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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAAGCTCCTGCTATTGTGAAGTCCTACTATGACAAGCGAATTGTGGGCTGCCCTGGTGGTGAAGGCGgtaagttcttcccttcttcaaactttagtcgcatattatggacaatctttaatcggcaatcgttgttgtcattgaatatatcaagacacattatttaccaatctaactttctcctgaaaactgcag

Basic information

species Arabidopsis thaliana
transcript AT3G15640.1
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G15640.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GRMZM2G064753_T01 (Zea mays), 5'ss of exon 4
GAAGCTCCTGCTATTGTGAAGTCCTACTATGACAAGCGAATTGTGGGCTGCCCTGGTGGTGAAGGCGgtaagttcttcccttcttcaaactttagtcgcatattatggacaatctttaatcggcaatcgttgttgtcattgaatatatcaagacacattatttaccaatctaactttctcctgaaaactgcag
|| |  ||  || | ||  ||||||||||| ||||||| || || ||||||||||||||||| || ||||||    |    |||     | ||| |    | || |  | | |    |   ||   | ||      ||||   | || | |    | |  |||     | ||  |  || ||        |||
GAGGAACCATCTGTAGTTGAGTCCTACTATAACAAGCGGATAGTCGGCTGCCCTGGTGGTGAGGGAGgtaagccagtgttgtctatcgccctta-tatttttttttctaaagttaacagctggtg-tggtgcgaagcatttg-tgtaaccaattgcttggtttttgcctttacttgcctgctttttctcccag

upper sequence: AT3G15640.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GRMZM2G477366_T01 (Zea mays), 5'ss of exon 3
GAAGCTCCTGCTATTGTGAAGTCCTACTATGACAAGCGAATTGTGGGCTGCCCTGGTGGTGAAGGCGgtaagttcttcccttcttcaaacttta-gtcgcatattatggacaatctttaatcggcaatcgttgttgtcattgaatatatcaagacacattatttaccaatctaactttctcctgaaaactgcag
|| |  ||  || | ||  ||||||||||| ||||||| || || ||||||||||||||||| || ||||||    |    |||     | |||  |    |  ||  |  ||  |||  |      | ||      ||||   | || | |    | |  |||   | | ||  |  ||  |       ||||
GAGGAACCATCTGTAGTTGAGTCCTACTATAACAAGCGGATAGTCGGCTGCCCTGGTGGTGAGGGAGgtaagccagtgttgtctctcgcccttatatttttttctaaagttaacatttggt-----gtggtgcgaagcatttg-tgtaaccaattgcttggtttttgactttacttgcctgttttttctcgcag

upper sequence: AT3G15640.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: AC215864.3_FGT010 (Zea mays), 5'ss of exon 2
GAAGCTCCTGCTATTGTGAAGTCCTACTATGACAAGCGAATTGTGGGCTGCCCTGGTGGTGAAGGCGgtaagttcttcccttcttcaaactttagtcgcatattatggacaatctttaatcggcaatcgttgttgtcattgaatatatcaagacacattatttaccaatctaactttctcctgaaaactgcag
|| |  ||  || | ||   |||||||||| ||||||| || || ||||||||||||||||| || ||||||    |    |||     | |||      | || |  | | |    |   ||   | ||      ||||   | || | |    | |  |||   | | ||  |  ||  |       ||||
GAGGAACCATCTGTAGTTGGGTCCTACTATAACAAGCGGATAGTCGGCTGCCCTGGTGGTGAGGGAGgtaagccagtgttgtctctcgcccttatat---ttttttctaaagttaacagctggtg-tggtgcgaagcatttg-tgtaaccaattgcttggtttttgactttacttgcctgttttttctcgcag

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|86043824|gb|DR339579.1|DR339579
EST:     GAAGTCCTACTATGACAAGCGAATTGTGGGCTGCC-TGGTGGTGAAGGCG                         AGGACGAGCACGATGTTGTCTGGTTCTGGCTGGAG
genomic: GAAGTCCTACTATGACAAGCGAATTGTGGGCTGCCCTGGTGGTGAAGGCGgtaagttctt ... aaaactgcagAGGACGAGCACGATGTTGTCTGGTTCTGGCTGGAG
EST: gi|86043837|gb|DR339592.1|DR339592
EST:     GAAGTCCTACTATGACAAGCGAATTGTGGGCTGCCCTGGTGGTGAAGGCG                         AGGACGAGCACGATGTTGTCTGGTTCTGGCTGGAGAAAGGAAAGTCCTTTG
genomic: GAAGTCCTACTATGACAAGCGAATTGTGGGCTGCCCTGGTGGTGAAGGCGgtaagttctt ... aaaactgcagAGGACGAGCACGATGTTGTCTGGTTCTGGCTGGAGAAAGGAAAGTCCTTTG
EST: gi|125003375|gb|EL075644.1|EL075644
EST:     GCTGCCCTGGTGGTGAAGGCG                         AGGACGAGCACGATGTTGTCTGGTTCTGGCTGGAGAAAGGAAAGTCCTTTG
genomic: GCTGCCCTGGTGGTGAAGGCGgtaagttctt ... aaaactgcagAGGACGAGCACGATGTTGTCTGGTTCTGGCTGGAGAAAGGAAAGTCCTTTG
EST: gi|124747382|gb|EH837518.1|EH837518
EST:     GAAGTCCTACTATGACAAGCGAATTGTGGGCTGCCCTGGTGGTGAAGGCG                         AGGACGAGCACGATGTTGTCTGGTTCTGGCTGGAGAAA
genomic: GAAGTCCTACTATGACAAGCGAATTGTGGGCTGCCCTGGTGGTGAAGGCGgtaagttctt ... aaaactgcagAGGACGAGCACGATGTTGTCTGGTTCTGGCTGGAGAAA
EST: gi|86043849|gb|DR339604.1|DR339604
EST:     GAAGTCCTACTATGACAAGCGAATTGTGGGCTGCCCTGGTGGTGAAGGCG                         AGGACGAGCACGATGTTGTCTGGTTC
genomic: GAAGTCCTACTATGACAAGCGAATTGTGGGCTGCCCTGGTGGTGAAGGCGgtaagttctt ... aaaactgcagAGGACGAGCACGATGTTGTCTGGTTC
EST: gi|86043829|gb|DR339584.1|DR339584
EST:     GAAGTCCTACTATGACAAGCGAATTGTGGGCTGCCCTGGTGGTGAAGGCG                         AGGACGAGCACGATGTTGTCTG
genomic: GAAGTCCTACTATGACAAGCGAATTGTGGGCTGCCCTGGTGGTGAAGGCGgtaagttctt ... aaaactgcagAGGACGAGCACGATGTTGTCTG
EST: gi|86043819|gb|DR339574.1|DR339574
EST:     GAAGTCNTACTATGACAAGCGAATTGTGGGCTGCC-TGGTGGTGAAGGCG                         AGGACGAGCACGATGTTGTCTGGTTCTGGCTG
genomic: GAAGTCCTACTATGACAAGCGAATTGTGGGCTGCCCTGGTGGTGAAGGCGgtaagttctt ... aaaactgcagAGGACGAGCACGATGTTGTCTGGTTCTGGCTG
EST: gi|164106396|gb|ES018146.1|ES018146
EST:     CTGGTGGTGAAGGCG                         AGGACGAGCACGATGTTGTCTGGTTCTGGCTGGAGAAAGGAAAGTCCTTTG
genomic: CTGGTGGTGAAGGCGgtaagttctt ... aaaactgcagAGGACGAGCACGATGTTGTCTGGTTCTGGCTGGAGAAAGGAAAGTCCTTTG
EST: gi|86043823|gb|DR339578.1|DR339578
EST:     GAAGTCCTACTATGACAAGCGAATTGTGGGCTGCCCTGGTGGTGAAGGCG                         AGGACGAGCACGATGTTGTCTGGTTCTGGCTGGAGAAAGGAAAGTCCTTTG
genomic: GAAGTCCTACTATGACAAGCGAATTGTGGGCTGCCCTGGTGGTGAAGGCGgtaagttctt ... aaaactgcagAGGACGAGCACGATGTTGTCTGGTTCTGGCTGGAGAAAGGAAAGTCCTTTG
EST: gi|124863334|gb|EH947771.1|EH947771
EST:     GAAGTCCTACTATGACAAGCGAATTGTGGGCTGCCCTGGTGGTGAAGGCG                         AGGACGAGCACGAT
genomic: GAAGTCCTACTATGACAAGCGAATTGTGGGCTGCCCTGGTGGTGAAGGCGgtaagttctt ... aaaactgcagAGGACGAGCACGAT
EST: gi|86043816|gb|DR339571.1|DR339571
EST:     GAAGTCCTACTATGACAAGCGAATTGTGGGCTGCCCTGGTGGTGAAGGCG                         AGGACGAGCACGATGTTGTCT
genomic: GAAGTCCTACTATGACAAGCGAATTGTGGGCTGCCCTGGTGGTGAAGGCGgtaagttctt ... aaaactgcagAGGACGAGCACGATGTTGTCT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAAGCTCCTGCTATTGTGAAGTCCTACTATGACAAGCGAATTGTGGGCTGCCCTGGTGGTGAAGGCGgtaagttcttcccttcttcaaactttagtcgcatattatggacaatctttaatcggcaatcgttgttgtcattgaatatatcaagacacattatttaccaatctaactttctcctgaaaactgcag

- - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG