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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagtaacaacaccctcttgaacttctcgatctttctccatacatttatcagtatctaaaacctgagttgttcctttgactgcagGTGAGGTGCTTGTACTTGAAGAGCACAATGGGTCCACCAAACCGAGTTTTCTAAGGTTATTATTATTACAAAGTTTCTCTAAGGTATCATCACTCTTTAG

Basic information

species Arabidopsis thaliana
transcript AT5G22440.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G22440.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: LOC_Os02g21660.1 (Oryza sativa), 3'ss of exon 5
-------------------------gttagtaacaacaccctcttgaacttctcgatctttctccatacatttatcagtatctaaaacctgagttgttcctttgactgcagGTGAGGTGCTTGTACTTGAAGAGCACAATGGGTCCACCAAACCGAGTTTTCTAAGGTTATTATTATTA-----CAAAGTTTCTCTAAGGTATCATCACTCTTTAG
                           |||  |||| |      ||  |  || |  | |   ||      || | |  || | | |  | | ||||  | | |  ||||||| |||||||||||| |||||||||| |||||        ||||||| ||||||| ||||| |  |||     | |  | | |   ||        |||      
gtatgtgatcatgtgttccttatagcatagatacaaaatttatctg--ccacttggacatcagcctagttattctgatgatttgacatgttatttgtatcatcg--tgcagGTTAGGTGCTTGTACCTGAAGAGCACCATGGGAAAGGTGTACCGAGTGTTCTAAG-TTATTTTCTTTAGGCTTCTAGATGTTTTGGAGACTAAGCTACTTG----

upper sequence: AT5G22440.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv06s0080g00400.t01 (Vitis vinifera), 3'ss of exon 8
------------gttagtaacaacaccctcttgaacttctcgatcttt-ctccatacatttatcagtatctaaaacctga-gttgttcctttgactgcagGTGAGGTGCTTGTACTTGAAGAGCACAATGGGTCCACCAAACCGAGTTTTCTAAGG--TTATTATTATTACAAAGTTTCTCTAAGGTATCATCACTCTTTAG
             ||   | |||   | | |||   ||||  || |||  | ||| |||| || |  |  ||     ||| | ||||   |  |   |||||||||||||||||| |||||||||| |||||   | ||||||| || ||||||||  |||    | ||||    | |   |   || |    |   |    
aaatcatctatctttgaaagcaaatgcattttgtttttctgtatttttgtttcatccattcatgataaattatctgatgaagctgtttgatgaaaatcagGTGAGGTGCTTGTACCTGAAGAGCACCATGGGGAGATCAAACCGCGTCTTCTAAGGAGTTAAATCTTTTACCTGTTATGGTTGGTGTGTAGGGAGAGTCC--
















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|116413764|gb|EG456356.1|EG456356
EST:     AGATGAGTGTTAACTTCCTCGTTTCTCTCTTGAAGAAAAACTGGCAAAAT                         GTGAGGTGCTTGTACTTGAAGAGCACAATGGGTCCACCAAACCGAGTTTTC
genomic: AGATGAGTGTTAACTTCCTCGTTTCTCTCTTGAAGAAAAACTGGCAAAATgttagtaaca ... ttgactgcagGTGAGGTGCTTGTACTTGAAGAGCACAATGGGTCCACCAAACCGAGTTTTC
EST: gi|116413742|gb|EG456334.1|EG456334
EST:     AGATGAGTGTTAACTTCCTCGTTTCTCTCTTGAAGAAAAACTGGCAAAAT                         GTGAGGTGCTTGTACTTGAAGAGCCCAATGGGTCCCCCAA
genomic: AGATGAGTGTTAACTTCCTCGTTTCTCTCTTGAAGAAAAACTGGCAAAATgttagtaaca ... ttgactgcagGTGAGGTGCTTGTACTTGAAGAGCACAATGGGTCCACCAA
EST: gi|116413756|gb|EG456348.1|EG456348
EST:     AGATGAGTGTTAACTTCCTCGTTTCTCTCTTGAAGAAAAACTGGCAAAAT                         GTGAGGTGCTTGTACTTGAAGAGCACAATGGGTCCACCAAACCGAGTTTTC
genomic: AGATGAGTGTTAACTTCCTCGTTTCTCTCTTGAAGAAAAACTGGCAAAATgttagtaaca ... ttgactgcagGTGAGGTGCTTGTACTTGAAGAGCACAATGGGTCCACCAAACCGAGTTTTC
EST: gi|116413757|gb|EG456349.1|EG456349
EST:     AGATGAGTGTTAACTTCCTCGTTTCTCTCTTGAAGAAAAACTGGCAAAAT                         GTGAGGTGCTTGTACTTGAAGAGCACAATGGGTCCACCAAACCGAGTTTTT
genomic: AGATGAGTGTTAACTTCCTCGTTTCTCTCTTGAAGAAAAACTGGCAAAATgttagtaaca ... ttgactgcagGTGAGGTGCTTGTACTTGAAGAGCACAATGGGTCCACCAAACCGAGTTTTC
EST: gi|86077020|gb|DR372777.1|DR372777
EST:     AGATGAGTGTTAACTTCCTCGTTTCTCTCTTGAAGAAAAACTGGCAAAAT                         GTGAGGTGCTTGTACTTGAAGAGCACAATGGGTCCACCAAACCGAGTTTTC
genomic: AGATGAGTGTTAACTTCCTCGTTTCTCTCTTGAAGAAAAACTGGCAAAATgttagtaaca ... ttgactgcagGTGAGGTGCTTGTACTTGAAGAGCACAATGGGTCCACCAAACCGAGTTTTC
EST: gi|164210785|gb|ES166040.1|ES166040
EST:     AGTGTTAACTTCCTCGTTTCTCTCTTGAAG-AAAACTGGCAAAAT                         GTGAGGTGCTTGTACTTGAAGAGCACAATGGG
genomic: AGTGTTAACTTCCTCGTTTCTCTCTTGAAGAAAAACTGGCAAAATgttagtaaca ... ttgactgcagGTGAGGTGCTTGTACTTGAAGAGCACAATGGG
EST: gi|164055778|gb|ES200563.1|ES200563
EST:     GATGAGTGTTAACTTCCTCGTTTCTCTCTTGAAGAAAAAACTGGCAAAAT                         GTGAGGTGCTTGTACTTGAAGAGCNCAATGGGTCCACCAAACCGAGTTTTC
genomic: GATGAGTGTTAACTTCCTCGTTTCTCTCTTGAAG-AAAAACTGGCAAAATgttagtaaca ... ttgactgcagGTGAGGTGCTTGTACTTGAAGAGCACAATGGGTCCACCAAACCGAGTTTTC
EST: gi|116413743|gb|EG456335.1|EG456335
EST:     AGATGAGTGTTAACTTCCTCGTTTCTCTCTTGAAGAAAAACTGGCAAAAT                         GTGAGGTGCTTGTACTTGAAGAGCACAATGGGTCCACCAAACCGAGTTTTC
genomic: AGATGAGTGTTAACTTCCTCGTTTCTCTCTTGAAGAAAAACTGGCAAAATgttagtaaca ... ttgactgcagGTGAGGTGCTTGTACTTGAAGAGCACAATGGGTCCACCAAACCGAGTTTTC
EST: gi|86080991|gb|DR376748.1|DR376748
EST:     AGATGAGTGTTAACTTCCTCGTTTCTCTCTTGAAGAAAAACTGGCAAAAT                         GTGAGGTGCTTGTACTTGAAGAGCACAATGGGTCCACCAAACCGAGTTTTC
genomic: AGATGAGTGTTAACTTCCTCGTTTCTCTCTTGAAGAAAAACTGGCAAAATgttagtaaca ... ttgactgcagGTGAGGTGCTTGTACTTGAAGAGCACAATGGGTCCACCAAACCGAGTTTTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctttctccatacatttatcagtatctaaaacctgagttgttcctttgactgcagGTGAGGTGCTTGTACTTGAAGAGCACAATGGGTCCACCAAACCGAGTTTTCTAAGGTTATTATTATTACAAAGTTTCTCTAAGGTATCATCACTCTTTAG
                                     ttgttccttt  CT-rich tract
         atacatttat  TA-rich tract