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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatcgatcgtcttcaccatacttttggattttttctgatcacgtttcaattccaatctgagagatcttccttgattcgatttctgaatatatctctgtaattttttttctggttttttctagGGTTTTAGTAATTTTCCGATGGCTTCAAGCTCAGAGAAAACACCTCTTATTCCTTCAG

Basic information

species Arabidopsis thaliana
transcript AT2G17390.1
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|86055531|gb|DR351288.1|DR351288
EST:     TTTGGGGGTTTTCATAATTTTTGGTTCTTCAGCTCCTCAAGCTTCGATAG                         GGTTTTAGTAATTTTCCGATGGCTTCAAGCTCAGAGAAAACACCTCTTATT
genomic: TTTGGGGGTTTTCATAATTTTTGGTTCTTCAGCTCCTCAAGCTTCGATAGgtatcgatcg ... ttttttctagGGTTTTAGTAATTTTCCGATGGCTTCAAGCTCAGAGAAAACACCTCTTATT
EST: gi|124997684|gb|EL069953.1|EL069953
EST:     TTTGGGGGTTTTCATAATTTTTGGTTCTTCAGCTCCTCAAGCTTCGATAG                         GGTTTTAGTAATTT-CCGATGG
genomic: TTTGGGGGTTTTCATAATTTTTGGTTCTTCAGCTCCTCAAGCTTCGATAGgtatcgatcg ... ttttttctagGGTTTTAGTAATTTTCCGATGG
EST: gi|86055530|gb|DR351287.1|DR351287
EST:     TTTGGGGGTTTTCATAATTTTTGGTTCTTCAGCTCCTCAAGCTTCGATAG                         GGTTTTAGTAATTTTCCGATGGCTTCAAGCTCAGAGAAAACACCTCTTATT
genomic: TTTGGGGGTTTTCATAATTTTTGGTTCTTCAGCTCCTCAAGCTTCGATAGgtatcgatcg ... ttttttctagGGTTTTAGTAATTTTCCGATGGCTTCAAGCTCAGAGAAAACACCTCTTATT
EST: gi|86055524|gb|DR351281.1|DR351281
EST:     ATTTTTGGTTCTTCAGCTCCTCAAGCTTCGATAG                         GGTTTTAGTAATTTTCCGATGGCTTCAAGCTCAGAGAAAACACCTCTTATT
genomic: ATTTTTGGTTCTTCAGCTCCTCAAGCTTCGATAGgtatcgatcg ... ttttttctagGGTTTTAGTAATTTTCCGATGGCTTCAAGCTCAGAGAAAACACCTCTTATT
EST: gi|116476826|gb|EG519418.1|EG519418
EST:     GGTTCTTCAGCTCCTCAAGCTTCGATAG                         GGTTTTAGTAATTTTCCGATGGCTTCAAGCTCAGAGAAAACACCTCTTATT
genomic: GGTTCTTCAGCTCCTCAAGCTTCGATAGgtatcgatcg ... ttttttctagGGTTTTAGTAATTTTCCGATGGCTTCAAGCTCAGAGAAAACACCTCTTATT
EST: gi|124909572|gb|EH983652.1|EH983652
EST:     GGGGGTTTTCATAATTTTTGGTTCTTCAGCTCCTCAAGCTTCGATAG                         GGTTTTAGTAATTTTCCGATGGCTTCAAGCTCAGAGAAAA
genomic: GGGGGTTTTCATAATTTTTGGTTCTTCAGCTCCTCAAGCTTCGATAGgtatcgatcg ... ttttttctagGGTTTTAGTAATTTTCCGATGGCTTCAAGCTCAGAGAAAA
EST: gi|125045414|gb|EL117683.1|EL117683
EST:     TTTGGGGGTTTTCATAATTTTTGGTTCTTCAGCTCCTCAAGCTTCGATAG                         GGTTTTAGTAATTTTCCGATGGCTTCAAGCT
genomic: TTTGGGGGTTTTCATAATTTTTGGTTCTTCAGCTCCTCAAGCTTCGATAGgtatcgatcg ... ttttttctagGGTTTTAGTAATTTTCCGATGGCTTCAAGCT
EST: gi|86055526|gb|DR351283.1|DR351283
EST:     AATTTTTGGTTCTTCAGCTCCTCAAGCTTCGATAG                         GGTTTTAGTAATTTTCCGATGGCTTCAAGCTCAGAGAAAACACCTCTTATT
genomic: AATTTTTGGTTCTTCAGCTCCTCAAGCTTCGATAGgtatcgatcg ... ttttttctagGGTTTTAGTAATTTTCCGATGGCTTCAAGCTCAGAGAAAACACCTCTTATT
EST: gi|86055536|gb|DR351293.1|DR351293
EST:     TTTGGGGGTTTTCATAATTTTTGGTTCTTCAGCTCCTCAAGCTTCGATAG                         GGTTTTAGTAATTTTCCGATGGCTTCAAGCTCAGAGAAAACACCTCTTATT
genomic: TTTGGGGGTTTTCATAATTTTTGGTTCTTCAGCTCCTCAAGCTTCGATAGgtatcgatcg ... ttttttctagGGTTTTAGTAATTTTCCGATGGCTTCAAGCTCAGAGAAAACACCTCTTATT
EST: gi|86055528|gb|DR351285.1|DR351285
EST:     TTTGGGGGTTTTCATAATTTTTGGTTCTTCAGCTCCTCAAGCTTCGATAG                         GGTTTTAGTAATTTTCCGATGGCTTCAAGCTCAGAGAAAACACCTCTTATT
genomic: TTTGGGGGTTTTCATAATTTTTGGTTCTTCAGCTCCTCAAGCTTCGATAGgtatcgatcg ... ttttttctagGGTTTTAGTAATTTTCCGATGGCTTCAAGCTCAGAGAAAACACCTCTTATT
EST: gi|86055533|gb|DR351290.1|DR351290
EST:     TTTGGGGGTTTTCATAATTTTTGGTTCTTCAGCTCCTCAAGCTTCGATAG                         GGTTTTAGTAATTTTCCGATGGCTTCAAGCTCAGAGAAAACACCTCTTATT
genomic: TTTGGGGGTTTTCATAATTTTTGGTTCTTCAGCTCCTCAAGCTTCGATAGgtatcgatcg ... ttttttctagGGTTTTAGTAATTTTCCGATGGCTTCAAGCTCAGAGAAAACACCTCTTATT
EST: gi|86055525|gb|DR351282.1|DR351282
EST:     TGGGGGTTTTCATAATTTTTGGTTCTTCAGCTCCTCAAGCTTCGATAG                         GGTTTTAGTAATTTTCCGATGGCTTCAAGCTCAGAGAAAACACCTCTTATT
genomic: TGGGGGTTTTCATAATTTTTGGTTCTTCAGCTCCTCAAGCTTCGATAGgtatcgatcg ... ttttttctagGGTTTTAGTAATTTTCCGATGGCTTCAAGCTCAGAGAAAACACCTCTTATT
EST: gi|86055527|gb|DR351284.1|DR351284
EST:     AATTTTTGGTTTTTCAGCTCCTCAAGCTTCGATAG                         GG-TTTAGTAATTTTCCGATGGCTTCAAGCTCAGAGAAAACACCTCTTATT
genomic: AATTTTTGGTTCTTCAGCTCCTCAAGCTTCGATAGgtatcgatcg ... ttttttctagGGTTTTAGTAATTTTCCGATGGCTTCAAGCTCAGAGAAAACACCTCTTATT
EST: gi|86055532|gb|DR351289.1|DR351289
EST:     TTTGGGGGTTTTCATAATTTTTGGTTCTTCAGCTCCTCAAGCTTCGATAG                         GGTTTTAGTAATTTKCSGATGGCTTCAAGCTCAGAGAAAACACCTCTTATT
genomic: TTTGGGGGTTTTCATAATTTTTGGTTCTTCAGCTCCTCAAGCTTCGATAGgtatcgatcg ... ttttttctagGGTTTTAGTAATTTTCCGATGGCTTCAAGCTCAGAGAAAACACCTCTTATT
EST: gi|86055534|gb|DR351291.1|DR351291
EST:     GGGGTTTTCATAATTTTTGGTTCTTCAGCTCCTCAAGCTTCGATAG                         GGTTTTAGTAATTTTCCGATGGCTTCAAGCTCAGAGAAAACACCTCTTATT
genomic: GGGGTTTTCATAATTTTTGGTTCTTCAGCTCCTCAAGCTTCGATAGgtatcgatcg ... ttttttctagGGTTTTAGTAATTTTCCGATGGCTTCAAGCTCAGAGAAAACACCTCTTATT
EST: gi|86055523|gb|DR351280.1|DR351280
EST:     TTTGGGGGTTTTCATAATTTTTGGTTCTTCAGCTCCTCAAGCTTCGATAG                         GGTTTTAGTAATTTTCCGATGGCTTCAAGCTCAGAGAAAACACCTCTTATT
genomic: TTTGGGGGTTTTCATAATTTTTGGTTCTTCAGCTCCTCAAGCTTCGATAGgtatcgatcg ... ttttttctagGGTTTTAGTAATTTTCCGATGGCTTCAAGCTCAGAGAAAACACCTCTTATT
EST: gi|116419184|gb|EG461776.1|EG461776
EST:     GGGGGTTTTCATAATTTTTGGTTCTTCAGCTCCTCAAGCTTCGATAG                         GGTTTTAGTAATTTTCCGATGGCTTCAAGCTCAGAGAAAACACCTCTTATT
genomic: GGGGGTTTTCATAATTTTTGGTTCTTCAGCTCCTCAAGCTTCGATAGgtatcgatcg ... ttttttctagGGTTTTAGTAATTTTCCGATGGCTTCAAGCTCAGAGAAAACACCTCTTATT
EST: gi|86055535|gb|DR351292.1|DR351292
EST:     AATTTTTGGTTCTTCAGCTCCTCAAGCTTCGATAG                         GGTTTTAGTAATTTTCCGATGGCTTCAAGCTCAGAGAAAACACCTCTTATT
genomic: AATTTTTGGTTCTTCAGCTCCTCAAGCTTCGATAGgtatcgatcg ... ttttttctagGGTTTTAGTAATTTTCCGATGGCTTCAAGCTCAGAGAAAACACCTCTTATT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tccttgattcgatttctgaatatatctctgtaattttttttctggttttttctagGGTTTTAGTAATTTTCCGATGGCTTCAAGCTCAGAGAAAACACCTCTTATTCCTTCAG
 ccttgat  putative branch site (score: 5)
                                 ttttttttctggtttt  putative PPT
                  aatatatctctgtaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatcgatcgtcttcaccatacttttggattttttctgatcacgtttcaattccaatctgagagatcttccttgattcgatttctgaatatatctctgtaattttttttctggttttttctagGGTTTTAGTAATTTTCCGATGGCTTCAAGCTCAGAGAAAACACCTCTTATTCCTTCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA