Sequence
atgc intronic sequence ATGC exonic sequence...tattaaagcaacatggcttctttttttttgtgagtattcatgcaaccatcgtaatcttgacgtgtaataatttggcttattgctatttgctacatcgcagAGGACCTGGACAAGCTGAGGGAGATGGAGATGTTCGGCGAGGACGGCCGGGACGGCGTGTGGACGGTGATGGCGAACGTGACGGACCCCGAGAGCCTGCA
Basic information
species | Oryza sativa |
transcript | LOC_Os01g45200.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g45200.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G029547_T01 (Zea mays), 3'ss of exon 1
tattaaagc-aacatggcttctttttttttgtgagt--att-catgcaaccatcgtaatcttgacgtgtaataatttggcttattgctatttgctacatcgcagAGGACCTGGACAAGCTGAGGGAGATGGAGATGTTCGGCGAGGACGGCCGGGACGGCGTGTGGACGGTGATGGCGAACGTGACGGACCCCGAGAGCCTGCA
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-gtggatgcgaatcccgattcagattgctagtgtttcaattatatttggttctc-tgagcgtgaagtctgaca-tgcggatcggtgggttctgtttt-tggcagAGGACATGGACAAGCTGCGGGAGATGGAGATGTTCGGCGACGACGGCAGGGACGGAGTGTGGACGGTGATGGCGAACGTGATGGACCCGGAGAGCCTGCA
upper sequence: LOC_Os01g45200.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G179685_T03 (Zea mays), 3'ss of exon 1
tattaaagcaacatggcttctttttttttgtgagtattcatgcaaccatcgtaatcttgacgtgtaa--taatttggcttattgctatttgctacatcg--cagAGGACCTGGACAAGCTGAGGGAGATGGAGATGTTCGGCGAGGACGGCCGGGACGGCG---TGTGGACGGTGATGGCGAACGTGACGGACCCCGAGAGCCTGCA
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----gttctgccgtgtcgtccgtcactagcgaatccccccggtcactcccaggtttcgagcgtttcggtttatttgatctctaagtacgtgtcttggcgtgcagAGGACATGGACAAGCTGCGGGAGATGGAGATGTTCGGCGAGGACGGCCGGGATGGGGGGGTGTCGACGGTGATGGCGAACGTGATGGACCCGGACGGCCT--- atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ccatcgtaatcttgacgtgtaataatttggcttattgctatttgctacatcgcagAGGACCTGGACAAGCTGAGGGAGATGGAGATGTTCGGCGAGGACGGCCGGGACGGCGTGTGGACGGTGATGGCGAACGTGACGGACCCCGAGAGCCTGCA
tcttgac putative branch site (score: 3)
tgtaataattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tattaaagcaacatggcttctttttttttgtgagtattcatgcaaccatcgtaatcttgacgtgtaataatttggcttattgctatttgctacatcgcagAGGACCTGGACAAGCTGAGGGAGATGGAGATGTTCGGCGAGGACGGCCGGGACGGCGTGTGGACGGTGATGGCGAACGTGACGGACCCCGAGAGCCTGCA
- - aaagcaa
- - - - - - - ggcttct
- - - - - - - - - - - - - - - - - - ttcatgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgctatt