Sequence
atgc intronic sequence ATGC exonic sequenceCTCCATGGGCCTCACCGTGTGCCGCACCTGGGCCTTCAACGACGGCTCCTACAACGCCCTCCAGCTCTCCCCCGGCCACTTCGACGAGCGCGTCTTCAAGgtaaccaaaaccaaacccatccattcccaaattccccagcagtaagaacgcgagatgcccactggtgcggatgctgatgcgcgcgcgcgtgcag
Basic information
species | Oryza sativa |
transcript | LOC_Os01g54300.1 |
intron # | 1 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g54300.1 (Oryza sativa), 5'ss of exon 1
lower sequence: GRMZM2G140201_T01 (Zea mays), 5'ss of exon 1
CTCCATGGGCCTCACCGTGTGCCGCACCTGGGCCTTCAACGACGGCTCCTACAACGCCCTCCAGCTCTCCCCCGGCCACTTCGACGAGCGCGTCTTCAAGgtaaccaaaaccaaacccatccattcccaaattccccagcagtaagaacgcgagatgcccactggtgcgga-tgct-gatgcgcgcgcgcgtg-cag
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CGAGATGGGCCTCACCGTGTGCCGCTCCTGGGCGTTCAATGACGGCGCCTACAACGCCCTCCAGGTCTCCCCCGGCCACTTCGACGAGCGCGTCTTCAAGgtaaaaaaaaggaaacc-gccccccgttaattttagc--cgaaaatgccgcgccttctggggtggtgctaactgcttaacaatggagtgcgcgtcag
upper sequence: LOC_Os01g54300.1 (Oryza sativa), 5'ss of exon 1
lower sequence: PP1S41_160V6.1 (Physcomitrella patens), 5'ss of exon 1
CTCCATGGGCCTCACCGTGTGCCGCACCTGGGCCTTCAACGACGGCTCCTACAACGCCCTCCAGCTCTCCCCCGGCCACTTCGACGAGCGCGTCTTCAAGgtaaccaaaaccaaacccatccattcccaaattccccagcagtaagaacgcgagatgcccactggtgcggatgctgatgcgcgcgcgcgtgcag---------
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TGCACTGGGGCTCACCGTGTGCCGCACCTGGGCCTTCAACGACGGCACCCACCTTGCTTTGCAGATGTCGCCGGGGAATTATGACGAGAATGTGTTTCAGgtg---gaattcggaccttgctttttggatctctctctctctctctctctctctctctctttttgctgttttgttcacgcttctccttgttgaggttaggtcg
upper sequence: LOC_Os01g54300.1 (Oryza sativa), 5'ss of exon 1
lower sequence: PP1S53_47V6.1 (Physcomitrella patens), 5'ss of exon 3
CTCCATGGGCCTCACCGTGTGCCGCACCTGGGCCTTCAACGACGGCTCCTACAACGCCCTCCAGCTCTCCCCCGGCCACTTCGACGAGCGCGTCTTCAAGgtaa--ccaaaaccaaacccatccattcccaaattccccagcagtaagaacgcgagatgcccactggtgcggatgctgatgcgcgcgcgcgtgcag--------
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GGCGCTCGGGCTCACCTTGTGCCGCACCTGGGCCTTCAACGACGACAGCTACCTCGCTTTGCAGACGTTGCCGGGGACATACGACGAGAAGGTTTTCAAGgtgagttttcgagcttcctcttcgatttgcaa-tcctttgctagtacgg-ttcaagcttcttttcggc-tgtttgttggt-tttatggtcgagcaagcttctggMapped 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|58613302|gb|CK041014.1|CK041014EST: ACAACGCCCTCCAGCTCTCCCCCGGCCACTTCGACGAGCGCGTCTTCAAG GCGCTGGACCGGGTGGTGGCGGAGGCGGGGGAGCACGGCGTGCGGCTGATC
genomic: ACAACGCCCTCCAGCTCTCCCCCGGCCACTTCGACGAGCGCGTCTTCAAGgtaaccaaaa ... gcgcgtgcagGCGCTGGACCGGGTGGTGGCGGAGGCGTCGGAGCACGGCGTGCGGCTGATC
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
CTCCATGGGCCTCACCGTGTGCCGCACCTGGGCCTTCAACGACGGCTCCTACAACGCCCTCCAGCTCTCCCCCGGCCACTTCGACGAGCGCGTCTTCAAGgtaaccaaaaccaaacccatccattcccaaattccccagcagtaagaacgcgagatgcccactggtgcggatgctgatgcgcgcgcgcgtgcag
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