Sequence
atgc intronic sequence ATGC exonic sequence...ttaattaacatgtataggcaaatgagaaagttttggactattaggctagatattttcccaactacgaccagaggctgaagctttgcttttttgtttgcagATAACAGTAGATGGTGAAGTTGCCACTGATCCAGATATGATTCTCAG
Basic information
species | Oryza sativa |
transcript | LOC_Os03g17920.3 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os03g17920.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G158261_T03 (Zea mays), 3'ss of exon 3
-------ttaattaacatgtatag---gcaaatgagaaagttttggactattaggctagatattttcccaactacgaccagaggctgaagctttgcttttttgtttgcagATAACAGTAGATGGTGAAGTTGCCACTGATCCAGATATGATTCTCAG-----------------------------------------------------
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accccccaaaaatgtcatgtgtactttggaaaaatgagagtttatgatttttctggcaaat--tttcttggatgtg--caaatgatg--gtttcg----tttgtttgcagATAACCGTTGATGGTGAAGTTGTCACTGATCCAGATATGACTCTGGTGTAATTTTTTTCCTCTCAGCAAGCTTATTATTGTTATATTCTTCCCAATCTCC
upper sequence: LOC_Os03g17920.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G158261_T02 (Zea mays), 3'ss of exon 3
-------ttaattaacatgtatag---gcaaatgagaaagttttggactattaggctagatattttcccaactacgaccagaggctgaagctttgcttttttgtttgcagATAACAGTAGATGGTGAAGTTGCCACTGATCCAGATATGATTCTCAG
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accccccaaaaatgtcatgtgtactttggaaaaatgagagtttatgatttttctggcaaat--tttcttggatgtg--caaatgatg--gtttcg----tttgtttgcagATAACCGTTGATGGTGAAGTTGTCACTGATCCAGATATGACTCTG--
upper sequence: LOC_Os03g17920.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G158261_T01 (Zea mays), 3'ss of exon 3
-------ttaattaacatgtatag---gcaaatgagaaagttttggactattaggctagatattttcccaactacgaccagaggctgaagctttgcttttttgtttgcagATAACAGTAGATGGTGAAGTTGCCACTGATCCAGATATGATTCTCAG
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accccccaaaaatgtcatgtgtactttggaaaaatgagagtttatgatttttctggcaaat--tttcttggatgtg--caaatgatg--gtttcg----tttgtttgcagATAACCGTTGATGGTGAAGTTGTCACTGATCCAGATATGACTCTGGTMapped 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|88420693|gb|CI564529.1|CI564529EST: GTTGTATTGTTGCGCTTTGCAGGTGGATTAAGAGGATTCGTGATGGACAG ATAACAGTAGATGGTGAAGTTGCCACTGATCCAGATATGATTCTCAG
genomic: GTTGTATTGTTGCGCTTTGCAGGTGGATTAAGAGGATTCGTGATGGACAGgtaggtcatc ... ttgtttgcagATAACAGTAGATGGTGAAGTTGCCACTGATCCAGATATGATTCTCAG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctagatattttcccaactacgaccagaggctgaagctttgcttttttgtttgcagATAACAGTAGATGGTGAAGTTGCCACTGATCCAGATATGATTCTCAG
ctttgcttttttgttt CT-rich tract
ttttttgttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttaattaacatgtataggcaaatgagaaagttttggactattaggctagatattttcccaactacgaccagaggctgaagctttgcttttttgtttgcagATAACAGTAGATGGTGAAGTTGCCACTGATCCAGATATGATTCTCAG
- - - - catgtat
- - - - - - - - -gcaaatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gctgaag