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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tcattccatagcttaagagtttatcgaatccagttgaatttgaaaagatgcatttttggttattgattttgagtgttcttgtatcaaacttgttgtgtagAAGATGAGAGGTGGGAGTCTATGGCAGCTAGGGCAATCAATAACCCGTCGTCTTGCTCAATCTGACAAGAAGGTTGTGTCACGTCGCTACTTTGCCTCTG

Basic information

species Arabidopsis thaliana
transcript AT1G11860.1
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|124856135|gb|EH940572.1|EH940572
EST:     AGTGGCAAAGACTCAACATTT                         AAGATGAGAGGTGGGAGTCTATGGCAGCTAGGGCAATCAATAACCCGTCG
genomic: AGTGGCAAAGACTCAACATTTgtaagatttc ... tgttgtgtagAAGATGAGAGGTGGGAGTCTATGGCAGCTAGGGCAATCAATAACCCGTCG
EST: gi|164163075|gb|ES196651.1|ES196651
EST:     GAGGAATCTGGGAAGAAGCTCCAGTGGCAAAGACTCAACATTT                         AAGATGAGAGGTGGGAGTCTATGGCAG
genomic: GAGGAATCTGGGAAGAAGCTCCAGTGGCAAAGACTCAACATTTgtaagatttc ... tgttgtgtagAAGATGAGAGGTGGGAGTCTATGGCAG
EST: gi|164027155|gb|ES121633.1|ES121633
EST:     GAGGAATCTGGGAAGAAGCTCCAGTGGCAAAGACTCAACATTT                         AAGATGAGAGGTGGGA-TCTATGGCAG
genomic: GAGGAATCTGGGAAGAAGCTCCAGTGGCAAAGACTCAACATTTgtaagatttc ... tgttgtgtagAAGATGAGAGGTGGGAGTCTATGGCAG
EST: gi|125284548|gb|EL298633.1|EL298633
EST:     GAGGAATCTGGGAAGAAGCTCCAGTGGCAAAGACTCAACATTT                         AAGATGAGAGGTGGGAGTCTATGGCAGCTAGGG
genomic: GAGGAATCTGGGAAGAAGCTCCAGTGGCAAAGACTCAACATTTgtaagatttc ... tgttgtgtagAAGATGAGAGGTGGGAGTCTATGGCAGCTAGGG
EST: gi|124941618|gb|EL017956.1|EL017956
EST:     GAGGAATCTGGGAAGAAGCTCCAGTGGCAAAGACTCAACATTT                         AAGATGAGAGGTGGGAGTCTATGG
genomic: GAGGAATCTGGGAAGAAGCTCCAGTGGCAAAGACTCAACATTTgtaagatttc ... tgttgtgtagAAGATGAGAGGTGGGAGTCTATGG
EST: gi|47832124|gb|CK121808.1|CK121808
EST:     GAAGAAGCTCCAGTGGCAAAGACTCAACATTT                         AAGATGAGAGGTGGGAGTCTATGGCAGCTAGGGCAATCAATAACCCGTCGT
genomic: GAAGAAGCTCCAGTGGCAAAGACTCAACATTTgtaagatttc ... tgttgtgtagAAGATGAGAGGTGGGAGTCTATGGCAGCTAGGGCAATCAATAACCCGTCGT
EST: gi|47832114|gb|CK121798.1|CK121798
EST:     GTAGTTTGAGGAATCTGGGAAGAAGCTCCAGTGGCAAAGACTCAACATTT                         AAGATGAGAGGTGGGAGTCTATGGCAGCTAGGGCAATCAATAACCCGTCGT
genomic: GTAGTTTGAGGAATCTGGGAAGAAGCTCCAGTGGCAAAGACTCAACATTTgtaagatttc ... tgttgtgtagAAGATGAGAGGTGGGAGTCTATGGCAGCTAGGGCAATCAATAACCCGTCGT
EST: gi|125021833|gb|EL094102.1|EL094102
EST:     AGTTTGAGGAATCTGGGAAGAAGCTCCAGTGGCAAAGACTCAACATTT                         AAGATGAGAGGTGGGAGTCTA
genomic: AGTTTGAGGAATCTGGGAAGAAGCTCCAGTGGCAAAGACTCAACATTTgtaagatttc ... tgttgtgtagAAGATGAGAGGTGGGAGTCTA
EST: gi|125211999|gb|EL226953.1|EL226953
EST:     GTAGTTTGAGGAATCTGGGAAGAAGCTCCAGTGGCAAAGACTCAACATTT                         AAGATGAGAGGTGGG
genomic: GTAGTTTGAGGAATCTGGGAAGAAGCTCCAGTGGCAAAGACTCAACATTTgtaagatttc ... tgttgtgtagAAGATGAGAGGTGGG
EST: gi|86059623|gb|DR355380.1|DR355380
EST:     GTAGTATCAGGAATCTGGGAAGAAGCTCCAGTGGCAAAGACTCAACATTT                         AAGATGAGAGGTGGGAGTCTATGGCAGCTAGGGCAATCAATAACCCGTCGT
genomic: GTAGTTTGAGGAATCTGGGAAGAAGCTCCAGTGGCAAAGACTCAACATTTgtaagatttc ... tgttgtgtagAAGATGAGAGGTGGGAGTCTATGGCAGCTAGGGCAATCAATAACCCGTCGT
EST: gi|124931700|gb|EL009033.1|EL009033
EST:     AGGAATCTGGGAAGAAGCTCCAGTGGCAAAGACTCAACATTT                         T
genomic: AGGAATCTGGGAAGAAGCTCCAGTGGCAAAGACTCAACATTTgtaagatttc ... tgttgtgtag-
EST: gi|124931700|gb|EL009033.1|EL009033
EST:     AGGAATCTGGGAAGAAGCTCCAGTGGCAAAGACTCAACATTT                         T
genomic: AGGAATCTGGGAAGAAGCTCCAGTGGCAAAGACTCAACATTTgtaagatttc ... tgttgtgtag-
EST: gi|47829607|gb|CK119291.1|CK119291
EST:     GTAGTTTGAGGAATCTGGGAAGAAGCTCCAGTGGCAAAGACTCAACATTT                         AAGATGAGAGGTGGGAGTCTATGGCAGCTAGGGCAATCAATAACCCGTCGT
genomic: GTAGTTTGAGGAATCTGGGAAGAAGCTCCAGTGGCAAAGACTCAACATTTgtaagatttc ... tgttgtgtagAAGATGAGAGGTGGGAGTCTATGGCAGCTAGGGCAATCAATAACCCGTCGT
EST: gi|125320523|gb|EL334608.1|EL334608
EST:     GTAGTTTGAGGAATCTGGGAAGAAGCTCCAGTGGCAAAGACTCAACATTT                         AAGATGAGAGGTGGGAGT
genomic: GTAGTTTGAGGAATCTGGGAAGAAGCTCCAGTGGCAAAGACTCAACATTTgtaagatttc ... tgttgtgtagAAGATGAGAGGTGGGAGT
EST: gi|116483791|gb|EG526383.1|EG526383
EST:     GAGGAATCTGGGAAGAAGCTCCAGTGGCAAAGACTCAACATTT                         AAGATGAGAGGTGGGAGTCTATGGCAGCTAGGGCAATCAATAACCCGTCGT
genomic: GAGGAATCTGGGAAGAAGCTCCAGTGGCAAAGACTCAACATTTgtaagatttc ... tgttgtgtagAAGATGAGAGGTGGGAGTCTATGGCAGCTAGGGCAATCAATAACCCGTCGT
EST: gi|124923084|gb|EL001311.1|EL001311
EST:     AGTTTGAGGAATCTGGGAAGAAGCTCCAGTGGCAAAGACTCAACATTT                         AAGATGAGAGGTGGGAGTCTATGG
genomic: AGTTTGAGGAATCTGGGAAGAAGCTCCAGTGGCAAAGACTCAACATTTgtaagatttc ... tgttgtgtagAAGATGAGAGGTGGGAGTCTATGG
EST: gi|124823045|gb|EH907911.1|EH907911
EST:     GTAGTTTGAGGAATCTGGGAAGAAGCTCCAGTGGCAAAGACTCAACATTT                         AAGATGAGAGGTGGG
genomic: GTAGTTTGAGGAATCTGGGAAGAAGCTCCAGTGGCAAAGACTCAACATTTgtaagatttc ... tgttgtgtagAAGATGAGAGGTGGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agatgcatttttggttattgattttgagtgttcttgtatcaaacttgttgtgtagAAGATGAGAGGTGGGAGTCTATGGCAGCTAGGGCAATCAATAACCCGTCGTCTTGCTCAATCTGACAAGAAGGTTGTGTCACGTCGCTACTTTGCCTCTG
               tattgat  putative branch site (score: 3)
              ttattgatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tcattccatagcttaagagtttatcgaatccagttgaatttgaaaagatgcatttttggttattgattttgagtgttcttgtatcaaacttgttgtgtagAAGATGAGAGGTGGGAGTCTATGGCAGCTAGGGCAATCAATAACCCGTCGTCTTGCTCAATCTGACAAGAAGGTTGTGTCACGTCGCTACTTTGCCTCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG