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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgtaacaatttctcaatgctttgtccataattgagtcagaagagagttgatttgttttgtgtgtatcataagaagagttgaacaaccaaccctttgaatttctacttatcttcataggttaattaactattgatgtacacgattgcagGGAGACGCTGACAGTGGTGTCGACAGGTTGTGGCAGAAGAAGAAGGTTGAAGCCAAACAAAACTAAGAGCTTAATCTGTCTTGTTTTTTGTCGAATCTTG

Basic information

species Arabidopsis thaliana
transcript AT5G27700.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G27700.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G125300_T02 (Zea mays), 3'ss of exon 3
gtttgtaacaatttctcaatgctttgtccataattgagtcagaagagagttgatttgtt--ttgtgtgtatcataagaagagttgaacaaccaaccctttgaatttctact-tatcttcataggttaattaactattgatgtacacgattgcagGGAGACGCTGACAGTGGTGTCGACAGGTTGTGGCAGAAGAAGAAGGTTGAAGCCAAACAAAACTAAGAGCTTAATCTGTCTTGTTTTTTGTCGAATCTTG---
                                                  | || ||||  |   ||| ||         |  ||     | |    ||||  | ||   | |||  |  ||| ||   | | |    || |    |    ||||| ||||| |||||     | |||||||||||||||||||||||||||||   ||| ||    ||     |  ||||   ||        | | |   ||   
--------------------------------------------------ttatatgttagtctagtggattgcccagttacctggtttgcta--tgtttggttgtccgttgtatagtggtagatt--ctgattccatattttgttgtgcacagGGCGACGCAGACAGCTCCTTGGACAGGTTGTGGCAGAAGAAGAAGGTTGATATCAAGCAG---TAGATTTTACATCTAGTTTACCAAGAATTGGACACTGCCT
















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|164042349|gb|ES079101.1|ES079101
EST:     ACACCGGACAGTTCACAACCTTTGCTCTCTGCGGTTTTGTCCGTGCTCAG                         GGAGACGCTGACAGTGGTGTCGACAGGTTGTGGCAGAAGAAGAAGGTTGAA
genomic: ACACCGGACAGTTCACAACCTTTGCTCTCTGCGGTTTTGTCCGTGCTCAGgtttgtaaca ... acgattgcagGGAGACGCTGACAGTGGTGTCGACAGGTTGTGGCAGAAGAAGAAGGTTGAA
EST: gi|125193143|gb|EL208097.1|EL208097
EST:     GCGGTTTTGTCCGTGCTCAG                         GGAGACGCTGACAGTGGTGTCGACAGGTTGTGGCAGAAGAAGAAGGTTGAA
genomic: GCGGTTTTGTCCGTGCTCAGgtttgtaaca ... acgattgcagGGAGACGCTGACAGTGGTGTCGACAGGTTGTGGCAGAAGAAGAAGGTTGAA
EST: gi|125019277|gb|EL091546.1|EL091546
EST:     CACCGGACAGTTCACAACCTTTGCTCTCTGCGGTTTTGTCCGTGCTCAG                         GGAGACGCTGACAGTGGTGTCGACAGGTTGTGGCAGAAGAAGAAGGTTGAA
genomic: CACCGGACAGTTCACAACCTTTGCTCTCTGCGGTTTTGTCCGTGCTCAGgtttgtaaca ... acgattgcagGGAGACGCTGACAGTGGTGTCGACAGGTTGTGGCAGAAGAAGAAGGTTGAA
EST: gi|164117972|gb|ES141297.1|ES141297
EST:     TGCGGTTTTGTCCGTGCTCAG                         GGAGACGCGTGACAGTGGTGTCGACAGGTTTGTGGCAGAAGAAGAAGGTTG
genomic: TGCGGTTTTGTCCGTGCTCAGgtttgtaaca ... acgattgcagGGAGACGC-TGACAGTGGTGTCGACAGG-TTGTGGCAGAAGAAGAAGGTTG
EST: gi|164058103|gb|ES003696.1|ES003696
EST:     CTTTGCTCTCTGCGGTTTTGTCCGTGCTCAG                         GGAGACGCTGACAGTGGTGTCGACAGGTTGTGGCAGAAGAAGAAGGTTGAA
genomic: CTTTGCTCTCTGCGGTTTTGTCCGTGCTCAGgtttgtaaca ... acgattgcagGGAGACGCTGACAGTGGTGTCGACAGGTTGTGGCAGAAGAAGAAGGTTGAA
EST: gi|164224419|gb|EL985050.1|EL985050
EST:     ACACTGGACAGTTCACAACCTTTGCTCTCTGCGGTTTTGTCCGTGCTCAG                         GGAGACGCTGACAGTGGTGTCGACAGGTTGTGGCA
genomic: ACACCGGACAGTTCACAACCTTTGCTCTCTGCGGTTTTGTCCGTGCTCAGgtttgtaaca ... acgattgcagGGAGACGCTGACAGTGGTGTCGACAGGTTGTGGCA
EST: gi|164075679|gb|ES074435.1|ES074435
EST:     ACACCGGACAGTTCACAACCTTTGCTCTCTGCGGTTTTGTCCGTGCTCAG                         GGAGACGCTGACAGTGGTGTCGA
genomic: ACACCGGACAGTTCACAACCTTTGCTCTCTGCGGTTTTGTCCGTGCTCAGgtttgtaaca ... acgattgcagGGAGACGCTGACAGTGGTGTCGA
EST: gi|164207808|gb|ES029087.1|ES029087
EST:     CTCTCTGCGGTTTTG-CCGTGCTCAG                         GGAGACGCTGACAGTGGTGTCGACAGGTTGTGGCAGAAGAAGAAGGTTGAA
genomic: CTCTCTGCGGTTTTGTCCGTGCTCAGgtttgtaaca ... acgattgcagGGAGACGCTGACAGTGGTGTCGACAGGTTGTGGCAGAAGAAGAAGGTTGAA
EST: gi|164045278|gb|ES195909.1|ES195909
EST:     ACACCGGACAGTTCACAACCTTTGCTCTCTGCGGTTT-GTCCGTGCTCAG                         GGAGACGCTGACAGTGGTG
genomic: ACACCGGACAGTTCACAACCTTTGCTCTCTGCGGTTTTGTCCGTGCTCAGgtttgtaaca ... acgattgcagGGAGACGCTGACAGTGGTG
EST: gi|163991824|gb|ES087501.1|ES087501
EST:     ACAGTTCACAACCTTTGCTCTCTGCGGTTTTGTCCGTGCTCAG                         GGAGACGCTGACAGTGGTGTCGACAGGTTGTGGCAGAAGAAGAAGGTTGAA
genomic: ACAGTTCACAACCTTTGCTCTCTGCGGTTTTGTCCGTGCTCAGgtttgtaaca ... acgattgcagGGAGACGCTGACAGTGGTGTCGACAGGTTGTGGCAGAAGAAGAAGGTTGAA
EST: gi|163967277|gb|ES028452.1|ES028452
EST:     TCACAACCTTTGCTCTCTGCGGTTTTGTCCGTGCTCAG                         GGAGACGCTGACAGTGGTGTCGACAGGTTGTGGCAGAAGAAGAAGGTTGAA
genomic: TCACAACCTTTGCTCTCTGCGGTTTTGTCCGTGCTCAGgtttgtaaca ... acgattgcagGGAGACGCTGACAGTGGTGTCGACAGGTTGTGGCAGAAGAAGAAGGTTGAA
EST: gi|125089682|gb|EL147958.1|EL147958
EST:     GGTTTTGTCCGTGCTCAG                         GGAGACGCTGACAGTGGTGTCGACAGGTTGTGGCAGAAGAAGAAGGTTGAA
genomic: GGTTTTGTCCGTGCTCAGgtttgtaaca ... acgattgcagGGAGACGCTGACAGTGGTGTCGACAGGTTGTGGCAGAAGAAGAAGGTTGAA
EST: gi|164078354|gb|ES098790.1|ES098790
EST:     CTCTCTGCGGTTTTGTCCGTGCTCAG                         GGAGACGCTGACAGTGGTGTCGACAGGTTGTGGCAGAAGAAGAAGGTTGAA
genomic: CTCTCTGCGGTTTTGTCCGTGCTCAGgtttgtaaca ... acgattgcagGGAGACGCTGACAGTGGTGTCGACAGGTTGTGGCAGAAGAAGAAGGTTGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgaatttctacttatcttcataggttaattaactattgatgtacacgattgcagGGAGACGCTGACAGTGGTGTCGACAGGTTGTGGCAGAAGAAGAAGGTTGAAGCCAAACAAAACTAAGAGCTTAATCTGTCTTGTTTTTTGTCGAATCTTG
                         ttaattaactattgat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttgtaacaatttctcaatgctttgtccataattgagtcagaagagagttgatttgttttgtgtgtatcataagaagagttgaacaaccaaccctttgaatttctacttatcttcataggttaattaactattgatgtacacgattgcagGGAGACGCTGACAGTGGTGTCGACAGGTTGTGGCAGAAGAAGAAGGTTGAAGCCAAACAAAACTAAGAGCTTAATCTGTCTTGTTTTTTGTCGAATCTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCTT