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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatcctgctgatacacatcttttttcaatctgttcccattactcacacagtaaaaatgcattgtgtaacaaaggtacttaccgttctgctgcagCTTGACTGTGACAGGTAGACGCACATCTATCTGTCAAAAAGTTGATGCAGGCACCAAAGCTTCGATCCTTGGATATCATAAGCAAGAAATACTACAAGGA

Basic information

species Arabidopsis thaliana
transcript AT1G06460.1
intron # 5
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|86077661|gb|DR373418.1|DR373418
EST:     CTACCAGGAGCCAGTATCAATGATATAAGAGTGGAGGTTGACAACACAAA                         CTTGACTGTGACAGGTAGACGCACATCTATCTGTCAAAAAGTTGATGCAGG
genomic: CTACCAGGAGCCAGTATCAATGATATAAGAGTGGAGGTTGACAACACAAAgtaatcctgc ... tctgctgcagCTTGACTGTGACAGGTAGACGCACATCTATCTGTCAAAAAGTTGATGCAGG
EST: gi|86084351|gb|DR380110.1|DR380110
EST:     CTACCAGGAGCCAGTATCAATGATATAAGAGTGGAGGTTGACAACACAAA                         CTTGACTGTGACAGGTAGACGCACATCTATCTGTCAAAAAGTTGATGCAGG
genomic: CTACCAGGAGCCAGTATCAATGATATAAGAGTGGAGGTTGACAACACAAAgtaatcctgc ... tctgctgcagCTTGACTGTGACAGGTAGACGCACATCTATCTGTCAAAAAGTTGATGCAGG
EST: gi|124735403|gb|EH826805.1|EH826805
EST:     TAAGAGTGGAGGTTGACAACACAAA                         CTTGACTGTGACAGGTAGACGCACATCTATCTGTCAAAAAGTTGATGCAGG
genomic: TAAGAGTGGAGGTTGACAACACAAAgtaatcctgc ... tctgctgcagCTTGACTGTGACAGGTAGACGCACATCTATCTGTCAAAAAGTTGATGCAGG
EST: gi|125103287|gb|EL157751.1|EL157751
EST:     CTACCAGGAGCCAGTATCAATGATATAAGAGTGGAGGTTGACAACACAAA                         CTTGACTGTGACAGGTAGACGCACAT
genomic: CTACCAGGAGCCAGTATCAATGATATAAGAGTGGAGGTTGACAACACAAAgtaatcctgc ... tctgctgcagCTTGACTGTGACAGGTAGACGCACAT
EST: gi|124903423|gb|EH977503.1|EH977503
EST:     CTACCAGGAGCCAGTATCAATGATATAAGAGTGGAGGTTGACAACACAAA                         CTTGAACTGTGACAGGTAGACGCACATCT
genomic: CTACCAGGAGCCAGTATCAATGATATAAGAGTGGAGGTTGACAACACAAAgtaatcctgc ... tctgctgcagCTTGA-CTGTGACAGGTAGACGCACATCT
EST: gi|124831363|gb|EH915802.1|EH915802
EST:     CTACCAGGAGCCAGTATCAATGATATAAGAGTGGAGGTTGACAACACAAA                         CTTGACTGTGACAGGTAG
genomic: CTACCAGGAGCCAGTATCAATGATATAAGAGTGGAGGTTGACAACACAAAgtaatcctgc ... tctgctgcagCTTGACTGTGACAGGTAG
EST: gi|86086217|gb|DR381976.1|DR381976
EST:     CTACCAGGAGCCAGTATCAATGATATAAGAGTGGAGGTTGACAACACAAA                         CTTGACTGTGACAGGTAGACGCACATCTATCTGTCAAAAAGTTGATGCAGG
genomic: CTACCAGGAGCCAGTATCAATGATATAAGAGTGGAGGTTGACAACACAAAgtaatcctgc ... tctgctgcagCTTGACTGTGACAGGTAGACGCACATCTATCTGTCAAAAAGTTGATGCAGG
EST: gi|47831960|gb|CK121644.1|CK121644
EST:     CTACCAGGAGCCAGTATCAATGATATAAGAGTGGAGGTTGACAACACAAA                         CTTGACTGTGACAGGTAGACGCACATCTATCTGTCAAAAAGTTGATGCAGG
genomic: CTACCAGGAGCCAGTATCAATGATATAAGAGTGGAGGTTGACAACACAAAgtaatcctgc ... tctgctgcagCTTGACTGTGACAGGTAGACGCACATCTATCTGTCAAAAAGTTGATGCAGG
EST: gi|47830420|gb|CK120104.1|CK120104
EST:     CTACCAGGAGCCAGTATCAATGATATAAGAGTGGAGGTTGACAACACAAA                         CTTGACTGTGACAGGTAGACGCACATCTATCTGTCAAAAAGTTGATGCAGG
genomic: CTACCAGGAGCCAGTATCAATGATATAAGAGTGGAGGTTGACAACACAAAgtaatcctgc ... tctgctgcagCTTGACTGTGACAGGTAGACGCACATCTATCTGTCAAAAAGTTGATGCAGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tactcacacagtaaaaatgcattgtgtaacaaaggtacttaccgttctgctgcagCTTGACTGTGACAGGTAGACGCACATCTATCTGTCAAAAAGTTGATGCAGGCACCAAAGCTTCGATCCTTGGATATCATAAGCAAGAAATACTACAAGGA
                                   tacttac  putative branch site (score: 1)
                                         ccgttct  CT-rich tract
         agtaaaaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaatcctgctgatacacatcttttttcaatctgttcccattactcacacagtaaaaatgcattgtgtaacaaaggtacttaccgttctgctgcagCTTGACTGTGACAGGTAGACGCACATCTATCTGTCAAAAAGTTGATGCAGGCACCAAAGCTTCGATCCTTGGATATCATAAGCAAGAAATACTACAAGGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA