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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTAGAACTCTATGCAGAATACGATACTAAGATGCTGCTTCCGTTCCTACGTAGCAGTCAACATTACAAGTTAGAAAAGgtacttaacattacaagcaacccagcttactgaaatgaactatctctgggttatgtctttgtgaacttgatctattgcaatatctcag

Basic information

species Arabidopsis thaliana
transcript AT1G08190.1
intron # 14
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G08190.1 (Arabidopsis thaliana), 5'ss of exon 14
lower sequence: GLYMA11G19660.2 (Glycine max), 5'ss of exon 14
GTAGAACTCTATGCAGAATACGATACTAAGATGCTGCTTCCGTTCCTACGTAGCAGTCAACATTACAAGTTAGAAAAGgtacttaac--attacaagcaacccagcttactgaaatgaactatctctgggttatgtctttgtgaacttgatctattgcaatatctcag
    ||||||||||||| || ||| ||||||||||||| || || || |||||||||||||| ||||   | || |||||  | ||   || |||| |        |||     |  |  |  || ||  | |  || |    || ||| | |   |           
----AACTCTATGCAGACTATGATCCTAAGATGCTGCTACCTTTTCTCCGTAGCAGTCAACACTACACCCTTGAGAAGgtgatgaatcaatgacaaactttgacagttatatgcacaacatgcctgtgaatcaaatcctca--aagttgtttttcag-----------

upper sequence: AT1G08190.1 (Arabidopsis thaliana), 5'ss of exon 14
lower sequence: GLYMA12G08840.1 (Glycine max), 5'ss of exon 14
GTAGAACTCTATGCAGAATACGATACTAAGATGCTGCTTCCGTTCCTACGTAGCAGTCAACATTACAAGTTAGAAAAGgtacttaac--attacaagcaacccagcttactgaaatgaactatctctgggttatgtctttgtgaacttgatctattgcaatatctcag
|||||||||||||| || || ||| | ||||||||||| || || || |||||||||||||| ||||   | || |||||  | |||  |||||||   ||   |     |  |   |  ||| |      |   | |  || || ||     || |   | | ||||
GTAGAACTCTATGCGGACTATGATCCAAAGATGCTGCTACCTTTTCTCCGTAGCAGTCAACACTACACCCTTGAGAAGgtgatgaaccaattacaa---actttgacagttatatgtagttatttacaacatgcttgtgagtcaaatt--ctcatagttgtttttcag
















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|47830127|gb|CK119811.1|CK119811
EST:     AGATGCTGCTTCCGTTCCTACGTAGCAGTCAACATTACAAGTTAGAAAAG                         GCATATGAACTTTGTGTCAAGAAAGATTTTTTAAGAGAGCAAGTGTTTGTC
genomic: AGATGCTGCTTCCGTTCCTACGTAGCAGTCAACATTACAAGTTAGAAAAGgtacttaaca ... aatatctcagGCATATGAACTTTGTGTCAAGAAAGATTTTTTAAGAGAGCAAGTGTTTGTC
EST: gi|124772363|gb|EH862492.1|EH862492
EST:     AGATGCTGCTTCCGTTCCTACGTAGCAGTCAACATTACAAGTTAGAAAAG                         GCATATGAACTTTGTGTC
genomic: AGATGCTGCTTCCGTTCCTACGTAGCAGTCAACATTACAAGTTAGAAAAGgtacttaaca ... aatatctcagGCATATGAACTTTGTGTC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTAGAACTCTATGCAGAATACGATACTAAGATGCTGCTTCCGTTCCTACGTAGCAGTCAACATTACAAGTTAGAAAAGgtacttaacattacaagcaacccagcttactgaaatgaactatctctgggttatgtctttgtgaacttgatctattgcaatatctcag

- - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - GCTGCT