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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgttgtgatcttttatttcatcttgaaaataaagaaacttgagagttttcatcttttgattaataactgaatcaaaattgatgaatcagGCCACTGGAGAGGACTTTTCTGTGGAACCAACTGATTCCAGAAGACCTTTCCGTGCTCTTCTTGATGTTGGACTTATCAGGACTACCACTGGAAACCGTG

Basic information

species Arabidopsis thaliana
transcript AT5G39740.2
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G39740.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: LOC_Os01g67126.1 (Oryza sativa), 3'ss of exon 5
gtatgt-tgtgatcttttatttcatcttgaaaataaagaaacttgagagttttcatcttttgattaataactgaatcaaaattgatgaatcagGCCACTGGAGAGGACTTTTCTGTGGAACCAACTGATTCCAGAAGACCTTTCCGTGCTCTTCTTGATGTTGGACTTATCAGGACTACCACTGGAAACCGTG
|||    | | ||| || ||    | || |   || |    | ||   || || |||||   ||  || | |   |             |||||||||||| |||||||  | ||| |||||| |||||   || || ||||||||||||||  | |||||||| || || ||||| ||||||||||||||||
gtacaaatataatcctt-ataatttttttactctatatgctcatgctggtcttgatcttgatatgtatgattcctttgg----------tcagGCCACTGGGGAGGACTACTATGTTGAACCAGCTGATGAAAGGAGGCCTTTCCGTGCTCTCTTGGATGTTGGCCTCATTAGGACAACCACTGGAAACCGTG

upper sequence: AT5G39740.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: LOC_Os01g67134.1 (Oryza sativa), 3'ss of exon 5
gtatgttgtgatcttttatttcatcttgaaaataaagaaacttgagagttttcatcttttgattaataactgaatcaaaattgatgaatcagGCCACTGGAGAGGACTTTTCTGTGGAACCAACTGATTCCAGAAGACCTTTCCGTGCTCTTCTTGATGTTGGACTTATCAGGACTACCACTGGAAACCGTG
|||       |    ||||    | || |   || |    | ||    |  | || ||    || |||  || ||   | |   |   | |||||||||| |||||||  | ||| |||||| |||||   ||  | ||||||||||||||  | |||||||| || || ||||| ||||||||||||||||
gtacaaatacaatccttataaattttttactctatatgctcatgctcatgctgattttgatcttgata--tgtat--gattcctttggttagGCCACTGGGGAGGACTACTATGTTGAACCAGCTGATGAAAGGCGGCCTTTCCGTGCTCTCTTGGATGTTGGCCTCATTAGGACAACCACTGGAAACCGTG

upper sequence: AT5G39740.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G163081_T04 (Zea mays), 3'ss of exon 5
gtatgttgtgatcttttatttcatcttgaaaataaagaaacttgagagttttcatcttttgattaataactgaatcaaaattgatgaatcagGCCACTGGAGAGGACTTTTCTGTGGAACCAACTGATTCCAGAAGACCTTTCCGTGCTCTTCTTGATGTTGGACTTATCAGGACTACCACTGGAAACCGTG
|||   | ||  |   ||| | |||||    ||    | |  |||    || |||   ||   || |             ||  |  ||||||||||||| |||||||| ||||| || ||| |||||   || || ||||||||||||||  | |||||||| |||||||||||||| || || |||||||
gtaaaatttggccaaatatataatctt----attttaatatctgatg--ttgcattggtttggtatttctgacggttctttttgttcatcagGCCACTGGTGAGGACTTCTCTGTTGAGCCAGCTGATGAGAGGAGGCCTTTCCGTGCTCTCTTGGATGTTGGCCTTATCAGGACTACAACAGGGAACCGTG

upper sequence: AT5G39740.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM5G815894_T03 (Zea mays), 3'ss of exon 5
gtatgttgtgatcttttatttcatcttgaaaataaagaaacttgagagttttcatcttttgattaataactgaatcaaaattgatgaatcagGCCACTGGAGAGGACTTTTCTGTGGAACCAACTGATTCCAGAAGACCTTTCCGTGCTCTTCTTGATGTTGGACTTATCAGGACTACCACTGGAAACCGTG
       || |  |||   |  || | ||   ||        |||    |  |||   |||   | | |     |     ||  |  ||||||||||||| |||||||| ||||| || ||| |||||   || || ||||||||||||||  | |||||||| ||||| |||||||| ||||| |||||||
-------gtaaaatttggctaaatttcgatcttattttttgctgatg--tcacattggttgggcatttatattgtttcttttcgttcatcagGCCACTGGTGAGGACTTCTCTGTTGAGCCAGCTGATGAGAGGAGGCCTTTCCGTGCTCTCTTGGATGTTGGCCTTATTAGGACTACAACTGGGAACCGTG

upper sequence: AT5G39740.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA16G03170.1 (Glycine max), 3'ss of exon 5
gtatgttgtgatcttttatttcatct-tgaaaataaagaaacttgagagttttcatcttttgattaataactgaatcaaaattgatgaatcagGCCACTGGAGAGGACTTTTCTGTGGAACCAACTGATTCCAGAAGACCTTTCCGTGCTCTTCTTGATGTTGGACTTATCAGGACTACCACTGGAAACCGTG
|||| |    || |  |||    | | ||    |    ||         || ||    |||  ||||| | |   |   |     |  ||||||| ||||||||||||| ||| ||||||||  ||||   ||| || || ||||||||||| ||||||||||| ||||| |||||||| ||||| |||||||
gtatttatgaatttgctatgctgtgtgtgtgtgtgtgcaactgctgcctttctctcagttttgttaattaattggttgtatccttttcatcagGCTACTGGAGAGGACTATTCAGTGGAACCTGCTGAGAGCAGGAGGCCATTCCGTGCTCTCCTTGATGTTGGTCTTATTAGGACTACAACTGGCAACCGTG

upper sequence: AT5G39740.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA07G06580.1 (Glycine max), 3'ss of exon 5
gtatgttgtgatcttttatttcatcttgaaaataaagaaacttgagagttttcatcttttgattaat-aactgaatcaaaattgatgaatcagGCCACTGGAGAGGACTTTTCTGTGGAACCAACTGATTCCAGAAGACCTTTCCGTGCTCTTCTTGATGTTGGACTTATCAGGACTACCACTGGAAACCGTG
|||| |     | |  |||    | |       |  ||          |||   | | |    |||| |  || |||  | ||  |   |||||| ||||||||||| | ||| ||||||||  ||||   ||| || || ||||||||||| ||||||||||| ||||| |||||||| || || |||||||
gtatttatgagtttgctatgctgtttgtgccccagcgagtgcctttcttttggctgtgtaagctaatgagttgtatcttattttttt--tcagGCTACTGGAGAGGATTATTCCGTGGAACCTGCTGAGAGCAGGAGGCCATTCCGTGCTCTCCTTGATGTTGGTCTTATTAGGACTACAACCGGTAACCGTG

upper sequence: AT5G39740.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA07G06590.1 (Glycine max), 3'ss of exon 5
gtatgttgtgatcttttatttcatcttgaaaataaagaaacttgagagttttcatcttttga-ttaat-aactgaatcaaaattgatgaatcagGCCACTGGAGAGGACTTTTCTGTGGAACCAACTGATTCCAGAAGACCTTTCCGTGCTCTTCTTGATGTTGGACTTATCAGGACTACCACTGGAAACCGTG
|||| |     |||  |||  | | |||      |   |         |||      | | |  |||| |  || |||  | ||  |   |||||| ||||||||||| | ||| ||||||||  ||||   ||| || || ||||||||||| ||||||||||| ||||| |||||||| || || |||||||
gtatttatgagtctgctatgcc-ttttgtgcccgagcgagtgcctttctttcagctgtgtaagctaatgagttgtatcttattttttt--tcagGCTACTGGAGAGGATTATTCCGTGGAACCTGCTGAGAGCAGGAGGCCATTCCGTGCTCTCCTTGATGTTGGTCTTATTAGGACTACAACCGGTAACCGTG

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|164064961|gb|ES119285.1|ES119285
EST:     TGGATGATGTAGTACGAGGGAAACGTAGAG                         GCCACTGGAGAGGACTTTTCTGTGGAACCAACTGATTCCAGAAGACCTTTA
genomic: TGGATGATG-AGTACGAGGGAAACGTAGAGgtatgttgtg ... gatgaatcagGCCACTGGAGAGGACTTTTCTGTGGAACCAACTGATTCCAGAAGACCTTT-
EST: gi|125288919|gb|EL303004.1|EL303004
EST:     GTGTTCTGAAAATGCTGGAAATGGATGATGAGTACGAGGGAAACGTAGAG                         GCCACTGGAGAGGACTTTTCTGTGGAACCA
genomic: GTGTTCTGAAAATGCTGGAAATGGATGATGAGTACGAGGGAAACGTAGAGgtatgttgtg ... gatgaatcagGCCACTGGAGAGGACTTTTCTGTGGAACCA
EST: gi|125207196|gb|EL222150.1|EL222150
EST:     GCTGGAAATGGATGATGAGTACGAGGGAAACGTAGAG                         GCCACTGGAGAGGACTTTTCTGTGGAACCAACTGATTCCAGAAGACCTTTC
genomic: GCTGGAAATGGATGATGAGTACGAGGGAAACGTAGAGgtatgttgtg ... gatgaatcagGCCACTGGAGAGGACTTTTCTGTGGAACCAACTGATTCCAGAAGACCTTTC
EST: gi|125034575|gb|EL106844.1|EL106844
EST:     GTGTTCTGAAAATGCTGGAAATGGATGATGAGTACGAGGGAAACGTAGAG                         GCCACTGGAGAGGACTTTTCTGTGGAACCAACTGATTCCAGAAGACCTTTC
genomic: GTGTTCTGAAAATGCTGGAAATGGATGATGAGTACGAGGGAAACGTAGAGgtatgttgtg ... gatgaatcagGCCACTGGAGAGGACTTTTCTGTGGAACCAACTGATTCCAGAAGACCTTTC
EST: gi|164191864|gb|EL977964.1|EL977964
EST:     GTGTTCTGAAAATGCTGGAAATGGATGATGAGTACGAGGGAAACGTAGAG                         GCCACTGGAGAGG
genomic: GTGTTCTGAAAATGCTGGAAATGGATGATGAGTACGAGGGAAACGTAGAGgtatgttgtg ... gatgaatcagGCCACTGGAGAGG
EST: gi|116398433|gb|EG441025.1|EG441025
EST:     GTGTTCTGAAAATGCTGGAAATGGATGATGAGTACGAGGGAAACGTAGAG                         GCCACTGGAGAGGACTTTTCTGTGGAACCAACTGATTCCAGAAGACCTTTC
genomic: GTGTTCTGAAAATGCTGGAAATGGATGATGAGTACGAGGGAAACGTAGAGgtatgttgtg ... gatgaatcagGCCACTGGAGAGGACTTTTCTGTGGAACCAACTGATTCCAGAAGACCTTTC
EST: gi|164128351|gb|ES100101.1|ES100101
EST:     GTGTTCTGAAAATGCTGGAAATGGATGATGAGTACGAGGGAAACGTAGAG                         GCCACTGGAGAAGGACTTTTCTGTGGAACCAACTGATTCCAGAAGACC
genomic: GTGTTCTGAAAATGCTGGAAATGGATGATGAGTACGAGGGAAACGTAGAGgtatgttgtg ... gatgaatcagGCCACTGGAGA-GGACTTTTCTGTGGAACCAACTGATTCCAGAAGACC
EST: gi|164209527|gb|ES079920.1|ES079920
EST:     TGGATGATGAGTACGAGGGAAACGTAGAG                         GCCACTGGAGAGGACTTTTCTGTGGAACCAACTGATTCCAGAAGACCTTTC
genomic: TGGATGATGAGTACGAGGGAAACGTAGAGgtatgttgtg ... gatgaatcagGCCACTGGAGAGGACTTTTCTGTGGAACCAACTGATTCCAGAAGACCTTTC
EST: gi|125158069|gb|EL186840.1|EL186840
EST:     GTGTTCTGAAAATGCTGGAAATGGATGATGAGTACGAGGGAAACGTAGAG                         GCCACTGGAGAGGACTTTTCTGTGGAACCAACTGATTCCAGAAGACCTTTC
genomic: GTGTTCTGAAAATGCTGGAAATGGATGATGAGTACGAGGGAAACGTAGAGgtatgttgtg ... gatgaatcagGCCACTGGAGAGGACTTTTCTGTGGAACCAACTGATTCCAGAAGACCTTTC
EST: gi|163972979|gb|ES099547.1|ES099547
EST:     GGAAATGGATGATGAGTACGAGGGAAACGTAGAG                         GCCACTGGAGAGGACTTTTCTGTGGAACCAACTGATTCCAGAAGACCTTTC
genomic: GGAAATGGATGATGAGTACGAGGGAAACGTAGAGgtatgttgtg ... gatgaatcagGCCACTGGAGAGGACTTTTCTGTGGAACCAACTGATTCCAGAAGACCTTTC
EST: gi|163972920|gb|ES197012.1|ES197012
EST:     GGAAATGGATGATGAGTACGAGGGAAACGTAGAG                         GCCACTGGAGAGGACTTTTCTGTGGAACCAACTGATTCCAGAAGACCTT-C
genomic: GGAAATGGATGATGAGTACGAGGGAAACGTAGAGgtatgttgtg ... gatgaatcagGCCACTGGAGAGGACTTTTCTGTGGAACCAACTGATTCCAGAAGACCTTTC
EST: gi|164097969|gb|EL977361.1|EL977361
EST:     GTGTTCTGAAAATGCTGGAAATGGATGATGAGTACGAGGGAAACGTAGAG                         GCCACTGGAGAGGACTTTTCTGTGGAACCAACTGATTCCA
genomic: GTGTTCTGAAAATGCTGGAAATGGATGATGAGTACGAGGGAAACGTAGAGgtatgttgtg ... gatgaatcagGCCACTGGAGAGGACTTTTCTGTGGAACCAACTGATTCCA
EST: gi|124764489|gb|EH854619.1|EH854619
EST:     GTGTTCTGAAAATGCTGGAAATGGATGATGAGTACGAGGGAAACGTAGAG                         GCCACTGGAGAGGACTTTTCTGTGGAACCAACTGATTCCAGA
genomic: GTGTTCTGAAAATGCTGGAAATGGATGATGAGTACGAGGGAAACGTAGAGgtatgttgtg ... gatgaatcagGCCACTGGAGAGGACTTTTCTGTGGAACCAACTGATTCCAGA
EST: gi|116398349|gb|EG440941.1|EG440941
EST:     GTGTTCTGAAAATGCTGGAAATGGATGATGAGTACGAGGGAAACGTAGAG                         GCCACTGGAGAGGACTTTTCTGTGGAACCAACTGATTCCAGAAGACCTTTC
genomic: GTGTTCTGAAAATGCTGGAAATGGATGATGAGTACGAGGGAAACGTAGAGgtatgttgtg ... gatgaatcagGCCACTGGAGAGGACTTTTCTGTGGAACCAACTGATTCCAGAAGACCTTTC
EST: gi|124841955|gb|EH926392.1|EH926392
EST:     GTGTTCTGAAAATGCTGGAAATGGATGATGAGTACGAGGGAAACGTAGAG                         GCCACTGGAGAGGACTTTTCT
genomic: GTGTTCTGAAAATGCTGGAAATGGATGATGAGTACGAGGGAAACGTAGAGgtatgttgtg ... gatgaatcagGCCACTGGAGAGGACTTTTCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaacttgagagttttcatcttttgattaataactgaatcaaaattgatgaatcagGCCACTGGAGAGGACTTTTCTGTGGAACCAACTGATTCCAGAAGACCTTTCCGTGCTCTTCTTGATGTTGGACTTATCAGGACTACCACTGGAAACCGTG
           ttttcatcttttgatt  TA-rich tract