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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atttttttttcaccaaattttcagctctgagatgaattatgatgattagtgtggttatgtcagtgattctgatatttgtttttcacaaaaaaatgaatagGTGACAGTTGCATACAACAAAGATCCTAGCCCAGTTAAGCTGAATTTAGGAGTTGGTGCTTACCGAACTGAG

Basic information

species Arabidopsis thaliana
transcript AT5G11520.1
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|301501584|gb|HO207124.1|HO207124
EST:     GTTCTGTTTTCTCTCATCTTGTTCAAGCTCCAGAGGATCCTATTCTTGGG                         GTGACAGTTGCATACAACAAAGATCCTAGCCCAGTTAAGCTGAATTTAGGA
genomic: GTTCTGTTTTCTCTCATCTTGTTCAAGCTCCAGAGGATCCTATTCTTGGGgtaccttctt ... aaatgaatagGTGACAGTTGCATACAACAAAGATCCTAGCCCAGTTAAGCTGAATTTAGGA
EST: gi|301502006|gb|HO207546.1|HO207546
EST:     GTTCTGTTTTCTCTCATCTTGTTCAAGCTCCAGAGGATCCTATTCTTGGG                         GTGACAGTTGCATACAACAAAGATCCTAGCCCAGTTAAGCTGAATTTAGGA
genomic: GTTCTGTTTTCTCTCATCTTGTTCAAGCTCCAGAGGATCCTATTCTTGGGgtaccttctt ... aaatgaatagGTGACAGTTGCATACAACAAAGATCCTAGCCCAGTTAAGCTGAATTTAGGA
EST: gi|86054405|gb|DR350162.1|DR350162
EST:     GTTCTGTTTTCTCTCATCTTGTTCAAGCTCCAGAGGATCCTATTCTTGGG                         GTGACAGTTGCATACAACAAAGATCCTAGCCCAGTTAAGCTGAATTTAGGA
genomic: GTTCTGTTTTCTCTCATCTTGTTCAAGCTCCAGAGGATCCTATTCTTGGGgtaccttctt ... aaatgaatagGTGACAGTTGCATACAACAAAGATCCTAGCCCAGTTAAGCTGAATTTAGGA
EST: gi|301501550|gb|HO207090.1|HO207090
EST:     GTTCTGTTTTCTCTCATCTTGTTCAAGCTCCAGAGGATCCTATTCTTGGG                         GTGACAGTTGCATACAACAAAGATCCTAGCCCAGTTAAGCTGAATTTAGGA
genomic: GTTCTGTTTTCTCTCATCTTGTTCAAGCTCCAGAGGATCCTATTCTTGGGgtaccttctt ... aaatgaatagGTGACAGTTGCATACAACAAAGATCCTAGCCCAGTTAAGCTGAATTTAGGA
EST: gi|86054401|gb|DR350158.1|DR350158
EST:     GTTCTGTTTTCTCTCATCTTGTTCAAGCTCCAGAGGATCCTATTCTTGGG                         GTGACAGTTGCATACAACAAAGATCCTAGCCCAGTTAAGCTGAATTTAGGA
genomic: GTTCTGTTTTCTCTCATCTTGTTCAAGCTCCAGAGGATCCTATTCTTGGGgtaccttctt ... aaatgaatagGTGACAGTTGCATACAACAAAGATCCTAGCCCAGTTAAGCTGAATTTAGGA
EST: gi|163990515|gb|ES114089.1|ES114089
EST:     GTTCTGTTTTCTCTCATCTTGTTCAAGCTCCAGAGGATCCTATTCTTGGG                         GTGACAGTTGCATACAACAAAGATCCTAG
genomic: GTTCTGTTTTCTCTCATCTTGTTCAAGCTCCAGAGGATCCTATTCTTGGGgtaccttctt ... aaatgaatagGTGACAGTTGCATACAACAAAGATCCTAG
EST: gi|86054406|gb|DR350163.1|DR350163
EST:     GTTCTGTTTTCTCTCATCTTGTTCAAGCTCCAGAGGATCCTATTCTTGGG                         GTGACAGTTGCATACAACAAAGATCCTAGCCCAGTTAAGCTGAATTTAGGA
genomic: GTTCTGTTTTCTCTCATCTTGTTCAAGCTCCAGAGGATCCTATTCTTGGGgtaccttctt ... aaatgaatagGTGACAGTTGCATACAACAAAGATCCTAGCCCAGTTAAGCTGAATTTAGGA
EST: gi|86054403|gb|DR350160.1|DR350160
EST:     GTTCTGTTTTCTCTCATCTTGTTCAAGCTCCAGAGGATCCTATTCTTGGG                         GTGACAGTTGCATACAACAAAGATCCTAGCCCAGTTAAGCTGAATTTAGGA
genomic: GTTCTGTTTTCTCTCATCTTGTTCAAGCTCCAGAGGATCCTATTCTTGGGgtaccttctt ... aaatgaatagGTGACAGTTGCATACAACAAAGATCCTAGCCCAGTTAAGCTGAATTTAGGA
EST: gi|301501070|gb|HO206610.1|HO206610
EST:     GTTCTGTTTTCTCTCATCTTGTTCAAGCTCCAGAGGATCCTATTCTTGGG                         GTGACAGTTGCATACAACAAAGATCCTAGCCCAGTTAAGCTGAATTTAGGA
genomic: GTTCTGTTTTCTCTCATCTTGTTCAAGCTCCAGAGGATCCTATTCTTGGGgtaccttctt ... aaatgaatagGTGACAGTTGCATACAACAAAGATCCTAGCCCAGTTAAGCTGAATTTAGGA
EST: gi|86054404|gb|DR350161.1|DR350161
EST:     GTTCTGTTTTCTCTCATCTTGTTCAAGCTCCAGAGGATCCTATTCTTGGG                         GTGACAGTTGCATACAACAAAGATCCTAGCCCAGTTAAGCTGAATTTAGGA
genomic: GTTCTGTTTTCTCTCATCTTGTTCAAGCTCCAGAGGATCCTATTCTTGGGgtaccttctt ... aaatgaatagGTGACAGTTGCATACAACAAAGATCCTAGCCCAGTTAAGCTGAATTTAGGA
EST: gi|86054407|gb|DR350164.1|DR350164
EST:     GNTCTGTTTTCTCTCATCTTGTTCAAGCTCCAGAGGATCCTATTCTTGGG                         GTGACAGTTGCATACAACAAAGATCCTAGCCCAGTTAAGCTGAATTTAGGA
genomic: GTTCTGTTTTCTCTCATCTTGTTCAAGCTCCAGAGGATCCTATTCTTGGGgtaccttctt ... aaatgaatagGTGACAGTTGCATACAACAAAGATCCTAGCCCAGTTAAGCTGAATTTAGGA
EST: gi|124990980|gb|EL063249.1|EL063249
EST:     GAGGATCCTATTCTTGGG                         GTGACAGTTGCATACAACAAAGATCCTAGCCCAGTTAAGCTGAATTTAGGA
genomic: GAGGATCCTATTCTTGGGgtaccttctt ... aaatgaatagGTGACAGTTGCATACAACAAAGATCCTAGCCCAGTTAAGCTGAATTTAGGA
EST: gi|86054402|gb|DR350159.1|DR350159
EST:     GTTCTGTTTTCTCTCATCTTGTTCAAGCTCCAGAGGATCCTATTCTTGGG                         GTGACAGTTGCATACAACAAAGATCCTAGCCCAGTTAAGCTGAATTTAGGA
genomic: GTTCTGTTTTCTCTCATCTTGTTCAAGCTCCAGAGGATCCTATTCTTGGGgtaccttctt ... aaatgaatagGTGACAGTTGCATACAACAAAGATCCTAGCCCAGTTAAGCTGAATTTAGGA
EST: gi|116468511|gb|EG511103.1|EG511103
EST:     GTTCTGTTTTCTCTCATCTTGTTCAAGCTCCAGAGGATCCTATTCTTGGG                         GTGACAGTTGCATACAACAAAGATCCTAGCCCAGTTAAGCTGAATTTAGGA
genomic: GTTCTGTTTTCTCTCATCTTGTTCAAGCTCCAGAGGATCCTATTCTTGGGgtaccttctt ... aaatgaatagGTGACAGTTGCATACAACAAAGATCCTAGCCCAGTTAAGCTGAATTTAGGA
EST: gi|86054408|gb|DR350165.1|DR350165
EST:     GTTCTGTTTTCTCTCATCTTGTTCAAGCTCCAGAGGATCCTATTCTTGGG                         GTGACAGTTGCATACAACAAAGATCCTAGCCCAGTTAAGCTGAATTTAGGA
genomic: GTTCTGTTTTCTCTCATCTTGTTCAAGCTCCAGAGGATCCTATTCTTGGGgtaccttctt ... aaatgaatagGTGACAGTTGCATACAACAAAGATCCTAGCCCAGTTAAGCTGAATTTAGGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttagtgtggttatgtcagtgattctgatatttgtttttcacaaaaaaatgaatagGTGACAGTTGCATACAACAAAGATCCTAGCCCAGTTAAGCTGAATTTAGGAGTTGGTGCTTACCGAACTGAG
                     ttctgat  putative branch site (score: 3)
                          atatttgtttttcaca  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atttttttttcaccaaattttcagctctgagatgaattatgatgattagtgtggttatgtcagtgattctgatatttgtttttcacaaaaaaatgaatagGTGACAGTTGCATACAACAAAGATCCTAGCCCAGTTAAGCTGAATTTAGGAGTTGGTGCTTACCGAACTGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA
- - - - - caccaaa
- - - - - - - - - - - - - - -agatgaa