Sequence
atgc intronic sequence ATGC exonic sequencegtaaaacccaataaaaggcgcctccttttcctttcctccgcctccctctcgctagcatttattgtcttgtattgttgcatacgtcgttgttcgtttaggttggatttgggttaggatttgtgtggcataatgcggtggttggaattgccttcgggagttgtggttgatggtggtgaggtttggcgcagGGACGCGTATGGATTCGCGGTGCGGCCGCAGCATCTGCAGCGTTTCCGCGAGTATGCCAAGATTTACAAG
Basic information
species | Oryza sativa |
transcript | LOC_Os03g17540.3 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os03g17540.3 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G095868_T03 (Zea mays), 3'ss of exon 1
gtaaaacccaataaaaggcgcctccttttcctttcctccgcctccctctcgctagcatttattgtcttgtattgttgcatacgtcgttgttcgtttaggttggatttgggttaggatttgtgtggcataatgcggtggttggaattgccttcgggagttgtggttgatggtggtgaggtttggcgcagGGACGCGTATGGATTCGCGGTGCGGCCGCAGCATCTGCAGCGTTTCCGCGAGTATGCCAAGATTTACAAG
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-------------------------------------------------------------------------------------cttgttcggttcc-ttgtattcgtatt--gccccgggggtgctaatgccgttgttggggttccctccgggagctgtggttgatgctcctgaggtttggcgcagGGACGCTTATGGATTCACGGTGCGGCCGCAGCATCTGCAGCGTTTCCGCGAGTACGCCAAGATTTACAAG
upper sequence: LOC_Os03g17540.3 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G154883_T02 (Zea mays), 3'ss of exon 1
gtaaaacccaataaaaggcgcctccttttcctttcctccgcctccctctcgctagcatttattgtcttgtattgttgcatacgtcgttgttcgtttaggttggatttgggttaggatttgtgtggcataatgcggtggttggaattgccttcgggagttgtggttgatggtggtgaggtttggcgcagGGACGCGTATGGATTCGCGGTGCGGCCGCAGCATCTGCAGCGTTTCCGCGAGTATGCCAAGATTTACAAG
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gtaaatcccacaaaaaggcgggtccctttgcccat-ttcgcctgcctccttttctctgctatggtctcttgttctc--------cgttccttgttt---tcatattggcctgagga-----gggggggaatgcctttgttggggttccctccgggagctgtggttgatggtcctgaggtttggcgcagGGACGCTTATGGTTTCGCGGTGCGGCCACAGCATCTGCAGCGTTTCCGCGAGTACGCCAAGATTTACAAG
upper sequence: LOC_Os03g17540.3 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G154883_T01 (Zea mays), 3'ss of exon 1
gtaaaacccaataaaaggcgcctccttttcctttcctccgcctccctctcgctagcatttattgtcttgtattgttgcatacgtcgttgttcgtttaggttggatttgggttaggatttgtgtggcataatgcggtggttggaattgccttcgggagttgtggttgatggtggtgaggtttggcgcagGGACGCGTATGGATTCGCGGTGCGGCCGCAGCATCTGCAGCGTTTCCGCGAGTATGCCAAGATTTACAAG
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-----------------------------------------------------------------------------------tctccgttccttgttttcatattggcctgagga-----gggggggaatgcctttgttggggttccctccgggagctgtggttgatggtcctgaggtttggcgcagGGACGCTTATGGTTTCGCGGTGCGGCCACAGCATCTGCAGCGTTTCCGCGAGTACGCCAAGATTTACAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ggtggttggaattgccttcgggagttgtggttgatggtggtgaggtttggcgcagGGACGCGTATGGATTCGCGGTGCGGCCGCAGCATCTGCAGCGTTTCCGCGAGTATGCCAAGATTTACAAG
ggttgat putative branch site (score: 5)
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaaacccaataaaaggcgcctccttttcctttcctccgcctccctctcgctagcatttattgtcttgtattgttgcatacgtcgttgttcgtttaggttggatttgggttaggatttgtgtggcataatgcggtggttggaattgccttcgggagttgtggttgatggtggtgaggtttggcgcagGGACGCGTATGGATTCGCGGTGCGGCCGCAGCATCTGCAGCGTTTCCGCGAGTATGCCAAGATTTACAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG