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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AATTGTCAAGGCCTCATCTCGGGTTGATAGGTTTTCGAAAAGTGATATCATTGTTTCTCCCTCTATTCTCTCGGCTAATTTCGCCAAATTAGGCGAGCAGgtaggtttttgttgctctcctctttggtttcttgtgtgtttgtttctccatttcactatttccggcttctttcag

Basic information

species Arabidopsis thaliana
transcript AT5G61410.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G61410.2 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: GLYMA05G00910.3 (Glycine max), 5'ss of exon 2
AATTGTCAAGGCCTCATCTCGGGTTGATAGGTTTTCGAAAAGTGATATCATTGTTTCTCCCTCTATTCTCTCGGCTAATTTCGCCAAATTAGGCGAGCAGgt--------aggtttttgttgctctcctc-----tttggtttcttgtgtgtttgtttctccatttcactat--------ttccggcttctttcag------------------------------------------------------------------------------------------------------
 |  || |||||  ||||||| ||||| | |||||| ||||| ||||||||||||||||| || ||||| || || || || || ||||| || ||||||||        | | |||   | || |  ||     ||  |||||   ||| |||||||  | | | || |||        |      || ||| |                                                                                                       
CACAGTGAAGGCTACATCTCGTGTTGACAAGTTTTCAAAAAGCGATATCATTGTTTCTCCATCCATTCTTTCTGCAAACTTTGCAAAATTGGGAGAGCAGgttctataacatgctttacattctgtaatcagtatttcagtttccaatgt-tttgttttgctactacaatatataatatttcataattttttttatcacgtttgctgattgccagtaaatctgtccttttgttttcaaggcatgtttttctattatcagcgatcatgattgttgtagtttgtgtgttatcttgtctag

upper sequence: AT5G61410.2 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: Vv17s0000g06450.t01 (Vitis vinifera), 5'ss of exon 2
AATTGTCAAGGCCTCATCTCGGGTTGATAGGTTTTCGAAAAGTGATATCATTGTTTCTCCCTCTATTCTCTCGGCTAATTTCGCCAAATTAGGCGAGCAGgtaggtttttgttgctctcctctttggtttcttgtgtgtttgtttctccatttcactatttccggcttctttcag---------------------------
 |  || ||||||||  |||||||||||| ||| || |||||||| |||||||||||||| |||||||| || |||||||| || || || || || |||||    |||| ||  | |  | | || |  |     || |   |||   || |  ||      |   |                                  
TACAGTGAAGGCCTCGGCTCGGGTTGATAAGTTCTCAAAAAGTGACATCATTGTTTCTCCATCTATTCTGTCTGCTAATTTTGCAAAGTTGGGAGAACAGgttctattttatttttgtgat-tatgctgccacaaatgct-acttccatatctttcttcccttgaactgcagggatcatatatccatttgacccaattttga
















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|124954229|gb|EL029342.1|EL029342
EST:     TTTCGCCGAAATTAGGCGAGCAG                         GTAAAAGCAGTGGAGTTGGCAGGTTGTGATTGGATTCATGTTGATGTCATG
genomic: TTTCGCC-AAATTAGGCGAGCAGgtaggttttt ... cttctttcagGTAAAAGCAGTGGAGTTGGCAGGTTGTGATTGGATTCATGTTGATGTCATG
EST: gi|125030610|gb|EL102879.1|EL102879
EST:     TTCTCTCGGCTAATTTCGCCAAATTAGGCGAGCAG                         GTAAAAGCAGTGGAGTTGGCAGGTTGTGATTGGATTCATGTTGATGTCATG
genomic: TTCTCTCGGCTAATTTCGCCAAATTAGGCGAGCAGgtaggttttt ... cttctttcagGTAAAAGCAGTGGAGTTGGCAGGTTGTGATTGGATTCATGTTGATGTCATG
EST: gi|116468994|gb|EG511586.1|EG511586
EST:     TTGTTTCTCCCTCTATTCTCTCGGCTAATTTCGCCAAATTAGGCGAGCAG                         GTAAAAGCAGTGGAGTCGGCAGGTTGTGATTGGATTCATGTTGATGTCATG
genomic: TTGTTTCTCCCTCTATTCTCTCGGCTAATTTCGCCAAATTAGGCGAGCAGgtaggttttt ... cttctttcagGTAAAAGCAGTGGAGTTGGCAGGTTGTGATTGGATTCATGTTGATGTCATG
EST: gi|125240220|gb|EL254305.1|EL254305
EST:     TGTTTCTCCCTCTATTCTCTCGGCTAATTTCGCCAAATTAGGCGAGCAG                         GTAAAAGCAGTGGAGTTGGCAGGTTGTGATTGGATTCATGTTGATGTCATG
genomic: TGTTTCTCCCTCTATTCTCTCGGCTAATTTCGCCAAATTAGGCGAGCAGgtaggttttt ... cttctttcagGTAAAAGCAGTGGAGTTGGCAGGTTGTGATTGGATTCATGTTGATGTCATG
EST: gi|124958286|gb|EL033040.1|EL033040
EST:     TTAGGCGAGCAG                         GTAAAAGCAGTGGAGTTGGCAGGTTGTGATTGGATTCATGTTGATGTCATG
genomic: TTAGGCGAGCAGgtaggttttt ... cttctttcagGTAAAAGCAGTGGAGTTGGCAGGTTGTGATTGGATTCATGTTGATGTCATG
EST: gi|124729174|gb|EH820576.1|EH820576
EST:     CTATTCTCTCGGCTAATTTCGCCAAATTAGGCGAGCAG                         GTAAAAGCAGTGGAGTTGGCAGGTTGTGATTGGATTCATGTTGATGTCATG
genomic: CTATTCTCTCGGCTAATTTCGCCAAATTAGGCGAGCAGgtaggttttt ... cttctttcagGTAAAAGCAGTGGAGTTGGCAGGTTGTGATTGGATTCATGTTGATGTCATG
EST: gi|124869977|gb|EH954414.1|EH954414
EST:     TTGTTTCTCCCTCTATTCTCTCGGCTAATTTCGCCAAATTAGGCGAGCAG                         GTAAAAGCAGTGGAGTTGGCAGGTTGTGATTGGATTCA
genomic: TTGTTTCTCCCTCTATTCTCTCGGCTAATTTCGCCAAATTAGGCGAGCAGgtaggttttt ... cttctttcagGTAAAAGCAGTGGAGTTGGCAGGTTGTGATTGGATTCA
EST: gi|125322217|gb|EL336302.1|EL336302
EST:     CTATTCTCTCGGCTAATTTCGCCAAATTAGGCGAGCAG                         GTAAAAGCAGTGGAGTTGGCAGGTTGTGATTGGATTCATGTTGATGTCATG
genomic: CTATTCTCTCGGCTAATTTCGCCAAATTAGGCGAGCAGgtaggttttt ... cttctttcagGTAAAAGCAGTGGAGTTGGCAGGTTGTGATTGGATTCATGTTGATGTCATG
EST: gi|124889316|gb|EH968218.1|EH968218
EST:     GGCTAATTTCGCCAAATTAGGCGAGCAG                         GTAAGAGCAGTGGAGTTGGCAGGTTGTGATTGGATTCATGTT
genomic: GGCTAATTTCGCCAAATTAGGCGAGCAGgtaggttttt ... cttctttcagGTAAAAGCAGTGGAGTTGGCAGGTTGTGATTGGATTCATGTT
EST: gi|125068265|gb|EL134470.1|EL134470
EST:     TTGTTTCTCCCTCTATTCTCTCGGCTAATTTCGCCAAATTAGGCGAGCAG                         GTAAAAGCAGTGGAGTTGGCAGGTT
genomic: TTGTTTCTCCCTCTATTCTCTCGGCTAATTTCGCCAAATTAGGCGAGCAGgtaggttttt ... cttctttcagGTAAAAGCAGTGGAGTTGGCAGGTT
EST: gi|124942332|gb|EL018607.1|EL018607
EST:     TTTCTCCCTCTATTCTCTCGGCTAATTTCGCCAAATTAGGCGAGCAG                         GTAAAAGCAGTGGAGTTGGCAGGTTGTGATTGGATTCATGTTGATGTCATG
genomic: TTTCTCCCTCTATTCTCTCGGCTAATTTCGCCAAATTAGGCGAGCAGgtaggttttt ... cttctttcagGTAAAAGCAGTGGAGTTGGCAGGTTGTGATTGGATTCATGTTGATGTCATG
EST: gi|124730299|gb|EH821701.1|EH821701
EST:     TTTCGCCAAATTAGGCGAGCAG                         GTAAAAGCAGTGGAGTTGGCAGGTTGTGATTGGATTCATGTTGATGTCATG
genomic: TTTCGCCAAATTAGGCGAGCAGgtaggttttt ... cttctttcagGTAAAAGCAGTGGAGTTGGCAGGTTGTGATTGGATTCATGTTGATGTCATG
EST: gi|124797170|gb|EH886849.1|EH886849
EST:     CTAATTTCGCCAAATTAGGCGAGCAG                         GTAAAAGCAGTGGAGTTGGCAGGTTGTGATTGGATTCATGTTGATGTCATG
genomic: CTAATTTCGCCAAATTAGGCGAGCAGgtaggttttt ... cttctttcagGTAAAAGCAGTGGAGTTGGCAGGTTGTGATTGGATTCATGTTGATGTCATG
EST: gi|125263076|gb|EL277161.1|EL277161
EST:     TTCTCCCTCTATTCTCTCGGCTAATTTCGCCAAATTAGGCGAGCAG                         GTAAAAGCAGTGGAGTTGGCAGGTTGTGATTGGATTCATGTTGATGTCATG
