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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagttgaaacaagaccaagatcataatccgatcagatctgtttcatttttttttttactgatttttgtttttttttgtgttcttgattgtgacagCGAAAGCTTCGTTTGGAGAACAAGAATGGTATTTTTTCAGTCCAAGAGATCGGAAATATCCCAACGGAGCTAGACCTAACCGAGCTGCGACTTCCGGTTA

Basic information

species Arabidopsis thaliana
transcript AT1G52880.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G52880.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv19s0014g03300.t01 (Vitis vinifera), 3'ss of exon 1
gtaagttgaaacaagaccaagatcataatccgatcagatctgtttcattttttttttt-actgatttttgttttttt----------ttgtgtt----cttgattg--tgacagCGAAAGCTTCGTTTGGAGAACAAGAATGGTATTTTTTCAGTCCAAGAGATCGGAAATATCCCAACGGAGCTAGACCTAACCGAGCTGCGACTTCCGGTTA
|||| ||  | |||  || || | || ||  ||| |    | | | ||| | | |  | | |  | | |      ||             || |     |||||    |  |||| || ||    ||||||||||| |||||||| || ||||| || ||||| ||||| || || ||||| ||| | ||||| ||||| |||||||| |||||
gtaacttacatcaaaccccagctaattat--gattaagattatgtgattatgtatgatgaattgtatgtaaaaggttagaaagaaagccatgctgatatttgatcaattctcagCTAAGGCCAGTTTTGGAGAACAGGAATGGTACTTCTTCAGCCCTAGAGACCGGAAGTACCCAAACGGGGCTCGGCCTAATCGAGCGGCGACTTCTGGTTA

upper sequence: AT1G52880.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: PP1S259_67V6.1 (Physcomitrella patens), 3'ss of exon 1
gtaagttgaaaca----agaccaagatcataatccgatcaga-tctgtttcatttttttttt-tactgatttttgtttttttttgtgttcttgattgtgacagCGAAAGCTTCGTTTGGAGAACAAGAATGGTATTTTTTCAGTCCAAGAGATCGGAAATATCCCAACGGAGCTAGACCTAACCGAGCTGCGACTTCCGGTTA
    |||||||||    ||| |    |  | ||       || |||||   | ||        ||   |||       |   || | | |||   | || |||  || |||   |||||||||  ||| |||||||||||||| ||||||||  ||||||| || || |||||| | ||||||||||||||  ||||||| ||
--ttgttgaaacatagcagagcggcctactgattttccgggaatctgtaaaagttcaagagcgtataaattaaaagaatcgattctctactttgatttg-cagGCAAGGCTATTTTTGGAGAAGGAGAGTGGTATTTTTTCAGCCCAAGAGACAGGAAATACCCAAATGGAGCTCGCCCTAACCGAGCTGCAGCTTCCGGATA
















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|86041643|gb|DR337398.1|DR337398
EST:     GATCATCGCCGACGTTGATCTTTACAAATTTGATCCATGGGAACTTCCCG                         CGAAAGCTTCGTTTGGAGAAC
genomic: GATCATCGCCGACGTTGATCTTTACAAATTTGATCCATGGGAACTTCCCGgtaagttgaa ... attgtgacagCGAAAGCTTCGTTTGGAGAAC
EST: gi|86041644|gb|DR337399.1|DR337399
EST:     GATCATCGCCGACGTTGATCTTTACAAATTTGATCCATGGGAACTTCCCG                         CGAAAGCTTCGTTTGGAGAACAAGAATGGTATTTTTTCAGTCCAAGAGATC
genomic: GATCATCGCCGACGTTGATCTTTACAAATTTGATCCATGGGAACTTCCCGgtaagttgaa ... attgtgacagCGAAAGCTTCGTTTGGAGAACAAGAATGGTATTTTTTCAGTCCAAGAGATC
EST: gi|86041638|gb|DR337393.1|DR337393
EST:     GATCATCGCCGACGTTGATCTTTACAAATTTGATCCATGGGAACTTCCCG                         CGAAAGCTTCGTTTGGAGAACAAGAATGGTATTTTTTCAGTCCAAGAGATC
genomic: GATCATCGCCGACGTTGATCTTTACAAATTTGATCCATGGGAACTTCCCGgtaagttgaa ... attgtgacagCGAAAGCTTCGTTTGGAGAACAAGAATGGTATTTTTTCAGTCCAAGAGATC
EST: gi|86041642|gb|DR337397.1|DR337397
EST:     GATCATCGCCGACGTTGATCTTTACAAATTTGATCCATGGGAACTTCCCG                         CGAAAGCTTCGTTTGGAGAACAAGAATGGTATTTTTTCAGTCCAAGAGATC
genomic: GATCATCGCCGACGTTGATCTTTACAAATTTGATCCATGGGAACTTCCCGgtaagttgaa ... attgtgacagCGAAAGCTTCGTTTGGAGAACAAGAATGGTATTTTTTCAGTCCAAGAGATC
EST: gi|86041640|gb|DR337395.1|DR337395
EST:     GATCATCGCCGACGTTGATCTTTACAAATTTGAT--ATGGGAACTTCCCG                         CGAAAGCTTCGTTTGGAGAACAAGAATGGTATTTTTTCAGTCCAAGAGATC
genomic: GATCATCGCCGACGTTGATCTTTACAAATTTGATCCATGGGAACTTCCCGgtaagttgaa ... attgtgacagCGAAAGCTTCGTTTGGAGAACAAGAATGGTATTTTTTCAGTCCAAGAGATC
EST: gi|86041645|gb|DR337400.1|DR337400
EST:     GATCATCGCCGACGTTGATCTTTACAAATTTGATCCATGGGAACTTCCCG                         CGAAAGCTTCGTTTGGAGAACAAGAATGGTATTTTTTCAGTCCAAGAGATC
genomic: GATCATCGCCGACGTTGATCTTTACAAATTTGATCCATGGGAACTTCCCGgtaagttgaa ... attgtgacagCGAAAGCTTCGTTTGGAGAACAAGAATGGTATTTTTTCAGTCCAAGAGATC
EST: gi|86041646|gb|DR337401.1|DR337401
EST:     GATCATCGCCGACGTTGATCTTTACAAATTTGATMMATGGGAACTTCCCG                         CGAAAGCTTCGTTTGGAGAMCAAGAATGGTATTTTTTCAGTCCAAGAGATC
genomic: GATCATCGCCGACGTTGATCTTTACAAATTTGATCCATGGGAACTTCCCGgtaagttgaa ... attgtgacagCGAAAGCTTCGTTTGGAGAACAAGAATGGTATTTTTTCAGTCCAAGAGATC
EST: gi|86041647|gb|DR337402.1|DR337402
EST:     GATCATCGCCGACGTTGATCTTTACAAATTTGATCCATGGGAACTTCCCG                         CGAAAGCTTCGTTTGGAGAACAAGAATGGTATTTTTTCAGTCCAAGAGATC
genomic: GATCATCGCCGACGTTGATCTTTACAAATTTGATCCATGGGAACTTCCCGgtaagttgaa ... attgtgacagCGAAAGCTTCGTTTGGAGAACAAGAATGGTATTTTTTCAGTCCAAGAGATC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttcatttttttttttactgatttttgtttttttttgtgttcttgattgtgacagCGAAAGCTTCGTTTGGAGAACAAGAATGGTATTTTTTCAGTCCAAGAGATCGGAAATATCCCAACGGAGCTAGACCTAACCGAGCTGCGACTTCCGGTTA
     tttttttttttactga  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagttgaaacaagaccaagatcataatccgatcagatctgtttcatttttttttttactgatttttgtttttttttgtgttcttgattgtgacagCGAAAGCTTCGTTTGGAGAACAAGAATGGTATTTTTTCAGTCCAAGAGATCGGAAATATCCCAACGGAGCTAGACCTAACCGAGCTGCGACTTCCGGTTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC