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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaattgcttaattgcttaagcttctcaaactccatctctcttctcgctgatttgacctagaaatcttcttccctaattttctttaccctgtctttgctgatttcgcagGTGAAGTACTCGCAAGAACCCGACAATCAGACCAAGT

Basic information

species Arabidopsis thaliana
transcript AT1G67430.1
intron # 1
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|124831911|gb|EH916350.1|EH916350
EST:     CAGCCGATTCTTCTATTAGCCGCCATG                         GTGAAGTACTCGCAAGAACCCGACAATCAGACCAAGT
genomic: CAGCCGATTCTTCTATTAGCCGCCATGgtaattgctt ... gatttcgcagGTGAAGTACTCGCAAGAACCCGACAATCAGACCAAGT
EST: gi|164153102|gb|EL993292.1|EL993292
EST:     CGATTCTTCTATTAGCCGCCATG                         GTGAAGTACTCGCAAGAACCCGACAATCAGACCAAGTCTTGCAAGG
genomic: CGATTCTTCTATTAGCCGCCATGgtaattgctt ... gatttcgcagGTGAAGTACTCGCAAGAACCCGACAATCAGACCAAGTCTTGCAAGG
EST: gi|164000956|gb|ES067483.1|ES067483
EST:     AGCCGATTCTTCTATTAGCCGCCATG                         GTGAAGTACTCGCAAGAACCCGACAATCAGACCAAGTCTTGC
genomic: AGCCGATTCTTCTATTAGCCGCCATGgtaattgctt ... gatttcgcagGTGAAGTACTCGCAAGAACCCGACAATCAGACCAAGTCTTGC
EST: gi|124737861|gb|EH829263.1|EH829263
EST:     AGCCGATTCTTCTATTAGCCGCCATG                         GTGAAGTACTCGCAAGAACCCGACAATCAGACTAAGTCTTGCAAGG
genomic: AGCCGATTCTTCTATTAGCCGCCATGgtaattgctt ... gatttcgcagGTGAAGTACTCGCAAGAACCCGACAATCAGACCAAGTCTTGCAAGG
EST: gi|164183703|gb|ES166737.1|ES166737
EST:     GCAGCCGATTCTTCTATTAGCCGCCATG                         GTGAAGTACTCGCAAGAACCCGANAATCAGACCAAGTCTTGC
genomic: GCAGCCGATTCTTCTATTAGCCGCCATGgtaattgctt ... gatttcgcagGTGAAGTACTCGCAAGAACCCGACAATCAGACCAAGTCTTGC
EST: gi|164044071|gb|ES199660.1|ES199660
EST:     GCAGCCGATTCTTCTATTAGCCGCCATG                         GTGAAGTACTCGCAAGAACCCGACAATCAGACCAAGTCTTGCAAGG
genomic: GCAGCCGATTCTTCTATTAGCCGCCATGgtaattgctt ... gatttcgcagGTGAAGTACTCGCAAGAACCCGACAATCAGACCAAGTCTTGCAAGG
EST: gi|125278342|gb|EL292427.1|EL292427
EST:     GCAGCCGATTCTTCTATTAGCCGCCATG                         GTGAAGTACTCGCAAGAACCCGACAATCAGACCAAGTCTTG
genomic: GCAGCCGATTCTTCTATTAGCCGCCATGgtaattgctt ... gatttcgcagGTGAAGTACTCGCAAGAACCCGACAATCAGACCAAGTCTTG
EST: gi|164194053|gb|ES102605.1|ES102605
EST:     CAGCCGATTCTTCTATTAGCCGCCATG                         GTGAAGTACTCGCAAGAACCCGACAATCAGACCAAGTC
genomic: CAGCCGATTCTTCTATTAGCCGCCATGgtaattgctt ... gatttcgcagGTGAAGTACTCGCAAGAACCCGACAATCAGACCAAGTC
EST: gi|125008017|gb|EL080286.1|EL080286
EST:     GCAGCCGATTCTTCTATTAGCCGCCATG                         GTGAAGTACTCGCAAGAACCCGACAATCAGACCAAGT
genomic: GCAGCCGATTCTTCTATTAGCCGCCATGgtaattgctt ... gatttcgcagGTGAAGTACTCGCAAGAACCCGACAATCAGACCAAGT
EST: gi|125165449|gb|EL191727.1|EL191727
EST:     ATCTCTTCTGCAGCCGATTCTTCTATTAGCCGCCATG                         GTGAAGTACTCGCAAGAACCCGACAATCAG
genomic: ATCTCTTCTGCAGCCGATTCTTCTATTAGCCGCCATGgtaattgctt ... gatttcgcagGTGAAGTACTCGCAAGAACCCGACAATCAG
EST: gi|164151622|gb|ES035571.1|ES035571
EST:     GCAGCCGATTCTTCTATTAGCCGCCATG                         GTGAAGTAACTCGCAAGAACCCGACAATCAGACCAAGTCTTGC
genomic: GCAGCCGATTCTTCTATTAGCCGCCATGgtaattgctt ... gatttcgcagGTGAAGTA-CTCGCAAGAACCCGACAATCAGACCAAGTCTTGC
EST: gi|116454165|gb|EG496757.1|EG496757
EST:     GCAGCCGATTCTTCTATTAGCCGCCATG                         GTGAAGTACTCGCAAGAACCCGACAATCAGACCAAGT
genomic: GCAGCCGATTCTTCTATTAGCCGCCATGgtaattgctt ... gatttcgcagGTGAAGTACTCGCAAGAACCCGACAATCAGACCAAGT
EST: gi|125000681|gb|EL072950.1|EL072950
EST:     GCCGATTCTTCTATTAGCCGCCATG                         GTGAAGTACTCGCAAGAACCCGACAATCAGACCAAGT
genomic: GCCGATTCTTCTATTAGCCGCCATGgtaattgctt ... gatttcgcagGTGAAGTACTCGCAAGAACCCGACAATCAGACCAAGT
EST: gi|152035881|gb|BP863620.2|BP863620
EST:     ATCTCTTCTGCAGCCGATTCTTCTATTAGCCGCCATG                         GTGAAGTACTCGCAAGAACCCGACAATCAGACCAAGT
genomic: ATCTCTTCTGCAGCCGATTCTTCTATTAGCCGCCATGgtaattgctt ... gatttcgcagGTGAAGTACTCGCAAGAACCCGACAATCAGACCAAGT
EST: gi|164087340|gb|ES039193.1|ES039193
EST:     ACATCTCTTCTGCAGCCGATTCTTCTATTAGCCGCCATG                         GTGAAGTACTCGCAAGAACCCGACAATC
genomic: ACATCTCTTCTGCAGCCGATTCTTCTATTAGCCGCCATGgtaattgctt ... gatttcgcagGTGAAGTACTCGCAAGAACCCGACAATC
EST: gi|125119451|gb|EL167668.1|EL167668
EST:     GCAGCCGATTCTTCTATTAGCCGCCATG                         GTGAAGTACTCGCAAGAACCCGACAATCAGGCCAAGTCTTG
genomic: GCAGCCGATTCTTCTATTAGCCGCCATGgtaattgctt ... gatttcgcagGTGAAGTACTCGCAAGAACCCGACAATCAGACCAAGTCTTG
EST: gi|125215165|gb|EL229331.1|EL229331
EST:     AGCCGATTCTTCTATTAGCCGCCATG                         GTGAAGTACTCGCAAGAACCCGACAATCAGACCAAGTCTTGCAAGG
genomic: AGCCGATTCTTCTATTAGCCGCCATGgtaattgctt ... gatttcgcagGTGAAGTACTCGCAAGAACCCGACAATCAGACCAAGTCTTGCAAGG
EST: gi|116451520|gb|EG494112.1|EG494112
EST:     ATCTCTTCTGCAGCCGATTCTTCTATTAGCCGCCATG                         GTGAAGTACTCGCAAGAACCCGACAATCAGACCAAGT
genomic: ATCTCTTCTGCAGCCGATTCTTCTATTAGCCGCCATGgtaattgctt ... gatttcgcagGTGAAGTACTCGCAAGAACCCGACAATCAGACCAAGT
EST: gi|163970163|gb|ES169461.1|ES169461
EST:     CTTCTGCAGCCGATTCTTCTATTAGCCGCCATG                         GTGAAGTACTCGCAAGAACCCGACAATCAGACCAAG
genomic: CTTCTGCAGCCGATTCTTCTATTAGCCGCCATGgtaattgctt ... gatttcgcagGTGAAGTACTCGCAAGAACCCGACAATCAGACCAAG
EST: gi|124906666|gb|EH980746.1|EH980746
EST:     GCAGCCGATTCTTCTATTAGCCGCCATG                         GTGAAGTACTCGCAAGAACCCGACAATCAG-CCAAGTCTTGCAAGG
genomic: GCAGCCGATTCTTCTATTAGCCGCCATGgtaattgctt ... gatttcgcagGTGAAGTACTCGCAAGAACCCGACAATCAGACCAAGTCTTGCAAGG
EST: gi|164048488|gb|ES142866.1|ES142866
EST:     GCAGCCGATTCTTCTATTAGCCGCCATG                         GTGAAGTACTCGCAAGAACCCGACAATCAGACCAAGTC
genomic: GCAGCCGATTCTTCTATTAGCCGCCATGgtaattgctt ... gatttcgcagGTGAAGTACTCGCAAGAACCCGACAATCAGACCAAGTC
EST: gi|125312644|gb|EL326729.1|EL326729
EST:     ATCTCTTCTGCAGCCGATTCTTCTATTAGCCGCCATG                         GTGAAGTACTCGCAAGAACCCCGACAATCAG
genomic: ATCTCTTCTGCAGCCGATTCTTCTATTAGCCGCCATGgtaattgctt ... gatttcgcagGTGAAGTACTCGCAAGAACCC-GACAATCAG
EST: gi|125157673|gb|EL186629.1|EL186629
EST:     GCAGCCGATTCTTCTATTAGCCGCCATG                         GTGAAGTACTCGCAAGAACCCGACAATCAGACCAAAGTCTTG
genomic: GCAGCCGATTCTTCTATTAGCCGCCATGgtaattgctt ... gatttcgcagGTGAAGTACTCGCAAGAACCCGACAATCAGACCAA-GTCTTG
EST: gi|124963858|gb|EL038165.1|EL038165
EST:     ACATCTCTTCTGCAGCCGATTCTTCTATTAGCCGCCATG                         GTGAAGTACTCGCAAGAACCCGACAAT
genomic: ACATCTCTTCTGCAGCCGATTCTTCTATTAGCCGCCATGgtaattgctt ... gatttcgcagGTGAAGTACTCGCAAGAACCCGACAAT
EST: gi|164012311|gb|ES085336.1|ES085336
EST:     TCACATCTCTTCTGCAGCCGATTCTTCTATTAGCCGCCATG                         GTGAAGTACTCGCAAGAACCCGACAA
genomic: TCACATCTCTTCTGCAGCCGATTCTTCTATTAGCCGCCATGgtaattgctt ... gatttcgcagGTGAAGTACTCGCAAGAACCCGACAA
EST: gi|164065892|gb|ES216334.1|ES216334
EST:     CCGATTCTTCTATTAGCCGCCATG                         GTGAAGTACTCGCAAGAACCCGACAATCAGACCAAGTCTTGC
genomic: CCGATTCTTCTATTAGCCGCCATGgtaattgctt ... gatttcgcagGTGAAGTACTCGCAAGAACCCGACAATCAGACCAAGTCTTGC
EST: gi|116454163|gb|EG496755.1|EG496755
EST:     GCAGCCGATTCTTCTATTAGCCGCCATG                         GTGAAGTACTCGCAAGAACCCGACAATCAGACCAAGT
genomic: GCAGCCGATTCTTCTATTAGCCGCCATGgtaattgctt ... gatttcgcagGTGAAGTACTCGCAAGAACCCGACAATCAGACCAAGT
EST: gi|125021887|gb|EL094156.1|EL094156
EST:     CCGATTCTTCTATTAGCCGCCATG                         GTGAAGTACTCGCAAGAACCCGACAATCAGACCAAGT
genomic: CCGATTCTTCTATTAGCCGCCATGgtaattgctt ... gatttcgcagGTGAAGTACTCGCAAGAACCCGACAATCAGACCAAGT
EST: gi|116451521|gb|EG494113.1|EG494113
EST:     ATCTCTTCTGCAGCCGATTCTTCTATTAGCCGCCATG                         GTGAAGTACTCGCAAGAACCCGACAATCAGACCAAGT
genomic: ATCTCTTCTGCAGCCGATTCTTCTATTAGCCGCCATGgtaattgctt ... gatttcgcagGTGAAGTACTCGCAAGAACCCGACAATCAGACCAAGT
EST: gi|164219594|gb|ES063028.1|ES063028
EST:     CTATTAGCCGCCATG                         GTGAAGTACTCGCAAGAACCCGACAATCAGACCAAGTCTTGCAAGGC
genomic: CTATTAGCCGCCATGgtaattgctt ... gatttcgcagGTGAAGTACTCGCAAGAACCCGACAATCAGACCAAGTCTTGCAAGGC
EST: gi|124749863|gb|EH839993.1|EH839993
EST:     GCAGCCGATTCTTCTATTAGCCGCCACG                         GTGAAGTACTCGCAAGAACCCGACAATCAGACCAAGTCTTGCAAGG
genomic: GCAGCCGATTCTTCTATTAGCCGCCATGgtaattgctt ... gatttcgcagGTGAAGTACTCGCAAGAACCCGACAATCAGACCAAGTCTTGCAAGG
EST: gi|164226224|gb|ES006494.1|ES006494
EST:     GCAGCCGATTCTTCTATTAGCCGCCATG                         GTGAAGTACTCGCAAGAACCCGACAATCAGACCAAGTCTTGC
genomic: GCAGCCGATTCTTCTATTAGCCGCCATGgtaattgctt ... gatttcgcagGTGAAGTACTCGCAAGAACCCGACAATCAGACCAAGTCTTGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gacctagaaatcttcttccctaattttctttaccctgtctttgctgatttcgcagGTGAAGTACTCGCAAGAACCCGACAATCAGACCAAGT
                                         tgctgat  putative branch site (score: 3)
                    taattttcttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaattgcttaattgcttaagcttctcaaactccatctctcttctcgctgatttgacctagaaatcttcttccctaattttctttaccctgtctttgctgatttcgcagGTGAAGTACTCGCAAGAACCCGACAATCAGACCAAGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC