Sequence
atgc intronic sequence ATGC exonic sequenceCGAATGTAGTGAAGCATCTGATTCTCATTCAGAAATGTCAAATGGGGTTTCAGAGGCTGCATCTTTGGAGCAGCGCCGAGCTTACAAGATGGAACTTCAGgtggatgttattccatagttatttctatatgtgtagttgttggtgggaatttgctggatgctgtcctttgccgtatgactcgctgctgttctgttgcatatttgattttatccatttacttatctgtattggtcgattgatttatatgaatggcag
Basic information
species | Oryza sativa |
transcript | LOC_Os03g14260.2 |
intron # | 3 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os03g14260.2 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G058870_T01 (Zea mays), 5'ss of exon 3
CGAATGTAGTGAAGCATCTGATTCTCATTCAGAAATGTCAAATGGGGTTTCAGAGGCTGCATCTTTGGAGCAGCGCCGAGCTTACAAGATGGAACTTCAGgtggatgttattcca-tagttatttctatatgtgtagttgttggtgggaatttgctggatgctgtcctttgccgtatgactcgctgctgttctgttgcatatttgattttatccatttacttatctgtat-tggtcgattgatttata-tgaatggcag
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TGAGTCTAGTGAAGCATCTGATTCACATTCTGAGTTATCGAATGGAATTTCAGAGGCAGCATCATTGGAACAACGTCGAGCTTACAAGATAGAGCTTCAGgtggatgatactatactagttattt---tgctttcaattcttagcgggaatgtgcttg----------ttgctatacaacttgctgcatctccagttctcgattgtttttgttgattcgtttcttcttatatggttgattaattattgctgaataacag
upper sequence: LOC_Os03g14260.2 (Oryza sativa), 5'ss of exon 3
lower sequence: AT1G01960.1 (Arabidopsis thaliana), 5'ss of exon 3
CGAATGTAGTGAAGCATCTGATTCTCATTCAGAAATGTCAAATGGGGTTTCAGAGGCTGCATCTTTGGAGCAGCGCCGAGCTTACAAGATGGAACTTCAGgtggatgttattccatagtt-atttctatatgtgtagttgttggtgggaatttgctggatgctgtcctttgccgtatgactcgctgctgttctgttgcatatttgattttatccatttacttatctgtattggtcgattgatttatatgaatggcag
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TGGTGGTTTTGAAAGATCAGACTCTCAGTCTGAATTGTCCAGTGGGAATTCTGATGCCTTAGCAATAGAGCAGCGCCGAGCTTACAAGCTTGAACTTCAGgtaaaagtttacctaaagtttgattcagcgctcattgacttttgtctcagtctttcagcta--aaacctgattagctgatttgtttttatta-atggcag---------------------------------------------------------Mapped 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|88969992|gb|CI383494.1|CI383494EST: CAGAGGCTGCATCTTTGGAGCAGCGCCGAGCTTACAAGATGGAACTTCAG GAGGGTATCTCTCTATTTAATCGAAAGCCCAGGAAGGGAATTGAGTTCCTA
genomic: CAGAGGCTGCATCTTTGGAGCAGCGCCGAGCTTACAAGATGGAACTTCAGgtggatgtta ... tgaatggcagGAGGGTATCTCTCTATTTAATCGAAAGCCCAGGAAGGGAATTGAGTTCCTA
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
CGAATGTAGTGAAGCATCTGATTCTCATTCAGAAATGTCAAATGGGGTTTCAGAGGCTGCATCTTTGGAGCAGCGCCGAGCTTACAAGATGGAACTTCAGgtggatgttattccatagttatttctatatgtgtagttgttggtgggaatttgctggatgctgtcctttgccgtatgactcgctgctgttctgttgcatatttgattttatccatttacttatctgtattggtcgattgatttatatgaatggcag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA