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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gttgggttttgtgcgtttcgacgcgagttgtagatgatcttgcctatacgtctgcttacttgtgctaaatgactattaatttggtcttcctttttgacagTTGGCGTTAACTCTTGTTTATCTACCAGTTGAAAGATG

Basic information

species Arabidopsis thaliana
transcript AT4G38930.2
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|125263426|gb|EL277511.1|EL277511
EST:     CTTACCTTGCGGGAATCACGCGACCAATTGATTCTTCTTCTCACAAGCAG                         TTGGCGTTAACTCTTGTTTATCTA
genomic: CTTACCTTGCGGGAATCACGCGACCAATTGATTCTTCTTCTCACAAGCAGgtactctctc ... tttttgacagTTGGCGTTAACTCTTGTTTATCTA
EST: gi|86059107|gb|DR354864.1|DR354864
EST:     CTTACCTTGCGGGAATCACGCGACCAATTGATTCTTCTTCTCACAAGCAG                         TTGGCGTTAACTCTTGTTTATCTACCAGTTGAAAGATG
genomic: CTTACCTTGCGGGAATCACGCGACCAATTGATTCTTCTTCTCACAAGCAGgtactctctc ... tttttgacagTTGGCGTTAACTCTTGTTTATCTACCAGTTGAAAGATG
EST: gi|124955432|gb|EL030446.1|EL030446
EST:     CTTACCTTGCGGGAATCACGCGACCAATTGATTCTTCTTCTCACAAGCAG                         TTGGCGTTAACTCTTGTTTAT
genomic: CTTACCTTGCGGGAATCACGCGACCAATTGATTCTTCTTCTCACAAGCAGgtactctctc ... tttttgacagTTGGCGTTAACTCTTGTTTAT
EST: gi|164219915|gb|ES187003.1|ES187003
EST:     GATTCTTCTTCTCACAAGCAG                         TTGGCGTTAACTCTTGTTTATCTACCAGTTAGAAAGATG
genomic: GATTCTTCTTCTCACAAGCAGgtactctctc ... tttttgacagTTGGCGTTAACTCTTGTTTATCTACCAGTT-GAAAGATG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atacgtctgcttacttgtgctaaatgactattaatttggtcttcctttttgacagTTGGCGTTAACTCTTGTTTATCTACCAGTTGAAAGATG
                            tattaat  putative branch site (score: 2)
                                  tttggtcttccttttt  CT-rich tract
                    taaatgactattaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttgggttttgtgcgtttcgacgcgagttgtagatgatcttgcctatacgtctgcttacttgtgctaaatgactattaatttggtcttcctttttgacagTTGGCGTTAACTCTTGTTTATCTACCAGTTGAAAGATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG