGCTATTGCTTGATGAGCCGTCCAATCATCTT
||||  |     || |     |  |  |   |||||    || |||          |  |||||    |       | || ||  |  |||||||   |||  | |   |   ||||   ||| |||| ||   |||               || |    | ||||||||||||||||||| ||||| ||||| |||||||| || ||||| |||||| |  |||||||||||||||| ||||||||||| 
gtattgtcttcatagtcatcataattcataaacaattcgtta-atgttcttttggaacagaaataatgtatgttgggacacttggtgggtgttgtaagttgcaatggatatagatgtacctttctgttatgaattgtatttttacttctctaaacgctttactagGTGGTCAGAAAAGCAGGGTTGCCTTTGCAAAGATAACTTTTAAGAAGCCACACATAATATTGCTTGATGAGCCATCCAATCATCTG

upper sequence: AT1G64550.1 (Arabidopsis thaliana), 3'ss of exon 15
lower sequence: Vv02s0025g02160.t01 (Vitis vinifera), 3'ss of exon 15
gtatacttcgggtatttggagttgtataaccacaatattctagatgcaggccctagaatgaaattggaactag-tcaatttttatgtgttgtggcttgttacgttcactaatgtgt-tttatgttttggggtgtgaatgggaaattagGTGGTCAGAAAAGCAGAGTTGCATTTGCGAAGATAACATTCAAGAAACCACACTTGCTATTGCTTGATGAGCCGTCCAATCATCTT
                                               | ||   |        |   | | |  || || || |  ||||| |  |     | ||  || | |||| ||||||  |||   | |  |||    || |||||||||||||||||||||||||||||| || ||||| ||||| ||||| ||| |  || | |||||||| || || |||||||||
---------------------------------------------ttaagcttgaaggctttgtcacatcaatctctatattaacctgttg-gcataaaatcattttctcaggtgtatttatgaattg--ttctatatgatgtatcagGTGGTCAGAAAAGCAGAGTTGCATTTGCAAAAATAACTTTCAAAAAACCTCACATCATACTTCTTGATGAACCATCAAATCATCTT

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|164158328|gb|ES043623.1|ES043623
EST:     TCTTGGGGTAACTGGAAATCTTGCACTGCAGCCCATGTACACTTTATCAG                         GTGGTCAGAAAAGCA
genomic: TCTTGGGGTAACTGGAAATCTTGCACTGCAGCCCATGTACACTTTATCAGgtatacttcg ... gggaaattagGTGGTCAGAAAAGCA
EST: gi|124792949|gb|EH882628.1|EH882628
EST:     TCTTGGGGTAACTGGAAATCTTGCACTGCAGCCCATGTACACTTTATCAG                         GTGGTCAGAAAAGCAGAGTTGC
genomic: TCTTGGGGTAACTGGAAATCTTGCACTGCAGCCCATGTACACTTTATCAGgtatacttcg ... gggaaattagGTGGTCAGAAAAGCAGAGTTGC
EST: gi|124733842|gb|EH825244.1|EH825244
EST:     TCTTGGGGTAACTGGAAATCTTGCACTGCAGCCCATGTACACTTTATCAG                         GTGGTCAGAAAAGCAGAGTTGCATT
genomic: TCTTGGGGTAACTGGAAATCTTGCACTGCAGCCCATGTACACTTTATCAGgtatacttcg ... gggaaattagGTGGTCAGAAAAGCAGAGTTGCATT
EST: gi|125022392|gb|EL094661.1|EL094661
EST:     TGTACACTTTATCAG                         GTGGTCAGAAAAGCAGAGTTGCATTTGCGAAGATAACATTCAAGAAACCAC
genomic: TGTACACTTTATCAGgtatacttcg ... gggaaattagGTGGTCAGAAAAGCAGAGTTGCATTTGCGAAGATAACATTCAAGAAACCAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggcttgttacgttcactaatgtgttttatgttttggggtgtgaatgggaaattagGTGGTCAGAAAAGCAGAGTTGCATTTGCGAAGATAACATTCAAGAAACCACACTTGCTATTGCTTGATGAGCCGTCCAATCATCTT
             cactaat  putative branch site (score: 2)
                       ttttatgtttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatacttcgggtatttggagttgtataaccacaatattctagatgcaggccctagaatgaaattggaactagtcaatttttatgtgttgtggcttgttacgttcactaatgtgttttatgttttggggtgtgaatgggaaattagGTGGTCAGAAAAGCAGAGTTGCATTTGCGAAGATAACATTCAAGAAACCACACTTGCTATTGCTTGATGAGCCGTCCAATCATCTT

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