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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtatcacatataacttctctttaactctctcactgtggcttgaacatttatattgaagaagaagaaaaaacaaatgactgtgttttttaactttaacaatggtaaaattgcagGGATTCGAGAAACTGAAGGAGCTGATAGATACATACAAAGGAGTTTCTCAATGAGCACAACAGAGATCATCTTTCGTTTTATAATTCATGTAATGTAATG

Basic information

species Arabidopsis thaliana
transcript AT5G04590.1
intron # 7
splice site 3'
intron type U2

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|124714845|gb|EH806247.1|EH806247
EST:     AACTAGAGAGGCAAACTAAAGAATCATTTGGAGAATACACAACCCGCATG                         GGATTCGAGAAACTGAAGGAGCTGATAGATACATACAAAGGAGTT
genomic: AACTAGAGAGGCAAACTAAAGAATCATTTGGAGAATACACAACCCGCATGgtaagtatca ... aaaattgcagGGATTCGAGAAACTGAAGGAGCTGATAGATACATACAAAGGAGTT
EST: gi|125287375|gb|EL301460.1|EL301460
EST:     TAAAGAATCATTTGGAGAATACACAACCCGCATG                         GGATTCGAGAAACTGAAGGAGCTGATAGATACATACAAAGGGGTTTCTCAA
genomic: TAAAGAATCATTTGGAGAATACACAACCCGCATGgtaagtatca ... aaaattgcagGGATTCGAGAAACTGAAGGAGCTGATAGATACATACAAAGGAGTTTCTCAA
EST: gi|116451400|gb|EG493992.1|EG493992
EST:     AACTAGAGAGGCAAACTAAAGAATCATTTGGAGAATACACAACCCGCATG                         GGATTCGAGAAACTGAAGGAGCTGATAGAAACATACAAAGGAGTTTCTCAA
genomic: AACTAGAGAGGCAAACTAAAGAATCATTTGGAGAATACACAACCCGCATGgtaagtatca ... aaaattgcagGGATTCGAGAAACTGAAGGAGCTGATAGATACATACAAAGGAGTTTCTCAA
EST: gi|124879287|gb|EH958724.1|EH958724
EST:     AACTAGAGAGGCAAACTAAAGAATCATTTGGAGAATACACAACCCGCATG                         GGATTCGAGAAACTGAAGGAGCTGATAGA
genomic: AACTAGAGAGGCAAACTAAAGAATCATTTGGAGAATACACAACCCGCATGgtaagtatca ... aaaattgcagGGATTCGAGAAACTGAAGGAGCTGATAGA
EST: gi|124880768|gb|EH959670.1|EH959670
EST:     ACTAGAGAGGCAAACTAAAGAATCATTTGGAGAATACACAAACCCGCATG                         GGATTCGAGAAACTGAAGGAG
genomic: ACTAGAGAGGCAAACTAAAGAATCATTTGGAGAATACACAA-CCCGCATGgtaagtatca ... aaaattgcagGGATTCGAGAAACTGAAGGAG
EST: gi|164134583|gb|ES021903.1|ES021903
EST:     AACTAGAGAGGCAAACTAAAGAATCATTTGGAGAATACACAACCCGCATG                         GGATTCGAGAAACTGAAGGAGCTGATAGATACATACAAAGGAG
genomic: AACTAGAGAGGCAAACTAAAGAATCATTTGGAGAATACACAACCCGCATGgtaagtatca ... aaaattgcagGGATTCGAGAAACTGAAGGAGCTGATAGATACATACAAAGGAG
EST: gi|125026987|gb|EL099256.1|EL099256
EST:     AACTAGAGAGGCAAACTAAAGAATCATTTGGAGAATACACAACCCGCATG                         GGATTCGAGAAACTGAAGGAGCTGATAGATACA
genomic: AACTAGAGAGGCAAACTAAAGAATCATTTGGAGAATACACAACCCGCATGgtaagtatca ... aaaattgcagGGATTCGAGAAACTGAAGGAGCTGATAGATACA
EST: gi|125014391|gb|EL086660.1|EL086660
EST:     AACTAGAGAGGCAAACTAAAGAATCATTTGGAGAATACACAACCCGCATG                         GGATTCGAGAAACTGAAGGAGCTGATAGATACATACAAAGGAGTTTCTCAA
genomic: AACTAGAGAGGCAAACTAAAGAATCATTTGGAGAATACACAACCCGCATGgtaagtatca ... aaaattgcagGGATTCGAGAAACTGAAGGAGCTGATAGATACATACAAAGGAGTTTCTCAA
EST: gi|125026751|gb|EL099020.1|EL099020
EST:     AACTAGAGAGGCAAACTAAAGAATCATTTGGAGAATACACAACCCGCATG                         GGATTCGAGAAACTGAAGGAGCTGATAGAT
genomic: AACTAGAGAGGCAAACTAAAGAATCATTTGGAGAATACACAACCCGCATGgtaagtatca ... aaaattgcagGGATTCGAGAAACTGAAGGAGCTGATAGAT
EST: gi|124942754|gb|EL018989.1|EL018989
EST:     AACTAGAGAGGCAAACTAAAGAATCATTTGGAGAATACACAACCCGCATG                         GGATTCGAGAAACTGAAGGAGCTGATAGATACATACAAAGGAGTTTCTC
genomic: AACTAGAGAGGCAAACTAAAGAATCATTTGGAGAATACACAACCCGCATGgtaagtatca ... aaaattgcagGGATTCGAGAAACTGAAGGAGCTGATAGATACATACAAAGGAGTTTCTC
EST: gi|124788942|gb|EH878621.1|EH878621
EST:     TACACAACCCGCATG                         GGATTCGAGAAACTGAAGGAGCTGATAGATACATACAAAGGAGTTTCTCAA
genomic: TACACAACCCGCATGgtaagtatca ... aaaattgcagGGATTCGAGAAACTGAAGGAGCTGATAGATACATACAAAGGAGTTTCTCAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aagaagaaaaaacaaatgactgtgttttttaactttaacaatggtaaaattgcagGGATTCGAGAAACTGAAGGAGCTGATAGATACATACAAAGGAGTTTCTCAATGAGCACAACAGAGATCATCTTTCGTTTTATAATTCATGTAATGTAATG
                        ttttttaactttaaca  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtatcacatataacttctctttaactctctcactgtggcttgaacatttatattgaagaagaagaaaaaacaaatgactgtgttttttaactttaacaatggtaaaattgcagGGATTCGAGAAACTGAAGGAGCTGATAGATACATACAAAGGAGTTTCTCAATGAGCACAACAGAGATCATCTTTCGTTTTATAATTCATGTAATGTAATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA