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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagttttctatcacgcatgaatacggcatatctactccttgcatcaaaggctcaattgtagctacacttaaaagcttatcttgaaaagcttataagacagagctgttttctttatagcacaagtttttaacttttgttgacaagttttgcttttgggttcttgcagGAGGGTGCCTTGCCAGCGAACCAACTCGTTGAGCGTATTGAGAATTCTTTGCAAGTGAAACAGTAGGTTTGAGAAACCAAGAAAACTTGTCATCTATGAA

Basic information

species Arabidopsis thaliana
transcript AT1G43560.1
intron # 3
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|86072280|gb|DR368037.1|DR368037
EST:     CTTTGCCCACATTCATCTTATTCAAAGACGGCAAACTCTGGGACCGTTTC                         GAGGGTGCCTTGCCAGCGAACCAACTCGTTGAGCGTATTGAGAATTCTTTG
genomic: CTTTGCCCACATTCATCTTATTCAAAGACGGCAAACTCTGGGACCGTTTCgtaagttttc ... gttcttgcagGAGGGTGCCTTGCCAGCGAACCAACTCGTTGAGCGTATTGAGAATTCTTTG
EST: gi|86088328|gb|DR384087.1|DR384087
EST:     CTTTGCCCACATTCATCTTATTCAAAGACGGCAAACTCTGGGACCGTTTC                         GAGGGTGCCTTGCCAGCGAACCAACTCGTTGAGCGTATTGAGAATTCTTTG
genomic: CTTTGCCCACATTCATCTTATTCAAAGACGGCAAACTCTGGGACCGTTTCgtaagttttc ... gttcttgcagGAGGGTGCCTTGCCAGCGAACCAACTCGTTGAGCGTATTGAGAATTCTTTG
EST: gi|125294034|gb|EL308119.1|EL308119
EST:     GCAAACTCTGGGACCGTTTC                         GAGGGTGCCTTGCCTAGCGAACCAACTCGTTGAGCGTATTGAGAATTCTTT
genomic: GCAAACTCTGGGACCGTTTCgtaagttttc ... gttcttgcagGAGGGTGCCTTGCC-AGCGAACCAACTCGTTGAGCGTATTGAGAATTCTTT
EST: gi|125025832|gb|EL098101.1|EL098101
EST:     CTTTGCCCACATTCATCTTATTCAAAGACGGCAAACTCTGGGACCGTTTC                         GAGGGTGCCTTGCCAGCGAACCAACTCGTTGAGCGTATTG
genomic: CTTTGCCCACATTCATCTTATTCAAAGACGGCAAACTCTGGGACCGTTTCgtaagttttc ... gttcttgcagGAGGGTGCCTTGCCAGCGAACCAACTCGTTGAGCGTATTG
EST: gi|124762474|gb|EH852604.1|EH852604
EST:     CATTCATCTTATTCAAAGACGGCAAACTCTGGGACCGTTTC                         GAGGGTGCCTTGCCAGCGAACCAACTCGTTGAGCGTATTGAGAATTCTTTG
genomic: CATTCATCTTATTCAAAGACGGCAAACTCTGGGACCGTTTCgtaagttttc ... gttcttgcagGAGGGTGCCTTGCCAGCGAACCAACTCGTTGAGCGTATTGAGAATTCTTTG
EST: gi|124761175|gb|EH851305.1|EH851305
EST:     CTTTGCCCACATTCATCTTATTCAAAGACGGCAAACTCTGGGACCGTTTC                         GAGGGTGCCTTGCCAGCGAACCAA
genomic: CTTTGCCCACATTCATCTTATTCAAAGACGGCAAACTCTGGGACCGTTTCgtaagttttc ... gttcttgcagGAGGGTGCCTTGCCAGCGAACCAA
EST: gi|124855119|gb|EH939556.1|EH939556
EST:     AAGACGGCAAACTCTGGGACCGTTTC                         GAGGGTGCCTTGCCAGCGAACCAACTCGTTGAGCGTATTGAGAATTCTTTG
genomic: AAGACGGCAAACTCTGGGACCGTTTCgtaagttttc ... gttcttgcagGAGGGTGCCTTGCCAGCGAACCAACTCGTTGAGCGTATTGAGAATTCTTTG
EST: gi|86072276|gb|DR368033.1|DR368033
EST:     CTTTGCCCACATTCATCTTATTCAAAGACGGCAAACTCTGGGACCGTTTC                         GAGGGTGCCTTGCCAGCGAACCAACTCGTTGAGCGTATTGAGAATTCTTTG
genomic: CTTTGCCCACATTCATCTTATTCAAAGACGGCAAACTCTGGGACCGTTTCgtaagttttc ... gttcttgcagGAGGGTGCCTTGCCAGCGAACCAACTCGTTGAGCGTATTGAGAATTCTTTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttatagcacaagtttttaacttttgttgacaagttttgcttttgggttcttgcagGAGGGTGCCTTGCCAGCGAACCAACTCGTTGAGCGTATTGAGAATTCTTTGCAAGTGAAACAGTAGGTTTGAGAAACCAAGAAAACTTGTCATCTATGAA
                                              ttcttgc  CT-rich tract
         aagtttttaactttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagttttctatcacgcatgaatacggcatatctactccttgcatcaaaggctcaattgtagctacacttaaaagcttatcttgaaaagcttataagacagagctgttttctttatagcacaagtttttaacttttgttgacaagttttgcttttgggttcttgcagGAGGGTGCCTTGCCAGCGAACCAACTCGTTGAGCGTATTGAGAATTCTTTGCAAGTGAAACAGTAGGTTTGAGAAACCAAGAAAACTTGTCATCTATGAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA