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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtattaaaaatcatagctttattgaaggtttaggtcctattgagcgattctatttggtgactaactggttttttaattgcagGGACCTCGTATGGTTCGTGATGTCTTCCGTCTTGCCAAGGAAAATGCTCCAGCTATCATCTTCATTGATGAGGTAGATGCCATCGCTACTGCTAGGTTTG

Basic information

species Arabidopsis thaliana
transcript AT5G58290.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G58290.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: LOC_Os02g21970.1 (Oryza sativa), 3'ss of exon 2
--------------gtattaaaaatc-----atagctttattgaaggtttaggtcctattgagcgattctatttggtgactaactggttttttaattgcagGGACCTCGTATGGTTCGTGATGTCTTCCGTCTTGCCAAGGAAAATGCTCCAGCTATCATCTTCATTGATGAGGTAGATGCCATCGCTACTGCTAGGTTTG
               | || | | |       ||| |||  |   | ||| || | || |      ||   |   |    |   |  ||  ||  ||  |||||||| | |||||||| ||||| |||||| | || || || ||||| ||||||||||| ||||| |||||||| ||||| || || |||||| | ||||
gctttatgttttggatgttgagacttcgtttgtagattttctatggtttttgggcatactagttcttttcttgatgaagttcttttattcatttgtt-tagGGACCTAGGATGGTTCGAGATGTATTCCGTTTGGCTAAAGAGAATGCCCCAGCTATCATATTCATCGATGAGGTTGATGCTATAGCAACTGCTCGTTTTG

upper sequence: AT5G58290.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G038126_T01 (Zea mays), 3'ss of exon 2
-------gtattaaaaatcatagctt-----tattgaaggtt-taggtcctattgagcgattctatttggtgactaactggttttttaa-----ttgcagGGACCTCGTATGGTTCGTGATGTCTTCCGTCTTGCCAAGGAAAATGCTCCAGCTATCATCTTCATTGATGAGGTAGATGCCATCGCTACTGCTAGGTTTG
        ||||   |   |||  ||      ||  ||  ||  || |||| ||    | |  |      |    |      || ||||     ||| |||| ||| | ||||| |||||||| |||||| | || ||||| ||||||||||| ||||| |||||||||||||| ||||| || || |||||| | ||||
ttagtggttattcgtagatatatgttgtcgacataaaaatttgcagttccttttttcggctgttcaacattagtcagtcatattcttaactcctttgtagGGCCCTAGAATGGTGCGTGATGTGTTCCGTTTGGCTAAGGAGAATGCTCCAGCAATCATTTTCATTGATGAGGTTGATGCTATAGCCACTGCTCGCTTTG

upper sequence: AT5G58290.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G090904_T01 (Zea mays), 3'ss of exon 2
----------gtattaaaaatcatagctttattgaaggtttag--gtcctattgagcgattctatt--tggtgactaactggtttttta----attgcagGGACCTCGTATGGTTCGTGATGTCTTCCGTCTTGCCAAGGAAAATGCTCCAGCTATCATCTTCATTGATGAGGTAGATGCCATCGCTACTGCTAGGTTTG
            || |||  |   |  ||| |      || ||  || | ||  | |  | |||||  ||  |  | |     ||| ||     ||| |||| ||| | ||||| ||||| || |||||| | |||||||| ||||| ||||| ||||| |||||||||||||| ||||| || || |||||| | ||||
cctgtcgtggacataaaattttgcatttttttcttcttttcagctgttcaatatatcagtcctattcttgacgtgttatgatctttctacttctttgtagGGCCCTAGAATGGTGCGTGACGTGTTCCGTTTGGCCAAGGAGAATGCCCCAGCAATCATTTTCATTGATGAGGTTGATGCTATAGCCACTGCTCGTTTTG

upper sequence: AT5G58290.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA11G31470.1 (Glycine max), 3'ss of exon 2
---------gtattaaaaatcatagctttattgaaggtttaggtcctattgagcgattc---------tatttggtgactaactggttttttaattgcagGGACCTCGTATGGTTCGTGATGTCTTCCGTCTTGCCAAGGAAAATGCTCCAGCTATCATCTTCATTGATGAGGTAGATGCCATCGCTACTGCTAGGTTTG
          |  ||  | |   |  |  |||||  || |  ||  |  | |  | ||          | ||       |  |||   |||| |||  |||| || || |||||||||||||| || ||||| || || || ||||| || ||||| || || ||||||||||| ||||| || || |||||||| ||||
tcctaaagtttcctaggagtttcaaatccattgattgtatgtgttttgatcaatggtttagagcaacatcttcaaatcttccctgccatttttattttagGGTCCACGAATGGTTCGTGATGTATTTCGTCTCGCTAAAGAGAATGCGCCTGCTATTATATTTATTGATGAGGTTGATGCAATAGCCACTGCTAGATTTG

upper sequence: AT5G58290.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv06s0004g08220.t01 (Vitis vinifera), 3'ss of exon 2
--gtattaaaaatcatagcttt-----attgaaggtttaggtcc--tattgagcgattctatttggtgactaactggttttttaattgc---------agGGACCTCGTATGGTTCGTGATGTCTTCCGTCTTGCCAAGGAAAATGCTCCAGCTATCATCTTCATTGATGAGGTAGATGCCATCGCTACTGCTAGGTTTG
  || ||||   |  || ||||     ||||    | | | | |  ||       ||| || ||  |   ||  |   |||||  |  |         |||| ||  | ||||| |||||||| ||||||||||||||||| |||||||| || || ||||||||||||||||| ||||| || ||||| ||||||||||
tggttttaattgttttatcttttctagattgccaatattgctgcaatacccttaaattttaatttatctatatatatattttttttctcttgttatcaagGGTCCGAGAATGGTCCGTGATGTTTTCCGTCTTGCCAAGGAGAATGCTCCTGCAATTATCTTCATTGATGAGGTTGATGCTATTGCTACCGCTAGGTTTG