genomic: TTCTCCCTCTATTCTCTCGGCTAATTTCGCCAAATTAGGCGAGCAGgtaggttttt ... cttctttcagGTAAAAGCAGTGGAGTTGGCAGGTTGTGATTGGATTCATGTTGATGTCATG
EST: gi|124926538|gb|EL004359.1|EL004359
EST:     TTGTTTCTCCCTCTATTCTCTCGGCTAATTTCGCCAAATTAGGCGAGCAG                         GTAAAAGCAGTGGAGTTGGCAGGTTGTGATTGGATTCA
genomic: TTGTTTCTCCCTCTATTCTCTCGGCTAATTTCGCCAAATTAGGCGAGCAGgtaggttttt ... cttctttcagGTAAAAGCAGTGGAGTTGGCAGGTTGTGATTGGATTCA
EST: gi|124781817|gb|EH871760.1|EH871760
EST:     TGTTTCTCCCTCTATTCTCTCGGCTAATTTCGCCAAATTAGGCGAGCAAG                         GTAAAAGCAGTGGAGTTGGCAGGT
genomic: TGTTTCTCCCTCTATTCTCTCGGCTAATTTCGCCAAATTAGGCGAGCA-Ggtaggttttt ... cttctttcagGTAAAAGCAGTGGAGTTGGCAGGT
EST: gi|125322073|gb|EL336158.1|EL336158
EST:     TCTATTCTCTCGGCTAATTTCGCCAAATTAGGTCGAGCAG                         GTAAAAGCAGTGGAGTTGGCAGGTTGTGATTGGATTCATGTTGATGTCAT
genomic: TCTATTCTCTCGGCTAATTTCGCCAAATTAGG-CGAGCAGgtaggttttt ... cttctttcagGTAAAAGCAGTGGAGTTGGCAGGTTGTGATTGGATTCATGTTGATGTCAT
EST: gi|116452333|gb|EG494925.1|EG494925
EST:     TTGTTTCTCCCTCTATTCTCTCGGCTAATTTCGCCAAATTAGGCGAGCAG                         GTAAAAGCAGTGGAGTTGGCAGGTTGTGATTGGATTCATGTTGATGTCACG
genomic: TTGTTTCTCCCTCTATTCTCTCGGCTAATTTCGCCAAATTAGGCGAGCAGgtaggttttt ... cttctttcagGTAAAAGCAGTGGAGTTGGCAGGTTGTGATTGGATTCATGTTGATGTCATG
EST: gi|125124365|gb|EL170359.1|EL170359
EST:     TTCTCCCTCTATTCTCTCGGCTAATTTCGCCTAAATTAGGCGAGCAG                         GTAAAAGCAGTGGAGTTGGCAGGTTGTGATTGGATTCATGTTGATGTCATG
genomic: TTCTCCCTCTATTCTCTCGGCTAATTTCGCC-AAATTAGGCGAGCAGgtaggttttt ... cttctttcagGTAAAAGCAGTGGAGTTGGCAGGTTGTGATTGGATTCATGTTGATGTCATG
EST: gi|124748355|gb|EH838485.1|EH838485
EST:     TTTCTCCCTCTATTCTCTCGGCTAATTTCGCCAAATTAGGCGAGCAG                         GTAAAAGCAGTGGAGTTGGCAGGTTGTGATTGGATTCATGTTGATGTCATG
genomic: TTTCTCCCTCTATTCTCTCGGCTAATTTCGCCAAATTAGGCGAGCAGgtaggttttt ... cttctttcagGTAAAAGCAGTGGAGTTGGCAGGTTGTGATTGGATTCATGTTGATGTCATG
EST: gi|124959908|gb|EL034611.1|EL034611
EST:     TTGTTTCTCCCTCTATTCTCTCGGCTAATTTCGCCAAATTAGGCGAGCAG                         GTAAAAGCAGTGGAGTTGGCAGGTTGTGATTGGA
genomic: TTGTTTCTCCCTCTATTCTCTCGGCTAATTTCGCCAAATTAGGCGAGCAGgtaggttttt ... cttctttcagGTAAAAGCAGTGGAGTTGGCAGGTTGTGATTGGA
EST: gi|124799789|gb|EH889468.1|EH889468
EST:     TCTCTCGGCTAATTTCGCCAAATTAGGCGAGCAG                         GTAAAAGCAGTGGAGTTGGCAGGTTGTGATTGGATTCATGTTGATGTCATG
genomic: TCTCTCGGCTAATTTCGCCAAATTAGGCGAGCAGgtaggttttt ... cttctttcagGTAAAAGCAGTGGAGTTGGCAGGTTGTGATTGGATTCATGTTGATGTCATG
EST: gi|125162269|gb|EL189039.1|EL189039
EST:     TCTCTCGGCTAATTTCGCCAAATTAGGCGAGTCAG                         GTAAAAGCAGTGGAGTTGGCAGGTTGTGATTGGATTCATGTTGATGTCAT
genomic: TCTCTCGGCTAATTTCGCCAAATTAGGCGAG-CAGgtaggttttt ... cttctttcagGTAAAAGCAGTGGAGTTGGCAGGTTGTGATTGGATTCATGTTGATGTCAT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AATTGTCAAGGCCTCATCTCGGGTTGATAGGTTTTCGAAAAGTGATATCATTGTTTCTCCCTCTATTCTCTCGGCTAATTTCGCCAAATTAGGCGAGCAGgtaggtttttgttgctctcctctttggtttcttgtgtgtttgtttctccatttcactatttccggcttctttcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG