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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagtattgtttaatccaaaactggtggtgtaaaattatactatgaatctttgctaatactaattttctatatattgcagCTCCAAGGGCATTAGAAAAGTGCAAGAACAGAAGTTGAGTTCTCGACGACATTTCGTGTTCTTACCTAAAAAAGGAAGAAAGCCTGTTTCGATCGGTTGG

Basic information

species Arabidopsis thaliana
transcript AT3G04730.1
intron # 4
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|124965490|gb|EL039674.1|EL039674
EST:     TCATGCAAACGTATACGAATAATGTAAGGGATCAGAAGCAATCGGACTTG                         CTCCAAGGGCATTAGAAAAGTGCAAGAACAGAAGTTGAGTT
genomic: TCATGCAAACGTATACGAATAATG-AAGGGATCAGAAGCAATCGGACTTGgttagtattg ... tatattgcagCTCCAAGGGCATTAGAAAAGTGCAAGAACAGAAGTTGAGTT
EST: gi|116458903|gb|EG501495.1|EG501495
EST:     TTCATGCAAACGTATACGAATAATGAAGGGATCAGAAGCAATCGGACTTG                         CTCCAAGGGCATTAGAAAAGTGCAAGAACAGAAGTTGAGTTCTCGACGACA
genomic: TTCATGCAAACGTATACGAATAATGAAGGGATCAGAAGCAATCGGACTTGgttagtattg ... tatattgcagCTCCAAGGGCATTAGAAAAGTGCAAGAACAGAAGTTGAGTTCTCGACGACA
EST: gi|47829393|gb|CK119077.1|CK119077
EST:     TTCATGCAAACGTATACGAATAATGAAGGGATCAGAAGCAATCGGACTTG                         CTCCAAGGGCATTAGAAAAGTGCAAGAACAGAAGTTGAGTTCTCGACGACA
genomic: TTCATGCAAACGTATACGAATAATGAAGGGATCAGAAGCAATCGGACTTGgttagtattg ... tatattgcagCTCCAAGGGCATTAGAAAAGTGCAAGAACAGAAGTTGAGTTCTCGACGACA
EST: gi|125072574|gb|EL137215.1|EL137215
EST:     AATGAAGGGATCAGAAGCAATCGGACTTG                         CTCCAAGGGCATTAGAAAAGTGCAAGAACAGAAGTTGAGTT
genomic: AATGAAGGGATCAGAAGCAATCGGACTTGgttagtattg ... tatattgcagCTCCAAGGGCATTAGAAAAGTGCAAGAACAGAAGTTGAGTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tggtgtaaaattatactatgaatctttgctaatactaattttctatatattgcagCTCCAAGGGCATTAGAAAAGTGCAAGAACAGAAGTTGAGTTCTCGACGACATTTCGTGTTCTTACCTAAAAAAGGAAGAAAGCCTGTTTCGATCGGTTGG
                                tactaat  putative branch site (score: 1)
                                      ttttctat  CT-rich tract
                        tttgctaatactaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttagtattgtttaatccaaaactggtggtgtaaaattatactatgaatctttgctaatactaattttctatatattgcagCTCCAAGGGCATTAGAAAAGTGCAAGAACAGAAGTTGAGTTCTCGACGACATTTCGTGTTCTTACCTAAAAAAGGAAGAAAGCCTGTTTCGATCGGTTGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA