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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtattttctgttctgcatttgattatagatatacattttcccctttcactcattctcattcttgatgcttcatttgtgtatcatattctagatttcaagatgtattgatcctctctctaactcgagccattcttctcttaacacagACAAGATTTGAAAGCAAAGAGTGACATGACAGACAATTGACTGATTTTGAAGACTATGATTGACTCCAAGACCACCAATGCAAGATCCTCTGTTTTCTCC

Basic information

species Arabidopsis thaliana
transcript AT3G54060.2
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|116394628|gb|EG437220.1|EG437220
EST:     CTGACCAGCCCTTTTTGGAATATACATCAACCGTGACTGATGTGATTCAA                         ACAAGATTTGAAAGCAAAGAGTGACATGACAGACAATTGACTGATTTTGAA
genomic: CTGACCAGCCCTTTTTGGAATATACATCAACCGTGACTGATGTGATTCAAgtgagtattt ... cttaacacagACAAGATTTGAAAGCAAAGAGTGACATGACAGACAATTGACTGATTTTGAA
EST: gi|116384866|gb|EG427458.1|EG427458
EST:     CTGCCCACCCCTTTTTGGAATATACATCACCCGTGACTGATGTGATTCAA                         ACAAGATTTGAAAGCAAAGAGTGACATGACAGACAATTGACTGATTTTGAA
genomic: CTGACCAGCCCTTTTTGGAATATACATCAACCGTGACTGATGTGATTCAAgtgagtattt ... cttaacacagACAAGATTTGAAAGCAAAGAGTGACATGACAGACAATTGACTGATTTTGAA
EST: gi|116412372|gb|EG454964.1|EG454964
EST:     TTGACCAGCCCTTTTTGGAATATACATCAACCGGGACTGATGTGATTCAA                         ACAAGATTTGAAAGCAAAGAGTGACATGACAG
genomic: CTGACCAGCCCTTTTTGGAATATACATCAACCGTGACTGATGTGATTCAAgtgagtattt ... cttaacacagACAAGATTTGAAAGCAAAGAGTGACATGACAG
EST: gi|116412394|gb|EG454986.1|EG454986
EST:     CTGCCCAGCCCTTTTTGGAATATACATCAACCGTGACTGATGTGATTCAA                         ACAAGATTTGAAAGCAAAGAGTGACATGACAGACAATTGACTGATTTTGAA
genomic: CTGACCAGCCCTTTTTGGAATATACATCAACCGTGACTGATGTGATTCAAgtgagtattt ... cttaacacagACAAGATTTGAAAGCAAAGAGTGACATGACAGACAATTGACTGATTTTGAA
EST: gi|116384858|gb|EG427450.1|EG427450
EST:     CTGACCAGCCCTTTTTGGAATATACATCAACCGTGACTGATGTGATTCAA                         ACAAGATTTGAAAGCAAAGAGTGACATGACAGACAATTGACTGATTTTGAA
genomic: CTGACCAGCCCTTTTTGGAATATACATCAACCGTGACTGATGTGATTCAAgtgagtattt ... cttaacacagACAAGATTTGAAAGCAAAGAGTGACATGACAGACAATTGACTGATTTTGAA
EST: gi|116412427|gb|EG455019.1|EG455019
EST:     CTGACCAGCCCTTTTTGGAATATACATCAACCGTGACTGATGTGATTCAA                         ACAAGATTTGAAAGCAAAGAGTGACATGACAGACAATTGACTGATTTTGAA
genomic: CTGACCAGCCCTTTTTGGAATATACATCAACCGTGACTGATGTGATTCAAgtgagtattt ... cttaacacagACAAGATTTGAAAGCAAAGAGTGACATGACAGACAATTGACTGATTTTGAA
EST: gi|116384868|gb|EG427460.1|EG427460
EST:     CTGACCAGCCCTTTTTGGAATATACATCAACCGTGACTGATGTGATTCAA                         ACAAGATTTGAAAGCAAAGAGTGACATGACAGACAATTGACTGATTTTGAA
genomic: CTGACCAGCCCTTTTTGGAATATACATCAACCGTGACTGATGTGATTCAAgtgagtattt ... cttaacacagACAAGATTTGAAAGCAAAGAGTGACATGACAGACAATTGACTGATTTTGAA
EST: gi|116394639|gb|EG437231.1|EG437231
EST:     CTGACCAGCCCTTTTTGGAATATACATCAACCGTGACTGATGTGATTCAA                         ACAAGATTTGAAAGCAAAGAGTGACATGACAGACAATTGACTGATTTTGAA
genomic: CTGACCAGCCCTTTTTGGAATATACATCAACCGTGACTGATGTGATTCAAgtgagtattt ... cttaacacagACAAGATTTGAAAGCAAAGAGTGACATGACAGACAATTGACTGATTTTGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atttcaagatgtattgatcctctctctaactcgagccattcttctcttaacacagACAAGATTTGAAAGCAAAGAGTGACATGACAGACAATTGACTGATTTTGAAGACTATGATTGACTCCAAGACCACCAATGCAAGATCCTCTGTTTTCTCC
                                            tcttaac  putative branch site (score: 2)
                                   ccattcttctctt  CT-rich tract
        atgtatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagtattttctgttctgcatttgattatagatatacattttcccctttcactcattctcattcttgatgcttcatttgtgtatcatattctagatttcaagatgtattgatcctctctctaactcgagccattcttctcttaacacagACAAGATTTGAAAGCAAAGAGTGACATGACAGACAATTGACTGATTTTGAAGACTATGATTGACTCCAAGACCACCAATGCAAGATCCTCTGTTTTCTCC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA