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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagttggcccttctgacattaactagtacagttaaagggcacatcagatttgctaaaatcttcccttatcagGCAGGGCATACCACTCCCACTGTCTTCTATCTTGCTTTGGGAGGATCATTGCTATCTTATATATACTCTGCTCCACCTCTTAAG

Basic information

species Arabidopsis thaliana
transcript AT3G51820.1
intron # 7
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|125009985|gb|EL082254.1|EL082254
EST:     GGGTGCTATTATTGGGAGGTCTTGGTATTGCTGGAATATTAGATGTGTGG                         GCAGGGCATAC
genomic: GGGTGCTATTATTGGGAGGTCTTGGTATTGCTGGAATATTAGATGTGTGGgtaagttggc ... cccttatcagGCAGGGCATAC
EST: gi|125137348|gb|EL177203.1|EL177203
EST:     GGGTGCTATTATTGGGAGGTCTTGGTATTGCTGGAATATTAGATGTGTGG                         GCAGGGCATACCACTCCCACTGTCTTCTATCTTGCTTTGGG
genomic: GGGTGCTATTATTGGGAGGTCTTGGTATTGCTGGAATATTAGATGTGTGGgtaagttggc ... cccttatcagGCAGGGCATACCACTCCCACTGTCTTCTATCTTGCTTTGGG
EST: gi|124923490|gb|EL001680.1|EL001680
EST:     GGGTGCTATTATTGGGAGGTCTTGGTATTGCTGGAATATTAGATGTGTGG                         GCAGGGCATACCACTCCCACTGTCTTCTATCTTG
genomic: GGGTGCTATTATTGGGAGGTCTTGGTATTGCTGGAATATTAGATGTGTGGgtaagttggc ... cccttatcagGCAGGGCATACCACTCCCACTGTCTTCTATCTTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attaactagtacagttaaagggcacatcagatttgctaaaatcttcccttatcagGCAGGGCATACCACTCCCACTGTCTTCTATCTTGCTTTGGGAGGATCATTGCTATCTTATATATACTCTGCTCCACCTCTTAAG
                                 tgctaaa  putative branch site (score: 2)
                                         tcttcccttatc  CT-rich tract
                                    taaaatctt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagttggcccttctgacattaactagtacagttaaagggcacatcagatttgctaaaatcttcccttatcagGCAGGGCATACCACTCCCACTGTCTTCTATCTTGCTTTGGGAGGATCATTGCTATCTTATATATACTCTGCTCCACCTCTTAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT