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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tctccttttgttaagatgtgctattatttacccattgtatatatgtcagcaaacacaacttcttgcatactaaaatttgtttattgtacattgttggcagTAAGCTCCTTGATATTCTGATAACAAACAAGGCAGCTGCAAAGGCTATATTCATCAAAATGGACCCAG

Basic information

species Oryza sativa
transcript LOC_Os01g72650.1
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|88315637|gb|CI615509.1|CI615509
EST:     ACGCTCCCCGGCGGGCTTCAATTTCGGTCGCCGGCGACAAGTACTACAGT                         TAAGCTCCTTGATATTCTGATAACAAACAAGGCAGCTGCAAAGGCTATATT
genomic: ACGCTCCCCGGCGGGCTTCAATTTCGGTCGCCGGCGACAAGTACTACAGTgtaagaagca ... ttgttggcagTAAGCTCCTTGATATTCTGATAACAAACAAGGCAGCTGCAAAGGCTATATT
EST: gi|58662600|gb|CK051286.1|CK051286
EST:     ACGCTCCCCGGCGGGCTTCAATTTCGGTCGCCGGCGACAAGTACTACAGT                         TAAGCTCCTTGATATTCTGATAACAAACAAGGCAGCTGCAAAGGCTATATT
genomic: ACGCTCCCCGGCGGGCTTCAATTTCGGTCGCCGGCGACAAGTACTACAGTgtaagaagca ... ttgttggcagTAAGCTCCTTGATATTCTGATAACAAACAAGGCAGCTGCAAAGGCTATATT
EST: gi|88305463|gb|CI630625.1|CI630625
EST:     ACGCTCCCCGGCGGGCTTCACTTTCGGTCGCCGGCGACAAGTACTACAGT                         TACGCTCCTTGATATTCTGATAACAAACAAGGCAGCTGCAAAGGCTATATT
genomic: ACGCTCCCCGGCGGGCTTCAATTTCGGTCGCCGGCGACAAGTACTACAGTgtaagaagca ... ttgttggcagTAAGCTCCTTGATATTCTGATAACAAACAAGGCAGCTGCAAAGGCTATATT
EST: gi|88337451|gb|CI630748.1|CI630748
EST:     ACGCTCCCCGGCGGGCTTCAATTTCGGTCGCCGGCGACAAGTACTACAGT                         TAAGCTCCTTGATATTCTGATAACAAACAAGGCAGCTGCAAAGGCTATATT
genomic: ACGCTCCCCGGCGGGCTTCAATTTCGGTCGCCGGCGACAAGTACTACAGTgtaagaagca ... ttgttggcagTAAGCTCCTTGATATTCTGATAACAAACAAGGCAGCTGCAAAGGCTATATT
EST: gi|88315936|gb|CI618812.1|CI618812
EST:     ACGCTCCCCGGCGGGCTTCAATTTCGGTCGCCGGCGACAAGTACTACAGT                         TAAGCTCCTTGATATTCTGATAACAAACAAGGCAGCTGCAAAGGCTATATT
genomic: ACGCTCCCCGGCGGGCTTCAATTTCGGTCGCCGGCGACAAGTACTACAGTgtaagaagca ... ttgttggcagTAAGCTCCTTGATATTCTGATAACAAACAAGGCAGCTGCAAAGGCTATATT
EST: gi|88347090|gb|CI631170.1|CI631170
EST:     CGCTCCCCGGCGGGCNTT-AATTTCGGTCGGCGGCGACAAGTACTACAGT                         TAAGCTCCTTGATATTCTGATAACAAACAAGGCAGCTGCAAAGGCTATATT
genomic: CGCTCCCCGGCGGGC-TTCAATTTCGGTCGCCGGCGACAAGTACTACAGTgtaagaagca ... ttgttggcagTAAGCTCCTTGATATTCTGATAACAAACAAGGCAGCTGCAAAGGCTATATT
EST: gi|88582438|gb|CI699851.1|CI699851
EST:     ACGCTCCCCGGCGGGCTTCAATTTCGGTCGCCGGCGACAAGTACTACAGT                         TAAGCTCCTTGATATTCTGATAACAAACAAGGCAGCTGGAAAGGCTATATT
genomic: ACGCTCCCCGGCGGGCTTCAATTTCGGTCGCCGGCGACAAGTACTACAGTgtaagaagca ... ttgttggcagTAAGCTCCTTGATATTCTGATAACAAACAAGGCAGCTGCAAAGGCTATATT
EST: gi|88372401|gb|CI619731.1|CI619731
EST:     ACGCTCCCCGGCGGGCTTCAATTTCGGTCGCCGGCGACAAGTACTACAGT                         TAAGCTCCTTGATATTCTGATAACAAACAAGGCAGCTGCAAAGGCTATATT
genomic: ACGCTCCCCGGCGGGCTTCAATTTCGGTCGCCGGCGACAAGTACTACAGTgtaagaagca ... ttgttggcagTAAGCTCCTTGATATTCTGATAACAAACAAGGCAGCTGCAAAGGCTATATT
EST: gi|88345614|gb|CI629875.1|CI629875
EST:     ACGCTCCCCGGNGGGCTTCAATTTCGGTCGCCGGCGACAAGTACTACAGT                         TAAGCTCCTTGATATTCTGANTA-CAAACAAGGCAGCTGCAAAGGCTATAT
genomic: ACGCTCCCCGGCGGGCTTCAATTTCGGTCGCCGGCGACAAGTACTACAGTgtaagaagca ... ttgttggcagTAAGCTCCTTGATATTCTGA-TAACAAACAAGGCAGCTGCAAAGGCTATAT
EST: gi|88353355|gb|CI631540.1|CI631540
EST:     ACGCTCCCCGGCGGGCTTCAATTTCGGTCGCCGGCGACAAGTACTACAGT                         TAAGCTCCTTGATATTCTGATAACAAACAAGGCAGCTGCCAAGGCTATATT
genomic: ACGCTCCCCGGCGGGCTTCAATTTCGGTCGCCGGCGACAAGTACTACAGTgtaagaagca ... ttgttggcagTAAGCTCCTTGATATTCTGATAACAAACAAGGCAGCTGCAAAGGCTATATT
EST: gi|88337722|gb|CI632224.1|CI632224
EST:     ACGCTCCCCGGCGGGCTTCAATTTCGGTCGCCGGCGACAAGTACTACAGT                         TAAGCTCCTTGATATTCTGATAACAAACAAGGCAGCTGCAAAGGCTATATT
genomic: ACGCTCCCCGGCGGGCTTCAATTTCGGTCGCCGGCGACAAGTACTACAGTgtaagaagca ... ttgttggcagTAAGCTCCTTGATATTCTGATAACAAACAAGGCAGCTGCAAAGGCTATATT
EST: gi|88353396|gb|CI631581.1|CI631581
EST:     ACGCTCCCCGGCGGGCTTCAATTTCGGTCGCCGGCGACAAGTACTACAGT                         TAAGCTCCTTGATATTCTGATAACAAACAAGGGAGCTGCAAAGGCTATATT
genomic: ACGCTCCCCGGCGGGCTTCAATTTCGGTCGCCGGCGACAAGTACTACAGTgtaagaagca ... ttgttggcagTAAGCTCCTTGATATTCTGATAACAAACAAGGCAGCTGCAAAGGCTATATT
EST: gi|88587934|gb|CI705716.1|CI705716
EST:     ACGCTCCCCGGCGGGCTTCAATTTCGGTCGNGGGCGACAAGTACTACAGT                         TAAGCTCCTTGATATTCTGATAACAAACAAGGCAGCTGCAAAGGCTATATT
genomic: ACGCTCCCCGGCGGGCTTCAATTTCGGTCGCCGGCGACAAGTACTACAGTgtaagaagca ... ttgttggcagTAAGCTCCTTGATATTCTGATAACAAACAAGGCAGCTGCAAAGGCTATATT
EST: gi|66923971|gb|CX110819.1|CX110819
EST:     ACGCTCCCCGGCGGGCTTCAATTTCGGTCGCCGGCGACAAGTACTACAGT                         TAAGCTCCTTGATATTCTGATAACAAACAAGGCAGCTGCAAAGGCTATATT
genomic: ACGCTCCCCGGCGGGCTTCAATTTCGGTCGCCGGCGACAAGTACTACAGTgtaagaagca ... ttgttggcagTAAGCTCCTTGATATTCTGATAACAAACAAGGCAGCTGCAAAGGCTATATT
EST: gi|88305629|gb|CI631996.1|CI631996
EST:     ACGCTCCCCGGNGGGCTTCAATTTCGGTCGCCGGNGACAAGTACTACAGT                         TAAGCTCCTTGATATTCTGATAACAAACAAGGCAGCTGCAAAGGCTATATT
genomic: ACGCTCCCCGGCGGGCTTCAATTTCGGTCGCCGGCGACAAGTACTACAGTgtaagaagca ... ttgttggcagTAAGCTCCTTGATATTCTGATAACAAACAAGGCAGCTGCAAAGGCTATATT
EST: gi|88348771|gb|CI631465.1|CI631465
EST:     ACGCTCCCCGGCGGGCTTCAATTTCGGTCGCCGGCGACAAGTACTACAGT                         TAAGCTCCTTGATATTCTGATAACAAACAAGGCAGCTGCAAAGGCTATATT
genomic: ACGCTCCCCGGCGGGCTTCAATTTCGGTCGCCGGCGACAAGTACTACAGTgtaagaagca ... ttgttggcagTAAGCTCCTTGATATTCTGATAACAAACAAGGCAGCTGCAAAGGCTATATT
EST: gi|88353381|gb|CI631566.1|CI631566
EST:     ACGCT-CCCGGCGGGCTTCAATTTCGGTCGCCGGCGACAAGTACTACAGT                         TAACCTCCTTGATATTCTGATAACAAACAAGGCAGCTGCAAAGGCTATATT
genomic: ACGCTCCCCGGCGGGCTTCAATTTCGGTCGCCGGCGACAAGTACTACAGTgtaagaagca ... ttgttggcagTAAGCTCCTTGATATTCTGATAACAAACAAGGCAGCTGCAAAGGCTATATT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcagcaaacacaacttcttgcatactaaaatttgtttattgtacattgttggcagTAAGCTCCTTGATATTCTGATAACAAACAAGGCAGCTGCAAAGGCTATATTCATCAAAATGGACCCAG
                      tactaaa  putative branch site (score: 1)
                     atactaaaatttgttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tctccttttgttaagatgtgctattatttacccattgtatatatgtcagcaaacacaacttcttgcatactaaaatttgtttattgtacattgttggcagTAAGCTCCTTGATATTCTGATAACAAACAAGGCAGCTGCAAAGGCTATATTCATCAAAATGGACCCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAAG
- - cttttgt
- - - - - - - gatgtgc
- - - - - - - - - - - - - - - - - - - - - - - cagcaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - actaaaa