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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tataaatgaaatgaagtgagtccaaagctgtttctattttcttactaaacctcttgtgagacagattatttgtttacggattttttctgacttggtttagGACATGGGACGTTCAAATGAATCAAAGCATAATCAATATCATTCAAACACGGAGACTTCATTGAAGCAAGAG

Basic information

species Arabidopsis thaliana
transcript AT5G66600.1
intron # 2
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|116429915|gb|EG472507.1|EG472507
EST:     GAGATAAAACCTCAAATAGTTCTCATGAAGCCTCTCAACGAATGAAGCTG                         GACATGGGACGTTCAAATGAATCAAAGCATAATCAATATCATTCAACCACG
genomic: GAGATAAAACCTCAAATAGTTCTCATGAAGCCTCTCAACGAATGAAGCTGgtgagtacta ... cttggtttagGACATGGGACGTTCAAATGAATCAAAGCATAATCAATATCATTCAAACACG
EST: gi|116429923|gb|EG472515.1|EG472515
EST:     GAGATAAAACCTCAAATAGTTCTCATGAAGCCTCTCAACGAATGAAGCTG                         GACATGGGACGTTCAAATGAATCAAAGCATAATCAATATCATTCAAACACG
genomic: GAGATAAAACCTCAAATAGTTCTCATGAAGCCTCTCAACGAATGAAGCTGgtgagtacta ... cttggtttagGACATGGGACGTTCAAATGAATCAAAGCATAATCAATATCATTCAAACACG
EST: gi|116429925|gb|EG472517.1|EG472517
EST:     GAGATAAAACCTCAAATAGTTCTCATGAAGCCTCTCAACGAATGAAGCTG                         GACATGGGACGTTCAAATGAATCAAAGCATAATCAATATCATTCAAACACG
genomic: GAGATAAAACCTCAAATAGTTCTCATGAAGCCTCTCAACGAATGAAGCTGgtgagtacta ... cttggtttagGACATGGGACGTTCAAATGAATCAAAGCATAATCAATATCATTCAAACACG
EST: gi|116429918|gb|EG472510.1|EG472510
EST:     GAGATAAAACCTCAAATAGTTCTCATGAAGCCTCTCAACGAATGAAGCTG                         GACATGGGACGTTCAAATGAATCAAAGCATAATCAATATCATTCAAACACG
genomic: GAGATAAAACCTCAAATAGTTCTCATGAAGCCTCTCAACGAATGAAGCTGgtgagtacta ... cttggtttagGACATGGGACGTTCAAATGAATCAAAGCATAATCAATATCATTCAAACACG
EST: gi|116429924|gb|EG472516.1|EG472516
EST:     GAGATAAAACCTCAAATAGTTCTCATGAAGCCTCTCAACGAATGAAGCTG                         GACATGGGACGTTCAAATGAATCAAAGCATAATCAATATCATTCAAACACG
genomic: GAGATAAAACCTCAAATAGTTCTCATGAAGCCTCTCAACGAATGAAGCTGgtgagtacta ... cttggtttagGACATGGGACGTTCAAATGAATCAAAGCATAATCAATATCATTCAAACACG
EST: gi|116429922|gb|EG472514.1|EG472514
EST:     GAGATAAAACCTCAAATAGTTCTCATGAAGCCTCTCAACGAATGAAGCTG                         GACATGGGACGTTCAAATGAATCAAAGCATAATCAATATCATTCAAACACG
genomic: GAGATAAAACCTCAAATAGTTCTCATGAAGCCTCTCAACGAATGAAGCTGgtgagtacta ... cttggtttagGACATGGGACGTTCAAATGAATCAAAGCATAATCAATATCATTCAAACACG
EST: gi|116429926|gb|EG472518.1|EG472518
EST:     GAGATAAAACCTCAAATAGTTCTCATGAAGCCTCTCAACGAATGAAGCTG                         GACATGGGACGTTCAAATGAATCAAAGCATAATCAATATCATTCAAACACG
genomic: GAGATAAAACCTCAAATAGTTCTCATGAAGCCTCTCAACGAATGAAGCTGgtgagtacta ... cttggtttagGACATGGGACGTTCAAATGAATCAAAGCATAATCAATATCATTCAAACACG
EST: gi|116429914|gb|EG472506.1|EG472506
EST:     GAGATAAAACCTCAAATAGTTCTCATGAAGCCTCTCAACGAATGAAGCTG                         GACATGGGACGTTCAAATGAATCAAAGCATAATCAATATCATTCAAACACG
genomic: GAGATAAAACCTCAAATAGTTCTCATGAAGCCTCTCAACGAATGAAGCTGgtgagtacta ... cttggtttagGACATGGGACGTTCAAATGAATCAAAGCATAATCAATATCATTCAAACACG
EST: gi|116429904|gb|EG472496.1|EG472496
EST:     TAGTTCTCATGAAGCCTCTCAACGAATGAAGCTG                         GACATGGGACGTTCAAATGAATCAAAGCATAACCAATATCATTCAAACACG
genomic: TAGTTCTCATGAAGCCTCTCAACGAATGAAGCTGgtgagtacta ... cttggtttagGACATGGGACGTTCAAATGAATCAAAGCATAATCAATATCATTCAAACACG
EST: gi|116429907|gb|EG472499.1|EG472499
EST:     GAGATAAAACCTCAAATAGTTCTCATGAAGCCTCTCAACGAATGAAGCTG                         GACATGGGACGTTCAAATGAATCAAAGCATAATCAATATCATTCAAACACG
genomic: GAGATAAAACCTCAAATAGTTCTCATGAAGCCTCTCAACGAATGAAGCTGgtgagtacta ... cttggtttagGACATGGGACGTTCAAATGAATCAAAGCATAATCAATATCATTCAAACACG
EST: gi|116429919|gb|EG472511.1|EG472511
EST:     GAGATAAAACCTCAAATAGTTCTCATGAAGCCTCTCAACGAATGAAGCTG                         GACATGGGACGTTCAAATGAATCAAAGCATAATCAATATCATTCAAACACG
genomic: GAGATAAAACCTCAAATAGTTCTCATGAAGCCTCTCAACGAATGAAGCTGgtgagtacta ... cttggtttagGACATGGGACGTTCAAATGAATCAAAGCATAATCAATATCATTCAAACACG
EST: gi|116429916|gb|EG472508.1|EG472508
EST:     GAGATAAAACCTCAAATAGTTCTCATGAAGCCTCTCAACGAATGAAGCTG                         GACATGGGACGTTCAAATGAATCAAAGCATAATCAATATCATTCAACCACG
genomic: GAGATAAAACCTCAAATAGTTCTCATGAAGCCTCTCAACGAATGAAGCTGgtgagtacta ... cttggtttagGACATGGGACGTTCAAATGAATCAAAGCATAATCAATATCATTCAAACACG
EST: gi|116429909|gb|EG472501.1|EG472501
EST:     AACCTCAAATAGTTCTCATGAAGCCTCTCAACGAATGAAGCTG                         GACATGGGACGTTCAAATGAATCAAAGCATAATCAATATCATTCAAACACG
genomic: AACCTCAAATAGTTCTCATGAAGCCTCTCAACGAATGAAGCTGgtgagtacta ... cttggtttagGACATGGGACGTTCAAATGAATCAAAGCATAATCAATATCATTCAAACACG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taaacctcttgtgagacagattatttgtttacggattttttctgacttggtttagGACATGGGACGTTCAAATGAATCAAAGCATAATCAATATCATTCAAACACGGAGACTTCATTGAAGCAAGAG
                                       ttctgac  putative branch site (score: 2)
                 agattatttgttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tataaatgaaatgaagtgagtccaaagctgtttctattttcttactaaacctcttgtgagacagattatttgtttacggattttttctgacttggtttagGACATGGGACGTTCAAATGAATCAAAGCATAATCAATATCATTCAAACACGGAGACTTCATTGAAGCAAGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA
- - aatgaaa
- - - - - - - - - - -ccaaagc
- - - - - - - - - - - - - - - - - - - - - - ctaaacc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - agacaga