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|125085979|gb|EL145619.1|EL145619
EST:     GTGCAAAAGTATCTCGGCGAG                         GGACCTCGTATGGTTCGTGATGTCTTCCGTCTTGCCAAGGAAAATGCTCCA
genomic: GTGCAAAAGTATCTCGGCGAGgtattaaaaa ... ttaattgcagGGACCTCGTATGGTTCGTGATGTCTTCCGTCTTGCCAAGGAAAATGCTCCA
EST: gi|116423148|gb|EG465740.1|EG465740
EST:     CCTTCATTAGGGTTGTTGGATCCGAGTTTGTGCAAAAGTATCTCGGCGAG                         GGACCTCGTATGGTTCGTGATGTCTTCCGTCTTGCCAAGGAAAATGCTCCA
genomic: CCTTCATTAGGGTTGTTGGATCCGAGTTTGTGCAAAAGTATCTCGGCGAGgtattaaaaa ... ttaattgcagGGACCTCGTATGGTTCGTGATGTCTTCCGTCTTGCCAAGGAAAATGCTCCA
EST: gi|124996123|gb|EL068392.1|EL068392
EST:     CCGAGTTTGTGCAAAAGTATCTCGGCGAG                         GGACCTCGTATGGTTCGTGATGTCTTCCGTCTTGCCAAGGAAAATGCTCCA
genomic: CCGAGTTTGTGCAAAAGTATCTCGGCGAGgtattaaaaa ... ttaattgcagGGACCTCGTATGGTTCGTGATGTCTTCCGTCTTGCCAAGGAAAATGCTCCA
EST: gi|163981724|gb|ES042210.1|ES042210
EST:     GCAAAAGTATCTCGGCGAG                         GGACCTCGTATGGTTCGTGATGTCTTCCGTCTTGCCAAGGAAAATGACTCC
genomic: GCAAAAGTATCTCGGCGAGgtattaaaaa ... ttaattgcagGGACCTCGTATGGTTCGTGATGTCTTCCGTCTTGCCAAGGAAAATG-CTCC
EST: gi|164070613|gb|ES210827.1|ES210827
EST:     CCTTCATTAGGGTTGTTGGATCCGAGTTTGTGCAAAAGTATCTCGGCGAG                         GGACCTCGTATGGTTCGTGATGTCTTCCGTCTTGCCAAGGAAA
genomic: CCTTCATTAGGGTTGTTGGATCCGAGTTTGTGCAAAAGTATCTCGGCGAGgtattaaaaa ... ttaattgcagGGACCTCGTATGGTTCGTGATGTCTTCCGTCTTGCCAAGGAAA
EST: gi|125044376|gb|EL116645.1|EL116645
EST:     TTCATTAGGGTTGTTGGATCCGAGTTTGTGCAAAAGTATCTCGGCGAG                         GGACCTCGTATGGTTCGTGATGTCTTCCGTCTTGCCAAGGAAAATG
genomic: TTCATTAGGGTTGTTGGATCCGAGTTTGTGCAAAAGTATCTCGGCGAGgtattaaaaa ... ttaattgcagGGACCTCGTATGGTTCGTGATGTCTTCCGTCTTGCCAAGGAAAATG
EST: gi|164176288|gb|ES028940.1|ES028940
EST:     CCTTCATTAGGGTTGTTGGATCCGAGTTTGTGCAAGAGTATCTCGGCGAG                         GGACCTCGTATGGTTCGTGATGTCTTCCGTCTTGCAAAGG
genomic: CCTTCATTAGGGTTGTTGGATCCGAGTTTGTGCAAAAGTATCTCGGCGAGgtattaaaaa ... ttaattgcagGGACCTCGTATGGTTCGTGATGTCTTCCGTCTTGCCAAGG
EST: gi|164206071|gb|ES170606.1|ES170606
EST:     TTAGGGTTGTTGGATCCGAGTTTGTGCAAAAGTATCTCGGCGAG                         GGACCTCGTATGGTTCGTGATGTCTTCCGTCTTGCCAAGGAAAATGCTCCA
genomic: TTAGGGTTGTTGGATCCGAGTTTGTGCAAAAGTATCTCGGCGAGgtattaaaaa ... ttaattgcagGGACCTCGTATGGTTCGTGATGTCTTCCGTCTTGCCAAGGAAAATGCTCCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtttaggtcctattgagcgattctatttggtgactaactggttttttaattgcagGGACCTCGTATGGTTCGTGATGTCTTCCGTCTTGCCAAGGAAAATGCTCCAGCTATCATCTTCATTGATGAGGTAGATGCCATCGCTACTGCTAGGTTTG
                                         tttttt  CT-rich tract
                                         ttttttaatt  TA-rich tract