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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cttaattggccaatggtggcagaattgtttggaactatccgttgatataaccctttagcaatcttcaatgccacttacaagacttaaattttgtgtacagGACACTGTTGTTGGATTTTTGATGGCTGGAGTTGGTAATGTTGACATAAGGAGGAAGACAAATTACCTCATCGTGGATTCAA

Basic information

species Arabidopsis thaliana
transcript AT4G02620.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G02620.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: LOC_Os02g57854.1 (Oryza sativa), 3'ss of exon 2
cttaattggccaatggtggcagaattgtttggaactatc-cgttgatataaccctttagcaatcttcaatgccacttacaagacttaaattttgtgtacagGACACTGTTGTTGGATTTTTGATGGCTGGAGTTGGTAATGTTGACATAAGGAGGAAGACAAATTACCTCATCGTGGATTCAA
||| |        || |   ||| | |   ||  |      ||| |   |    | |||  ||||  || |    ||      | |    | ||| | |||||||| ||   ||| |||||| ||||||||||||| ||||||||  | ||||  |||||||||||||| || || |||   |
cttgacataa-gctgctctaagagtagccaggttccccagtgtttaatcatgattatagtcatctgaaaggaatattctgtttcctcccctgtgtttgcagGACACGGTCACTGGGTTTTTGTTGGCTGGAGTTGGCAATGTTGATCTGAGGAAAAAGACAAATTACCTTATTGTTGATAACA

upper sequence: AT4G02620.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA05G26580.1 (Glycine max), 3'ss of exon 2
----cttaattggccaatggtggcagaattg---tttggaactatccgttgatataaccctttagcaatcttcaatgccacttacaa-gacttaaattttgtgtacagGACACTGTTGTTGGATTTTTGATGGCTGGAGTTGGTAATGTTGACATAAGGAGGAAGACAAATTACCTCATCGTGGATTCAA
      || |||   |||  |  |  |||||   ||  |||  |    |||| || |   || |   ||| | || ||   |||||| ||||   || || |  |||||| ||||| |||||||||||| |||||||||| || |||||||||||| | |||||||||||||||||||| ||||||||||
ctgttatagttg--taattttttcgtaattggtattctgaataactgattgaaatga---ttaaaacatcctgaaggc---ttacaatgactactatattttacacagGATACTGTAGTTGGATTTTTGTTGGCTGGAGTGGGAAATGTTGACATACGTAGGAAGACAAATTACCTCATTGTGGATTCAA

upper sequence: AT4G02620.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA08G09570.1 (Glycine max), 3'ss of exon 2
----cttaattggccaatggtggcagaattg---tttggaactatccgttgatataaccctttagcaatcttcaatgccacttacaagacttaaatt-ttgtgtacagGACACTGTTGTTGGATTTTTGATGGCTGGAGTTGGTAATGTTGACATAAGGAGGAAGACAAATTACCTCATCGTGGATTCAA
      || |||  || |  |     |||||   ||  ||| |     |||| || |   || |   ||| | || ||   ||||||    ||  || || |  |||||| ||||| ||||||||| || |||||||||| || |||||||||||| | |||||||||||||||||||| ||||||||||
ctgttatagttg--cagtttttttgtaattggtattctgaatttctgattgaaatga---ttaaaacatcctgaaggc---ttacaatgaatactttattttacacagGATACTGTAGTTGGATTTCTGTTGGCTGGAGTGGGAAATGTTGACATACGTAGGAAGACAAATTACCTCATTGTGGATTCAA

upper sequence: AT4G02620.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv05s0062g00210.t01 (Vitis vinifera), 3'ss of exon 2
cttaattggcca--atggtggcagaattgtttg-gaactatc-cgttgatataaccctttagcaatcttcaatgccacttacaagacttaaattttgtgtacagGACACTGTTGTTGGATTTTTGATGGCTGGAGTTGGTAATGTTGACATAAGGAGGAAGACAAATTACCTCATCGTGGATTCAA
    | ||  ||  ||  |     | || ||    || | || |   |  | |    |||  | |  ||   |     |   | |  | |   ||  | | ||||||||| |   ||| |||||| |||||||||| |||||||||||| |  |||| ||||||||||| ||||| || || ||||
----actgtgcatcataattatttatttcttgataaattgtcacaaagccacatggttttcactaggttttttatttatctgatggatgattgttcatatgcagGACACTATAACTGGGTTTTTGCTGGCTGGAGTGGGTAATGTTGACTTGCGGAGAAAGACAAATTATCTCATTGTTGACTCAA

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|86018446|gb|DR314192.1|DR314192
EST:     CTACGATCCCTGCTCGCAACTCTGCCCTCATCGCAATGATCGCCGATGAG                         GACACTGTTGTTGGATTTTTGATGGCTGGAGTTGGTAATGTTGACATAAGG
genomic: CTACGATCCCTGCTCGCAACTCTGCCCTCATCGCAATGATCGCCGATGAGgtaaattcgt ... ttgtgtacagGACACTGTTGTTGGATTTTTGATGGCTGGAGTTGGTAATGTTGACATAAGG
EST: gi|86018455|gb|DR314201.1|DR314201
EST:     CTACGATCCCTGCTCGCAACTCTGCCCTCATCGCAATGATCGCCGATGAG                         GACACTGTTGTTGGATTTTTGATGGCTGGAGTTGGTAATGTTGACATAAGG
genomic: CTACGATCCCTGCTCGCAACTCTGCCCTCATCGCAATGATCGCCGATGAGgtaaattcgt ... ttgtgtacagGACACTGTTGTTGGATTTTTGATGGCTGGAGTTGGTAATGTTGACATAAGG
EST: gi|86018467|gb|DR314213.1|DR314213
EST:     CTACGATCCCTGCTCGCAACTCTGCCCTCATCGCAATGATCGCCGATGAG                         GACACTGTTGTTGGATTTTTGATGGCTGGAGTTGGTAATGTTGACATAAGG
genomic: CTACGATCCCTGCTCGCAACTCTGCCCTCATCGCAATGATCGCCGATGAGgtaaattcgt ... ttgtgtacagGACACTGTTGTTGGATTTTTGATGGCTGGAGTTGGTAATGTTGACATAAGG
EST: gi|124911120|gb|EH985200.1|EH985200
EST:     CGCAACTCTGCCCTCATCGCAATGATCGCCGATGAG                         GACACTGTTGTTGGATTTTTGATGGCTGGAGTTGGTAATGTTGACATAAGG
genomic: CGCAACTCTGCCCTCATCGCAATGATCGCCGATGAGgtaaattcgt ... ttgtgtacagGACACTGTTGTTGGATTTTTGATGGCTGGAGTTGGTAATGTTGACATAAGG
EST: gi|86018442|gb|DR314188.1|DR314188
EST:     CTACGATCCCTGCTCGCAACTCTGCCCTCATCGCAATGATCGCCGATGAG                         GACACTGTTGTTGGATTTTTGATGGCTGGAGTTGGTMATGTTGACATMAGG
genomic: CTACGATCCCTGCTCGCAACTCTGCCCTCATCGCAATGATCGCCGATGAGgtaaattcgt ... ttgtgtacagGACACTGTTGTTGGATTTTTGATGGCTGGAGTTGGTAATGTTGACATAAGG
EST: gi|86018460|gb|DR314206.1|DR314206
EST:     CTACGATCCCTGCTCGCAACTCTGCCCTCATCGCAATGATCGCCGATGAG                         GACACTGTTGTTGGATTTTTGATGGCTGGAGTTGGTAATGTTGACATAAGG
genomic: CTACGATCCCTGCTCGCAACTCTGCCCTCATCGCAATGATCGCCGATGAGgtaaattcgt ... ttgtgtacagGACACTGTTGTTGGATTTTTGATGGCTGGAGTTGGTAATGTTGACATAAGG
EST: gi|86018443|gb|DR314189.1|DR314189
EST:     CTACGATCCCTGCTCGCAACTCTGCCCTCATCGCAATGATCGCCGATGAG                         GACACTGTTGTTGGATTTTTGATGGCTGGAGTTGGTAATGTTGACATAAGG
genomic: CTACGATCCCTGCTCGCAACTCTGCCCTCATCGCAATGATCGCCGATGAGgtaaattcgt ... ttgtgtacagGACACTGTTGTTGGATTTTTGATGGCTGGAGTTGGTAATGTTGACATAAGG
EST: gi|86018454|gb|DR314200.1|DR314200
EST:     CTACGATCCCTGCTCGCAACTCTGCCCTCATCGCAATGATCGCCGATGAG                         GACACTGTTGTTGGATTTTTGATGGCTGGAGTTGGTAATGTTGACATAAGG
genomic: CTACGATCCCTGCTCGCAACTCTGCCCTCATCGCAATGATCGCCGATGAGgtaaattcgt ... ttgtgtacagGACACTGTTGTTGGATTTTTGATGGCTGGAGTTGGTAATGTTGACATAAGG
EST: gi|86018463|gb|DR314209.1|DR314209
EST:     CTACGATCCCTGCTCGCAACTCTGCCCTCATCGCAATGATCGCCGATGAG                         GACACTGTTGTTGGATTTTTGATGGCTGGAGTTGGTAATGTTGACATAAGG
genomic: CTACGATCCCTGCTCGCAACTCTGCCCTCATCGCAATGATCGCCGATGAGgtaaattcgt ... ttgtgtacagGACACTGTTGTTGGATTTTTGATGGCTGGAGTTGGTAATGTTGACATAAGG
EST: gi|86018451|gb|DR314197.1|DR314197
EST:     CTACGATCCCTGCTCGCAACTCTGCCCTCATCGCAATGATCGCCGATGAG                         GACACTGTTGTTGGATTTTTGATGGCTGGAGTTGGTAATGTTGACATAAGG
genomic: CTACGATCCCTGCTCGCAACTCTGCCCTCATCGCAATGATCGCCGATGAGgtaaattcgt ... ttgtgtacagGACACTGTTGTTGGATTTTTGATGGCTGGAGTTGGTAATGTTGACATAAGG
EST: gi|86018447|gb|DR314193.1|DR314193
EST:     CTACGATCCCTGCTCGCAACTCTGCCCTCATCGCAATGATCGCCGATGAG                         GACACTGTTGTTGGATTTTTGATGGCTGGAGTTGGTAATGTTGACATAAGG
genomic: CTACGATCCCTGCTCGCAACTCTGCCCTCATCGCAATGATCGCCGATGAGgtaaattcgt ... ttgtgtacagGACACTGTTGTTGGATTTTTGATGGCTGGAGTTGGTAATGTTGACATAAGG
EST: gi|86018456|gb|DR314202.1|DR314202
EST:     CTACGATCCCTGCTCGCAACTCTGCCCTCATCGCAATGATCGCCGATGAG                         GACACTGTTGTTGGATTTTTGATGGCTGGAGTTGGTAATGTTGACATAAGG
genomic: CTACGATCCCTGCTCGCAACTCTGCCCTCATCGCAATGATCGCCGATGAGgtaaattcgt ... ttgtgtacagGACACTGTTGTTGGATTTTTGATGGCTGGAGTTGGTAATGTTGACATAAGG
EST: gi|86018466|gb|DR314212.1|DR314212
EST:     CTACGATCCCTGCTCDCAACTCTGCCCTCATCGCAATGATCGCCGATGAG                         GACACTGTTGTTGGATTTTTGATGGCTGGAGTTGGTAATGTTGACATAAGG
genomic: CTACGATCCCTGCTCGCAACTCTGCCCTCATCGCAATGATCGCCGATGAGgtaaattcgt ... ttgtgtacagGACACTGTTGTTGGATTTTTGATGGCTGGAGTTGGTAATGTTGACATAAGG
EST: gi|86018458|gb|DR314204.1|DR314204
EST:     CTACGATCCCTGCTCGCAACTCTGCCCTCATCGCAATGATCGCCGATGAG                         GACACTGTTGTTGGATTTTTGATGGCTGGAGTTGGTAATGTTGACATAAGG
genomic: CTACGATCCCTGCTCGCAACTCTGCCCTCATCGCAATGATCGCCGATGAGgtaaattcgt ... ttgtgtacagGACACTGTTGTTGGATTTTTGATGGCTGGAGTTGGTAATGTTGACATAAGG
EST: gi|86018457|gb|DR314203.1|DR314203
EST:     CTACGATCCCTGCTCGCAACTCTGCCCTCATCGCAATGATCGCCGATGAG                         GACACTGTTGTTGGATTTTTGATGGCTGGAGTTGGTAATGTTGACATAAGG
genomic: CTACGATCCCTGCTCGCAACTCTGCCCTCATCGCAATGATCGCCGATGAGgtaaattcgt ... ttgtgtacagGACACTGTTGTTGGATTTTTGATGGCTGGAGTTGGTAATGTTGACATAAGG
EST: gi|86018461|gb|DR314207.1|DR314207
EST:     CTACGATCCCTGCTCGCAACTCTGCCCTCATCGCAATGATCGCCGATGAG                         GACACTGTTGTTGGATTTTTGATGGCTGGAGTTGGTAATGTTGACATAAGG
genomic: CTACGATCCCTGCTCGCAACTCTGCCCTCATCGCAATGATCGCCGATGAGgtaaattcgt ... ttgtgtacagGACACTGTTGTTGGATTTTTGATGGCTGGAGTTGGTAATGTTGACATAAGG
EST: gi|164035856|gb|ES204161.1|ES204161
EST:     CTACGATCCCTGCTCGCAACTCTGCCCTCATCGCAATGATCGCCGATGAG                         GACACTGTTGTTGGATTTTTGATGGCTGGAGT
genomic: CTACGATCCCTGCTCGCAACTCTGCCCTCATCGCAATGATCGCCGATGAGgtaaattcgt ... ttgtgtacagGACACTGTTGTTGGATTTTTGATGGCTGGAGT
EST: gi|86018462|gb|DR314208.1|DR314208
EST:     CTACGATCCCTGCTCGCAACTCTGCCCTCATCGCAATGATCGCCGATGAG                         GACACTGTTGTTGGATTTTTGATGGCTGGAGTTGGTAATGTTGACATAAGG
genomic: CTACGATCCCTGCTCGCAACTCTGCCCTCATCGCAATGATCGCCGATGAGgtaaattcgt ... ttgtgtacagGACACTGTTGTTGGATTTTTGATGGCTGGAGTTGGTAATGTTGACATAAGG
EST: gi|86018450|gb|DR314196.1|DR314196
EST:     CTACGATCCCTGCTCGCAACTCTGCCCTCATCGCAATGATCGCCGATGAG                         GACACTGTTGTTGGATTTTTGATGGCTGGAGTTGGTAATGTTGACATAAGG
genomic: CTACGATCCCTGCTCGCAACTCTGCCCTCATCGCAATGATCGCCGATGAGgtaaattcgt ... ttgtgtacagGACACTGTTGTTGGATTTTTGATGGCTGGAGTTGGTAATGTTGACATAAGG
EST: gi|86018444|gb|DR314190.1|DR314190
EST:     CTACGATCCCTGCTCGCAACTCTGCCCTCATCGCAATGATCGCCGATGAG                         GACACTGTTGTTGGATTTTTGATGGCTGGAGTTGGTAATGTTGACATAAGG
genomic: CTACGATCCCTGCTCGCAACTCTGCCCTCATCGCAATGATCGCCGATGAGgtaaattcgt ... ttgtgtacagGACACTGTTGTTGGATTTTTGATGGCTGGAGTTGGTAATGTTGACATAAGG
EST: gi|164113442|gb|ES061720.1|ES061720
EST:     CTACGATCCCTGCTCGCAACTCTGCCCTCATCGCAATGATCGCCGATGAG                         GACACTGTTGTTGGATTTTTGATGGCTGGAGTTGGTA
genomic: CTACGATCCCTGCTCGCAACTCTGCCCTCATCGCAATGATCGCCGATGAGgtaaattcgt ... ttgtgtacagGACACTGTTGTTGGATTTTTGATGGCTGGAGTTGGTA
EST: gi|86018453|gb|DR314199.1|DR314199
EST:     CTACGATCCCTGCTCGCAACTCTGCCCTCATCGCAATGATCGCCGATGAG                         GACACTGTTGTTGGATTTTTGATGGCTGGAGTTGGTAATGTTGACATAAGG
genomic: CTACGATCCCTGCTCGCAACTCTGCCCTCATCGCAATGATCGCCGATGAGgtaaattcgt ... ttgtgtacagGACACTGTTGTTGGATTTTTGATGGCTGGAGTTGGTAATGTTGACATAAGG
EST: gi|86075878|gb|DR371635.1|DR371635
EST:     CTACGATCCCTGCTCGCAACTCTGCCCTCATCGCAATGATCGCCGATGAG                         GACACTGTTGTTGGATTTTTGATGGCTGGAGTTGGTAATGTTGACATAAGG
genomic: CTACGATCCCTGCTCGCAACTCTGCCCTCATCGCAATGATCGCCGATGAGgtaaattcgt ... ttgtgtacagGACACTGTTGTTGGATTTTTGATGGCTGGAGTTGGTAATGTTGACATAAGG
EST: gi|86018449|gb|DR314195.1|DR314195
EST:     CTACGATCCCTGCTCGCAACTCTGCCCTCATCGCAATGATCGCCGATGAG                         GACACTGTTGTTGGATTTTTGATGGCTGGAGTTGGTAATGTTGACATAAGG
genomic: CTACGATCCCTGCTCGCAACTCTGCCCTCATCGCAATGATCGCCGATGAGgtaaattcgt ... ttgtgtacagGACACTGTTGTTGGATTTTTGATGGCTGGAGTTGGTAATGTTGACATAAGG
EST: gi|86018464|gb|DR314210.1|DR314210
EST:     CTACGATCCCTGCTCGCAACTCTGCCCTCATCGCAATGATCGCCGATGAG                         GACACTGTTGTTGGATTTTTGATGGCTGGAGTTGGTAATGTTGACATAAGG
genomic: CTACGATCCCTGCTCGCAACTCTGCCCTCATCGCAATGATCGCCGATGAGgtaaattcgt ... ttgtgtacagGACACTGTTGTTGGATTTTTGATGGCTGGAGTTGGTAATGTTGACATAAGG
EST: gi|86018452|gb|DR314198.1|DR314198
EST:     CTACGATCCCTGCTCGCAACTCTGCCCTCATCGCAATGATCGCCGATGAG                         GACACTGTTGTTGGATTTTTGATGGCTGGAGTTGGTAATGTTGACATAAGG
genomic: CTACGATCCCTGCTCGCAACTCTGCCCTCATCGCAATGATCGCCGATGAGgtaaattcgt ... ttgtgtacagGACACTGTTGTTGGATTTTTGATGGCTGGAGTTGGTAATGTTGACATAAGG
EST: gi|86018459|gb|DR314205.1|DR314205
EST:     CTACGATCCCTGCTCGCAACTCTGCCCTCATCGCAATGATCGCCGATGAG                         GACACTGTTGTTGGATTTTTGATGGCTGGAGTTGGTAATGTTGACATAAGG
genomic: CTACGATCCCTGCTCGCAACTCTGCCCTCATCGCAATGATCGCCGATGAGgtaaattcgt ... ttgtgtacagGACACTGTTGTTGGATTTTTGATGGCTGGAGTTGGTAATGTTGACATAAGG
EST: gi|86018448|gb|DR314194.1|DR314194
EST:     CTACGATCCCTGCTCGCAACTCTGCCCTCATCGCAATGATCGCCGATGAG                         GACACTGTTGTTGGATTTTTGATGGCTGGAGTTGGTAATGTTGACATAAGG
genomic: CTACGATCCCTGCTCGCAACTCTGCCCTCATCGCAATGATCGCCGATGAGgtaaattcgt ... ttgtgtacagGACACTGTTGTTGGATTTTTGATGGCTGGAGTTGGTAATGTTGACATAAGG
EST: gi|47828671|gb|CK118355.1|CK118355
EST:     CTACGATCCCTGCTCGCAACTCTGCCCTCATCGCAATGATCGCCGATGAG                         GACACTGTTGTTGGATTTTTGATGGCTGGAGTTGGTAATGTTGACATAAGG
genomic: CTACGATCCCTGCTCGCAACTCTGCCCTCATCGCAATGATCGCCGATGAGgtaaattcgt ... ttgtgtacagGACACTGTTGTTGGATTTTTGATGGCTGGAGTTGGTAATGTTGACATAAGG
EST: gi|86018445|gb|DR314191.1|DR314191
EST:     CTACGATCCCTGCTCGCAACTCTGCCCTCATCGCAATGATCGCCGATGAG                         GACACTGTTGTTGGATTTTTGATGGCTGGAGTTGGTAATGTTGACATAAGG
genomic: CTACGATCCCTGCTCGCAACTCTGCCCTCATCGCAATGATCGCCGATGAGgtaaattcgt ... ttgtgtacagGACACTGTTGTTGGATTTTTGATGGCTGGAGTTGGTAATGTTGACATAAGG
EST: gi|86018465|gb|DR314211.1|DR314211
EST:     CTACGATCCCTGCTCGCAACTCTGCCCTCATCGCAATGATCGCCGATGAG                         GACACTGTTGTTGGATTTTTGATGGCTGGAGTTGGTAATGTTGACATAAGG
genomic: CTACGATCCCTGCTCGCAACTCTGCCCTCATCGCAATGATCGCCGATGAGgtaaattcgt ... ttgtgtacagGACACTGTTGTTGGATTTTTGATGGCTGGAGTTGGTAATGTTGACATAAGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tataaccctttagcaatcttcaatgccacttacaagacttaaattttgtgtacagGACACTGTTGTTGGATTTTTGATGGCTGGAGTTGGTAATGTTGACATAAGGAGGAAGACAAATTACCTCATCGTGGATTCAA
                          cacttac  putative branch site (score: 2)
                                 aagacttaaatttt  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cttaattggccaatggtggcagaattgtttggaactatccgttgatataaccctttagcaatcttcaatgccacttacaagacttaaattttgtgtacagGACACTGTTGTTGGATTTTTGATGGCTGGAGTTGGTAATGTTGACATAAGGAGGAAGACAAATTACCTCATCGTGGATTCAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - -tgtttgg
- - - - - - - - - - - - - - - - - ctatccg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - acttaca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -acttaaa