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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgacttatggtttctgttaaagttcctgttatggtaatagagaggaatgtgttgtttactatttgttggtattgactctgtttttgttactctgtttcagACGGTTCCTATGTGCCAGAATCTCTACAGGAATTCATTCACTTATCATGGTCTTGATAATGAAAAAGTTTTACAGTTTGATGATGCTATTAAGTTCTTAG

Basic information

species Arabidopsis thaliana
transcript AT2G04550.3
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT2G04550.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: EFJ30059 (Selaginella moellendorffii), 3'ss of exon 1
tgacttatggtttctgttaaagttcctgttatggtaatagagaggaatgtgttgtttactatttgttggtattgactctgtttttgttactctgtttcagACGGTTCCTATGTGCCAGAATCTCTACAGGAATTCATTCACTTATCATGGTCTTGATAATGAAAAAGTTTTACAGTTTGATGATGCTATTAAGTTCTTAG
                                         |    || | |  | | ||  ||  | |  |   |||    | || |  | ||| | |||| ||  | |  |||||||||||||||| |||||| |||||||||||  |  |  |  | || | |   |||| | | || ||     |  | ||| | |
-----------------------------------------gtaagatctctcctctcctcctttctagggtatcctcatactgtggtg-tttgtcttagACTGTAGCGAGATGCCAGAATCTCTACAAGAATTCTTTCACTTATCACTGCATACAAGAGGAGAGA---TTACCGCTGGAAGAGTGCCTGGATTTCATCG
















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|86021655|gb|DR317401.1|DR317401
EST:     CTTCTCGCTCTGAGCTTCTTAAGACTCAAGGAATCTCTCGTGTTCTTAAT                         ACGGTTCCTATGTGCCAGAATCTCTACAGGAATTCATTCACTTATCATGGT
genomic: CTTCTCGCTCTGAGCTTCTTAAGACTCAAGGAATCTCTCGTGTTCTTAATgtgagtttct ... tctgtttcagACGGTTCCTATGTGCCAGAATCTCTACAGGAATTCATTCACTTATCATGGT
EST: gi|164069213|gb|ES171607.1|ES171607
EST:     CTTCTCGCTCTGAGCTTCTTAAGACTCAAGGAATCTCTCGTGTTCTTAAT                         ACGGTTCCTATGTGCCAGAATCTCTACAGGAATTC
genomic: CTTCTCGCTCTGAGCTTCTTAAGACTCAAGGAATCTCTCGTGTTCTTAATgtgagtttct ... tctgtttcagACGGTTCCTATGTGCCAGAATCTCTACAGGAATTC
EST: gi|125280926|gb|EL295011.1|EL295011
EST:     CTTCTCGCTCTGAGCTTCTTAAGACTCAAGGAATCTCTCGTGTTCTTAAT                         ACGGTTCCTATGTGCCAGAATCTCTACAGGAATTCATTCACTTA
genomic: CTTCTCGCTCTGAGCTTCTTAAGACTCAAGGAATCTCTCGTGTTCTTAATgtgagtttct ... tctgtttcagACGGTTCCTATGTGCCAGAATCTCTACAGGAATTCATTCACTTA
EST: gi|125326589|gb|EL340669.1|EL340669
EST:     CTGAGCTTCTTAAGACTCAAGGAATACTCTCGTGTTCTTAAT                         ACGGTTCCTATGTGC
genomic: CTGAGCTTCTTAAGACTCAAGGAAT-CTCTCGTGTTCTTAATgtgagtttct ... tctgtttcagACGGTTCCTATGTGC
EST: gi|124824938|gb|EH909804.1|EH909804
EST:     CTCGCTCTGAGCTTCTTAAGACTCAAGGAATCTCTCGTGTTCTTAAT                         ACGGTTCCTATGTGCCAAAATCTCTACAGGAATTCATTCACTTATCATGGT
genomic: CTCGCTCTGAGCTTCTTAAGACTCAAGGAATCTCTCGTGTTCTTAATgtgagtttct ... tctgtttcagACGGTTCCTATGTGCCAGAATCTCTACAGGAATTCATTCACTTATCATGGT
EST: gi|19876233|gb|AU237064.1|AU237064
EST:     CTTCTCGCTCTGAGCTTCTTAAGACTCAAGGAATCTCTCGTGTTCTTAAT                         ACGGTTCCTATGTGCCAGAATCTCTACAGGAATTCATTCACTTATCATGGT
genomic: CTTCTCGCTCTGAGCTTCTTAAGACTCAAGGAATCTCTCGTGTTCTTAATgtgagtttct ... tctgtttcagACGGTTCCTATGTGCCAGAATCTCTACAGGAATTCATTCACTTATCATGGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aatgtgttgtttactatttgttggtattgactctgtttttgttactctgtttcagACGGTTCCTATGTGCCAGAATCTCTACAGGAATTCATTCACTTATCATGGTCTTGATAATGAAAAAGTTTTACAGTTTGATGATGCTATTAAGTTCTTAG
                        tattgac  putative branch site (score: 2)
                                            ctctgtttc  putative PPT
         tttactattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgacttatggtttctgttaaagttcctgttatggtaatagagaggaatgtgttgtttactatttgttggtattgactctgtttttgttactctgtttcagACGGTTCCTATGTGCCAGAATCTCTACAGGAATTCATTCACTTATCATGGTCTTGATAATGAAAAAGTTTTACAGTTTGATGATGCTATTAAGTTCTTAG

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