Sequence
atgc intronic sequence ATGC exonic sequencegtggggcaattattgttaattacaaatttcttattatataatagttaagattatgcatttcataacatttctatgatgttcacagATAAGGGGTTCAGCTAAGCTGAAAAGGATTATGCAGACAATTCTTTCACTGGGAAATGCGTTAAACCAAGGAACTGCTAGAG
Basic information
species | Oryza sativa |
transcript | LOC_Os08g17820.2 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os08g17820.2 (Oryza sativa), 3'ss of exon 9
lower sequence: AC197714.3_FGT005 (Zea mays), 3'ss of exon 5
gtggggcaattattgttaattacaaatttcttattatataatagttaagattatgcatttcataacatttctatgatgttcacagATAAGGGGTTCAGCTAAGCTGAAAAGGATTATGCAGACAATTCTTTCACTGGGAAATGCGTTAAACCAAGGAACTGCTAGAG
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gttaggcactttatattgattgaaaa----ttaatat-taaca--tacagatattaatttcatgtatttgttataatgtttatagATACGAGGTTCAGTCAAGTTGAAAAGGATTATGCAGACAATTCTTTCTCTCGGAAATGCATTGAACCAAGGCACTGCTAGAG
upper sequence: LOC_Os08g17820.2 (Oryza sativa), 3'ss of exon 9
lower sequence: EFJ15040 (Selaginella moellendorffii), 3'ss of exon 10
gtggggcaattattgttaattacaaatttcttattatataatagttaagattatgcatttcataacatttctatgatgttcacagATAAGGGGTTCAGCTAAGCTGAAAAGGATTATGCAGACAATTCTTTCACTGGGAAATGCGTTAAACCAAGGAACTGCTAGAG
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--------------------------------gtaatttcgcactcttc-ttgtatgttgcctgaagccg----gattcttgcagGTGAAAGAGTCTCCTAAGCTTAAAAGAGTGATGCAAACGGTTCTGTCCCTGGGAAATGCGTTAAACCAAGGAACTGCTAGAG
upper sequence: LOC_Os08g17820.2 (Oryza sativa), 3'ss of exon 9
lower sequence: EFJ14916 (Selaginella moellendorffii), 3'ss of exon 6
gtggggcaattattgttaattacaaatttcttattatataatagttaagattatgcatttcataacatttctatgatgttcacagATAAGGGGTTCAGCTAAGCTGAAAAGGATTATGCAGACAATTCTTTCACTGGGAAATGCGTTAAACCAAGGAACTGCTAGAG
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---------------------------------------------------------------------------------gtaagttgcagagtctcctaagCTTGAAAGAGTGATGCAAACGGTTCTGTCCCTGGGAAATGTGTTAAACCAAGGAACTGCTAGAG
upper sequence: LOC_Os08g17820.2 (Oryza sativa), 3'ss of exon 9
lower sequence: EFJ36895 (Selaginella moellendorffii), 3'ss of exon 10
gtggggcaattattgttaattacaaatttcttattatataatagttaagattatgcatttcataacatttctatgatgttcacagATAAGGGGTTCAGCTAAGCTGAAAAGGATTATGCAGACAATTCTTTCACTGGGAAATGCGTTAAACCAAGGAACTGCTAGAG
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------------------------------gtaatctcccactgttt---ttgtaagtagcctgaagccg----gatttttgcagGTGAAAGAGTCTGCGAAGCTTAAAAGAGTAATGCAAACGGTTCTATCCTTGGGAAATGCGCTAAACCAAGGAACTGCTAGAG
upper sequence: LOC_Os08g17820.2 (Oryza sativa), 3'ss of exon 9
lower sequence: EFJ33545 (Selaginella moellendorffii), 3'ss of exon 10
gtggggcaattattgttaattacaaatttcttattatataatagttaagattatgcatttcataacatttctatgatgttcacagATAAGGGGTTCAGCTAAGCTGAAAAGGATTATGCAGACAATTCTTTCACTGGGAAATGCGTTAAACCAAGGAACTGCTAGAG
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------------------------------gtaatctcccactgttt---ttgtaagtagcctgaagccg----gatttttgcagGTGAAAGAGTCTGCTAAGCTTAAAAGAGTAATGCAAACGGTTCTATCCTTGGGAAATGCGCTAAACCAAGGAACTGCTAGAG
upper sequence: LOC_Os08g17820.2 (Oryza sativa), 3'ss of exon 9
lower sequence: EFJ38303 (Selaginella moellendorffii), 3'ss of exon 3
----------------------gtggggcaattattgttaatta-caaatttcttattatat-----aatagttaa-gattatgcatttcataacatttctatgatgttcacagATAAGGGGTTCAGCTAAGCTGAAAAGGATTATGCAGACAATTCTTTCACTGGGAAATGCGTTAAACCAAGGAACTGCTAGAG
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gtcaaaattattttgtctaccctttcaaacgttggtatcaggtgtcagatttacgagaaaatctggtagtagtcaatgaagcttcaacagaggtaatttcgactcttcttgtaagttgcagAGTCTCCTAAGCTTGAAAGAGTGATGCAAACGGTTCTGTCCCTGGGAAATGCGTTAAACCAAGGAACTGCTAGAGMapped 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|11442844|gb|BF430743.1|BF430743EST: TTTCTGACCTTAAGAGGAGCCTGAACATTGTCAACTCTTCCGCGGAAGAG ATAAGGGGTTCAGCTAAGCTGAAAAGGATTATGCAGACAATTCTTTCACTG
genomic: TTTCTGACCTTAAGAGGAGCCTGAACATTGTCAACTCTTCCGCGGAAGAGgtggggcaat ... atgttcacagATAAGGGGTTCAGCTAAGCTGAAAAGGATTATGCAGACAATTCTTTCACTG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttattatataatagttaagattatgcatttcataacatttctatgatgttcacagATAAGGGGTTCAGCTAAGCTGAAAAGGATTATGCAGACAATTCTTTCACTGGGAAATGCGTTAAACCAAGGAACTGCTAGAG
tcataac putative branch site (score: 2)
atataatagttaagat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtggggcaattattgttaattacaaatttcttattatataatagttaagattatgcatttcataacatttctatgatgttcacagATAAGGGGTTCAGCTAAGCTGAAAAGGATTATGCAGACAATTCTTTCACTGGGAAATGCGTTAAACCAAGGAACTGCTAGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA