Sequence
atgc intronic sequence ATGC exonic sequencegtgatcaatcttatcttgtaaattcatcacttgatgcagttctatgccaacttcctatattcatgtttttttcatttttcagGAAGAGGAGTTGATCTTAATAGAAATTGGAGTGTTGATTGGGGAAAGAAGGAAAAG
Basic information
species | Oryza sativa |
transcript | LOC_Os02g02710.2 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os02g02710.3 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G006069_T02 (Zea mays), 3'ss of exon 4
gtgatcaatct-tatcttgtaaattcatcacttgatgcagtt-ctatgccaacttcctatattcatgtttttttcattttt-cagGAAGAGGAGTTGATCTTAATAGAAATTGGAGTGTTGATTGGGGAAAGAAGGAAAAG
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gtgattggtccatttcttacaaattaatcactacaggcagttgttatgccaacatgttttttatatatatatttcccttcggcagGAAGAGGAGTTGATCTCAACAGAAATTGGAGTGTTGACTGGGGAAAGAAAGAAAAA
upper sequence: LOC_Os02g02710.3 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA06G02070.1 (Glycine max), 3'ss of exon 4
gtgatcaatcttatcttgtaaattcatcacttgatgcagttctatgccaacttcctatattcatg--tttttttcatttttcagGAAGAGGAGTTGATCTTAATAGAAATTGGAGTGTTGATTGGGGAAAGAAGGAAAAG
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gtattgtatttctcctt-taaaatcgtcagttaa----atgattgactagctttgaaaatgcctgagttttttttatgtggcagGTAGAGGAGTTGATCTCAACCGAAATTGGAGTGTAGATTGGGGAAAAAAGGAGAAG
upper sequence: LOC_Os02g02710.3 (Oryza sativa), 3'ss of exon 5
lower sequence: AT5G42320.1 (Arabidopsis thaliana), 3'ss of exon 5
gtgatcaatcttatcttgtaaattcatcact-tgatgcagttctatgccaacttcctatattcatgtttttttcatttttcagGAAGAGGAGTTGATCTTAATAGAAATTGGAGTGTTGATTGGGGAAAGAAGGAAAAG
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gtaaccatatttgagtctccattacatgattatgactgtgttttgttttgtattttatcttttaacatatctgtaaatcacagGAAGAGGAGTTGACCTGAACCGAAATTGGGGTGTTGACTGGGGCAAGAAAGAAAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cacttgatgcagttctatgccaacttcctatattcatgtttttttcatttttcagGAAGAGGAGTTGATCTTAATAGAAATTGGAGTGTTGATTGGGGAAAGAAGGAAAAG
acttgat putative branch site (score: 5)
ttcatgtttttttcat putative PPT
tatattcatgtttttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgatcaatcttatcttgtaaattcatcacttgatgcagttctatgccaacttcctatattcatgtttttttcatttttcagGAAGAGGAGTTGATCTTAATAGAAATTGGAGTGTTGATTGGGGAAAGAAGGAAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA