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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatatatgtttcttcttcttctcaacacattaaagaacatccctaacgaatttgttggacattttcagGGACCAATTCGTCTCTTACAGCAGCTGTAGTCGTTGTGACTGGTCTGATTGGAGCTAACTTTGTACAAGTTGTTCTTGACAAACTGCGTTTACGTGATCC

Basic information

species Arabidopsis thaliana
transcript AT1G32080.1
intron # 6
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|86080362|gb|DR376119.1|DR376119
EST:     TCGCTGCATCACGGTTGCATTGGCCCTTAGCATTGTATCACTCTTTGAAG                         GGACCAATTCGTCTCTTACAGCAGCTGTAGTCGTTGTGACTGGTCTGATTG
genomic: TCGCTGCATCACGGTTGCATTGGCCCTTAGCATTGTATCACTCTTTGAAGgtatatatgt ... acattttcagGGACCAATTCGTCTCTTACAGCAGCTGTAGTCGTTGTGACTGGTCTGATTG
EST: gi|47830990|gb|CK120674.1|CK120674
EST:     TCGCTGCATCACGGTTGCATTGGCCCTTAGCATTGTATCACTCTTTGAAG                         GGACCAATTCGTCTCTTACAGCAGCTGTAGTCGTTGTGACTGGTCTGATTG
genomic: TCGCTGCATCACGGTTGCATTGGCCCTTAGCATTGTATCACTCTTTGAAGgtatatatgt ... acattttcagGGACCAATTCGTCTCTTACAGCAGCTGTAGTCGTTGTGACTGGTCTGATTG
EST: gi|124893020|gb|EH971922.1|EH971922
EST:     TCGCTGCATCACGGTTGCATTGGCCCTTAGCATTGTATCACTCTTTGAAG                         GGACCAATTCGTCTCTTACA
genomic: TCGCTGCATCACGGTTGCATTGGCCCTTAGCATTGTATCACTCTTTGAAGgtatatatgt ... acattttcagGGACCAATTCGTCTCTTACA
EST: gi|86080193|gb|DR375950.1|DR375950
EST:     TCGCTGCATCACGGTTGCATTGGCCCTTAGCATTGTATCACTCTTTGAAG                         GGACCAATTCGTCTCTTACAGCAGCTGTAGTCGTTGTGACTGGTCTGATTG
genomic: TCGCTGCATCACGGTTGCATTGGCCCTTAGCATTGTATCACTCTTTGAAGgtatatatgt ... acattttcagGGACCAATTCGTCTCTTACAGCAGCTGTAGTCGTTGTGACTGGTCTGATTG
EST: gi|125199840|gb|EL214794.1|EL214794
EST:     TCGCTGCATCACGGTTGCATTGGCCCTTAGCATTGTATCACTCTTTGAAG                         GGACCAATTCGTCTCTTACAGCAGCT
genomic: TCGCTGCATCACGGTTGCATTGGCCCTTAGCATTGTATCACTCTTTGAAGgtatatatgt ... acattttcagGGACCAATTCGTCTCTTACAGCAGCT
EST: gi|124745337|gb|EH836297.1|EH836297
EST:     TCGCTGCATCACGGTTGCATTGGCCCTTAGCATTGTATCACTCTTTGAAG                         GGAACCAATTCGTCTCTTACAGCAGCTGTA
genomic: TCGCTGCATCACGGTTGCATTGGCCCTTAGCATTGTATCACTCTTTGAAGgtatatatgt ... acattttcagGGA-CCAATTCGTCTCTTACAGCAGCTGTA
EST: gi|124944133|gb|EL020266.1|EL020266
EST:     TCGCTGCATCACGGTTGCATTGGCCCTT-GCATTGTATCACTCTTTGAAG                         GGACCAATTCGTTCTCTTACAGCAGCT
genomic: TCGCTGCATCACGGTTGCATTGGCCCTTAGCATTGTATCACTCTTTGAAGgtatatatgt ... acattttcagGGACCAATTCGT-CTCTTACAGCAGCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcttcttctcaacacattaaagaacatccctaacgaatttgttggacattttcagGGACCAATTCGTCTCTTACAGCAGCTGTAGTCGTTGTGACTGGTCTGATTGGAGCTAACTTTGTACAAGTTGTTCTTGACAAACTGCGTTTACGTGATCC
                           ccctaac  putative branch site (score: 2)
                                              cattttc  putative PPT
               attaaagaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatatatgtttcttcttcttctcaacacattaaagaacatccctaacgaatttgttggacattttcagGGACCAATTCGTCTCTTACAGCAGCTGTAGTCGTTGTGACTGGTCTGATTGGAGCTAACTTTGTACAAGTTGTTCTTGACAAACTGCGTTTACGTGATCC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT