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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTTTCAGCTCCTGGATGCATTTCTGTGCTGTGCGTACATTCGCTGAGAGCATTATGAGATACGGTTTACCTCCGGCGTTCTTGgtaaattaggactccaagctatgctattttagagaattcctctaccctactatctcccttaccaaattactttctcttgtctttccag

Basic information

species Arabidopsis thaliana
transcript AT1G12840.1
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G12840.1 (Arabidopsis thaliana), 5'ss of exon 9
lower sequence: LOC_Os05g51530.1 (Oryza sativa), 5'ss of exon 9
GTTTTCAGCTCCTGGATGCATTTCTGTGCTGTGCGTACATTCGCTGAGAGCATTATGAGATACGGTTTACCTCCGGCGTTCTTGgtaaattaggactccaagctatgctattttagaga-attcctctaccctactatctcccttacca--aattactttctcttgtctttccag
|| ||||| ||||||||||| |||||||||||||||   || |  ||||||||| | ||||| ||| | || ||  | ||| ||||||  ||     |       |  ||| | | ||  |    | |||  |  |  ||    ||  |  |  | || | | |  | |   |||
GTATTCAGTTCCTGGATGCACTTCTGTGCTGTGCGTGTCTTTGTAGAGAGCATTCTTAGATATGGTCTTCCCCCATCATTCCTGgtaatctattctactgttacgtagtatatgatagtcaaatttgtactttgatgcctgatctaatatcatatgctgtttatgttttcatcag

upper sequence: AT1G12840.1 (Arabidopsis thaliana), 5'ss of exon 9
lower sequence: GRMZM2G128995_T01 (Zea mays), 5'ss of exon 9
GTTTTCAGCTCCTGGATGCATTTCTGTGCTGTGCGTACATTCGCTGAGAGCATTATGAGATACGGTTTACCTCCGGCGTTCTTGgtaaattaggactccaagctatgctattttagagaattcctc-taccctactatctcccttaccaaattactttctcttgtctttccag
|| ||||| ||||||||||| |||||||||||||||   || |  ||||||||  | ||||| ||| | |||||  | ||| |||||| ||        | ||| |  | |||  ||   |   |  ||  || |  | ||  ||  |  || | | | | |||  | ||   
GTATTCAGTTCCTGGATGCACTTCTGTGCTGTGCGTGTCTTTGTAGAGAGCATCCTTAGATATGGTCTCCCTCCATCATTCCTGgtaatttg----ctgaggctgt--tgtttatgatggtaaatagtatacttccgtttc--ttgtctgatca-tatgttttgcatatcag-

upper sequence: AT1G12840.1 (Arabidopsis thaliana), 5'ss of exon 9
lower sequence: GLYMA19G27360.1 (Glycine max), 5'ss of exon 9
GTTTTCAGCTCCTGGATGCATTTCTGTGCTGTGCGTACATTCGCTGAGAGCATTATGAGATACGGTTTACCTCCGGCGTTCTTGgtaaattaggactccaagctatgctattttagagaattcctctaccctactatctcccttaccaaattactttctcttgtct-ttccag
|||||||| ||||||||||| || ||||||||||||  ||| |||||||||||| ||||||| ||| | |||||  | ||||||||||  ||    || ||   ||   | || ||   | |   |   |||   || | |     |   | |||  |  |||  | ||||||
GTTTTCAGTTCCTGGATGCACTTTTGTGCTGTGCGTTTATTTGCTGAGAGCATTCTGAGATATGGTCTGCCTCCATCCTTCTTGgtaatatactcttctaaa--atcaaagttcagtctaatggcc---cctgggattttcaaatactgttcactgaccattgggtattccag

upper sequence: AT1G12840.1 (Arabidopsis thaliana), 5'ss of exon 9
lower sequence: GLYMA16G05470.1 (Glycine max), 5'ss of exon 9
GTTTTCAGCTCCTGGATGCATTTCTGTGCTGTGCGTACATTCGCTGAGAGCATTATGAGATACGGTTTACCTCCGGCGTTCTTGgtaaattaggactccaagctatgctattttagagaattcctcta--ccctactatctcccttaccaaattactttctcttgtct-ttccag
|||||||| ||||||||||| || ||||||||||||  ||| |||||||||||| ||||||| ||| | || ||  | ||||||||||  ||    || ||        ||   || | | ||   |   ||||   || | |     |  || |||   | |||  | ||||||
GTTTTCAGTTCCTGGATGCACTTTTGTGCTGTGCGTTTATTTGCTGAGAGCATTCTGAGATATGGTCTGCCACCATCTTTCTTGgtaatatactcttctaaa-------atcaaagtgcagtctaatgacccctgggattttcaaacactgatcactgagtattgggtattccag

upper sequence: AT1G12840.1 (Arabidopsis thaliana), 5'ss of exon 9
lower sequence: GLYMA02G07260.1 (Glycine max), 5'ss of exon 9
GTTTTCAGCTCCTGGATGCATTTCTGTGCTGTGCGTACATTCGCTGAGAGCATTATGAGATACGGTTTACCTCCGGCGTTCTTGgtaaat-taggactccaagctatgctattttagagaattcctctaccctactatctcccttaccaaa-ttactttctcttgtctttccag
|||||||||||||||||||| || ||||| ||||||  |||  ||||||||||| ||||||| ||| | || ||  | ||||||||| || ||    ||    | ||    ||       |||  |     | | ||| |    |   |   ||  ||  | | ||| ||||||
GTTTTCAGCTCCTGGATGCACTTTTGTGCAGTGCGTGTATTTACTGAGAGCATTCTGAGATATGGTCTTCCACCATCTTTCTTGgtagatatacccatctgtacaatagctttcaccttcattttttccttcaaatattttatctctgacccttgattcttgtggtcattccag

upper sequence: AT1G12840.1 (Arabidopsis thaliana), 5'ss of exon 9
lower sequence: GLYMA16G26220.1 (Glycine max), 5'ss of exon 9
GTTTTCAGCTCCTGGATGCATTTCTGTGCTGTGCGTACATTCGCTGAGAGCATTATGAGATACGGTTTACCTCCGGCGTTCTTGgtaaattaggactccaagctatgctattttagagaattcctctaccctactatctcccttaccaa-----attactttctcttgtctttccag
|||||||||||||||||||| || ||||| ||||||  |||  | ||||||||| ||||||| ||| | || ||  | ||||||||| ||     || |     |     ||| ||     || | | |         |   ||| ||       ||  ||  | | ||| ||||||
GTTTTCAGCTCCTGGATGCACTTTTGTGCAGTGCGTGTATTTACCGAGAGCATTCTGAGATATGGTCTTCCACCATCTTTCTTGgtagatatacccttctgtacaacagctttcagcttcatcttttccttcttcgaatattttatcacttatccttgattcttgtggtcattccag

upper sequence: AT1G12840.1 (Arabidopsis thaliana), 5'ss of exon 9
lower sequence: Vv14s0068g01280.t01 (Vitis vinifera), 5'ss of exon 9
GTTTTCAGCTCCTGGATGCATTTCTGTGCTGTGCGTACATTCGCTGAGAGCATTATGAGATACGGTTTACCTCCGGCGTTCTTGgtaaattaggactccaagct--atgctattttagagaattcctctaccctactatctcccttaccaa------attactttctcttgtctttccag
||||||||||||||||||||||| |||||||| |||   || || ||||| ||  | ||||| || || || ||  | |||||||||||| |    | |||     |   |  ||    |||| ||||   |      | ||  |||   |      |||  ||  |    |  || |||
GTTTTCAGCTCCTGGATGCATTTTTGTGCTGTACGTGTCTTTGCAGAGAGTATCCTTAGATATGGCTTGCCACCATCCTTCTTGgtaaataaaccattcaactccaacattccttcttggaatccctccctcacgaattttcttttattgattgaggattggttgttgagatgatttcag

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|86077243|gb|DR373000.1|DR373000
EST:     GTACATTCGCTGAGAGCATTATGAGATACGGTTTACCTCCGGCGTTCTTG                         GCATGTGTCTTATCTCCGGCTGTGAAAAGTGAAAAGAAAGTACGCTCCATT
genomic: GTACATTCGCTGAGAGCATTATGAGATACGGTTTACCTCCGGCGTTCTTGgtaaattagg ... gtctttccagGCATGTGTCTTATCTCCGGCTGTGAAAAGTGAAAAGAAAGTACGCTCCATT
EST: gi|124889160|gb|EH968062.1|EH968062
EST:     GTACATTCGCTGAGAGCATTATGAGATACGGTTTACCTCCGGCGTTCTTG                         GCATGTGTCTTATCTCCGGCTGTGAAAAG
genomic: GTACATTCGCTGAGAGCATTATGAGATACGGTTTACCTCCGGCGTTCTTGgtaaattagg ... gtctttccagGCATGTGTCTTATCTCCGGCTGTGAAAAG
EST: gi|125166687|gb|EL192368.1|EL192368
EST:     TCGCTGAGAGCATTATGAGATACGGTTTACCTCCGGCGTTCTTG                         GCATGTGTCTTATCTCCGGCTGTGAAAAGTGAAAAGAAAGTACGCTCCATT
genomic: TCGCTGAGAGCATTATGAGATACGGTTTACCTCCGGCGTTCTTGgtaaattagg ... gtctttccagGCATGTGTCTTATCTCCGGCTGTGAAAAGTGAAAAGAAAGTACGCTCCATT
EST: gi|86082327|gb|DR378086.1|DR378086
EST:     GTACATTCGCTGAGAGCATTATGAGATACGGTTTACCTCCGGCGTTCTTG                         GCATGTGTCTTATCTCCGGCTGTGAAAAGTGAAAAGAAAGTACGCTCCATT
genomic: GTACATTCGCTGAGAGCATTATGAGATACGGTTTACCTCCGGCGTTCTTGgtaaattagg ... gtctttccagGCATGTGTCTTATCTCCGGCTGTGAAAAGTGAAAAGAAAGTACGCTCCATT
EST: gi|116402070|gb|EG444662.1|EG444662
EST:     GTACATTCGCTGAGAGCATTATGAGATACGGTTTACCTCCGGCGTTCTTG                         GCATGTGTCTTATCTCCGGCTGTGAAAAGTGAAAAGAAAGTACGCTCCATT
genomic: GTACATTCGCTGAGAGCATTATGAGATACGGTTTACCTCCGGCGTTCTTGgtaaattagg ... gtctttccagGCATGTGTCTTATCTCCGGCTGTGAAAAGTGAAAAGAAAGTACGCTCCATT
EST: gi|124878731|gb|EH958168.1|EH958168
EST:     CGGTTTACCTCCGGCGTTCTTG                         GCATGTGTCTTATCTCCGGCTGTGAAAAGTGAAAAGAAAGTACGCTCCATT
genomic: CGGTTTACCTCCGGCGTTCTTGgtaaattagg ... gtctttccagGCATGTGTCTTATCTCCGGCTGTGAAAAGTGAAAAGAAAGTACGCTCCATT
EST: gi|124833467|gb|EH917906.1|EH917906
EST:     TCCGGCGTTCTTG                         GCATGTGTCTTATCTCCGGCTGTGAAAAGTGAAAAGAAAGTACGCTCCATT
genomic: TCCGGCGTTCTTGgtaaattagg ... gtctttccagGCATGTGTCTTATCTCCGGCTGTGAAAAGTGAAAAGAAAGTACGCTCCATT
EST: gi|124986503|gb|EL059020.1|EL059020
EST:     AGAGCATTATGAGATACGGTTTACCTCCGGCGTTCTTG                         GCATGTGTCTTATCTCCGGCTGTGAAAAGTGAAAAGAAAGTACGCTCCATT
genomic: AGAGCATTATGAGATACGGTTTACCTCCGGCGTTCTTGgtaaattagg ... gtctttccagGCATGTGTCTTATCTCCGGCTGTGAAAAGTGAAAAGAAAGTACGCTCCATT
EST: gi|124745098|gb|EH836198.1|EH836198
EST:     GTACATTCGCTGAGAGCATTATGAGATACGGTTTACCTCCGGCGTTCTTG                         GCATGTGTCTTATCTCCGGCTGTGAAAAGTGAAAAG
genomic: GTACATTCGCTGAGAGCATTATGAGATACGGTTTACCTCCGGCGTTCTTGgtaaattagg ... gtctttccagGCATGTGTCTTATCTCCGGCTGTGAAAAGTGAAAAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTTTCAGCTCCTGGATGCATTTCTGTGCTGTGCGTACATTCGCTGAGAGCATTATGAGATACGGTTTACCTCCGGCGTTCTTGgtaaattaggactccaagctatgctattttagagaattcctctaccctactatctcccttaccaaattactttctcttgtctttccag

- - - - - - - - - - - - - - - - - - - - - - - AGAGCA