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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TATACTGGGGAGATGCAAGAGAGAAGCTTGTTGATGCTGTTAAAGATCTTAAACTCGATTCTATTGTCATGGGAAGCAGAGGACTCAGTGCTCTTCAAAGgtaatttcttgctctctttttcttttttatgtaataaattccattttatattcttgccaaaatgccattattgcttagtgtttactgtttagtattgctg...

Basic information

species Arabidopsis thaliana
transcript AT3G53990.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G53990.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GLYMA01G26300.1 (Glycine max), 5'ss of exon 3
TATACTGGGGAGATGCAAGAGAGAAGCTTGTTGATGCTGTTAAAGATCTTAAACTCGATTCTATTGTCATGGGAAGCAGAGGACTCAGTGCTCTTCAAAGgtaatttcttgctctctttttcttttttatgtaataaattccattttatattct-tgccaaaatgccattattgcttagtgtttact-gtttag-tattgctg--
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TATATTGGGGGGATGCAAGAGAGAAGCTTTTGGATGCTATTGAAGATCTGAAGCTGGATTCGCTGGTTATGGGAAGCAGGGGCCTCAGCACAATCCAAAGgtg----cctactttttttgtccctta-atttctttattttactgttatattcagcatctctcatcaataatttcatgagaattattcgcatagatattattgga
















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|164193330|gb|ES027881.1|ES027881
EST:     AAACTCGATTCTATTGTCATGGGAAGCAGAGGACTCAGTGCTCTTCAAAG                         GATAATAATGGGAAGCGTGAGCAGCTTTGNGATCCAACACGCG
genomic: AAACTCGATTCTATTGTCATGGGAAGCAGAGGACTCAGTGCTCTTCAAAGgtaatttctt ... aatgaaacagGATAATAATGGGAAGCGTGAGCAGCTTTGTGATCCAACACGCG
EST: gi|124927850|gb|EL005547.1|EL005547
EST:     TGCTCTTCAAAG                         GATAATAATGGGAAGCGTGAGCAGCTTTGTGATCCAACACGCGCCTTGCCC
genomic: TGCTCTTCAAAGgtaatttctt ... aatgaaacagGATAATAATGGGAAGCGTGAGCAGCTTTGTGATCCAACACGCGCCTTGCCC
EST: gi|116402197|gb|EG444789.1|EG444789
EST:     AAACTCGATTCTATTGTCATGGGAAGCAGAGGACTCAGTGCTCTTCAAAG                         GATAATAATGGGAAGCGTGAGCAGCTTTGGGATCCAACACGCGCCTTGCCC
genomic: AAACTCGATTCTATTGTCATGGGAAGCAGAGGACTCAGTGCTCTTCAAAGgtaatttctt ... aatgaaacagGATAATAATGGGAAGCGTGAGCAGCTTTGTGATCCAACACGCGCCTTGCCC
EST: gi|164074110|gb|ES131782.1|ES131782
EST:     AAACTCGATTCTATTGTCATGGGAAGCAGAGGACTCAGTGCTCTTCAAAG                         GATAATAATGGG
genomic: AAACTCGATTCTATTGTCATGGGAAGCAGAGGACTCAGTGCTCTTCAAAGgtaatttctt ... aatgaaacagGATAATAATGGG
EST: gi|116458737|gb|EG501329.1|EG501329
EST:     AAACTCGATTCTATTGTCATGGGAAGCAGAGGACTCAGTGCTCTTCAAAG                         GATAATAATGGGAAGCGTGAGCAGCTTTGTGATCCAACACGCGCCTTGCCC
genomic: AAACTCGATTCTATTGTCATGGGAAGCAGAGGACTCAGTGCTCTTCAAAGgtaatttctt ... aatgaaacagGATAATAATGGGAAGCGTGAGCAGCTTTGTGATCCAACACGCGCCTTGCCC
EST: gi|164125351|gb|ES198765.1|ES198765
EST:     GTGCTCTTCAAAG                         GATAATAATGGGAAGCGTGAGCNGCTTTGTGATCCAACACGCGCCTTGCCC
genomic: GTGCTCTTCAAAGgtaatttctt ... aatgaaacagGATAATAATGGGAAGCGTGAGCAGCTTTGTGATCCAACACGCGCCTTGCCC
EST: gi|47828449|gb|CK118133.1|CK118133
EST:     AAACTCGATTCTATTGTCATGGGAAGCAGAGGACTCAGTGCTCTTCAAAG                         GATAATAATGGGAAGCGTGAGCAGCTTTGTGATCCAACACGCGCCTTGCCC
genomic: AAACTCGATTCTATTGTCATGGGAAGCAGAGGACTCAGTGCTCTTCAAAGgtaatttctt ... aatgaaacagGATAATAATGGGAAGCGTGAGCAGCTTTGTGATCCAACACGCGCCTTGCCC
EST: gi|164178981|gb|ES132772.1|ES132772
EST:     GTCATGGGAAGCAGAGGACTCAGTGCTCTTCAAAG                         GATAATAATGGGAAGCGTGAGCAGCTTTGTG
genomic: GTCATGGGAAGCAGAGGACTCAGTGCTCTTCAAAGgtaatttctt ... aatgaaacagGATAATAATGGGAAGCGTGAGCAGCTTTGTG
EST: gi|164007765|gb|ES007905.1|ES007905
EST:     AAACTCGATTCTATTGTCATGGGAAGCAGAGGACTCAGTGCTCTTCAAAG                         GATAATAATGGGAA
genomic: AAACTCGATTCTATTGTCATGGGAAGCAGAGGACTCAGTGCTCTTCAAAGgtaatttctt ... aatgaaacagGATAATAATGGGAA
EST: gi|125314356|gb|EL328441.1|EL328441
EST:     GGGAAGCAGAGGACTCAGTGCTCTTCAAAG                         GTATAATAATGGGAAGCGTGAGCAGCTTTGTGATCCAACACGCGCCTTGCC
genomic: GGGAAGCAGAGGACTCAGTGCTCTTCAAAGgtaatttctt ... aatgaaacagG-ATAATAATGGGAAGCGTGAGCAGCTTTGTGATCCAACACGCGCCTTGCC
EST: gi|125024836|gb|EL097105.1|EL097105
EST:     AGGACTCAGTGCTCTTCAAAG                         GATAATAATGGGAAGCGTGAGCAGCTTTGTGATCCAACACGCGACCTTGCC
genomic: AGGACTCAGTGCTCTTCAAAGgtaatttctt ... aatgaaacagGATAATAATGGGAAGCGTGAGCAGCTTTGTGATCCAACACGCG-CCTTGCC
EST: gi|164147276|gb|ES051464.1|ES051464
EST:     AAACTCGATTCTATTGTCATGGGAAGCAGAGGACTCAGTGCTCTTCAAAG                         GATAATAATGGGAAGCGTGAGCA
genomic: AAACTCGATTCTATTGTCATGGGAAGCAGAGGACTCAGTGCTCTTCAAAGgtaatttctt ... aatgaaacagGATAATAATGGGAAGCGTGAGCA
EST: gi|164025057|gb|EL993740.1|EL993740
EST:     AAACTCGATTCTATTGTCATGGGAAGCAGAGGACTCAGTGCTCTTCAAAG                         GATAATAATGGGAAGC
genomic: AAACTCGATTCTATTGTCATGGGAAGCAGAGGACTCAGTGCTCTTCAAAGgtaatttctt ... aatgaaacagGATAATAATGGGAAGC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TATACTGGGGAGATGCAAGAGAGAAGCTTGTTGATGCTGTTAAAGATCTTAAACTCGATTCTATTGTCATGGGAAGCAGAGGACTCAGTGCTCTTCAAAGgtaatttcttgctctctttttcttttttatgtaataaattccattttatattcttgccaaaatgccattattgcttagtgtttactgtttagtattgctg

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA