Sequence
atgc intronic sequence ATGC exonic sequencegtaagtatacttgcaacttccattcatgtggctttcattcaaagtccaagctacccacgataccatgtattttgtgctattgtataattaaactggattttacaattttagcatcgaacatctgtaatcctagacttttcttcacaaatgcttatttgttggttctgtaactttaaccactctatgattttgtgctccagAAAGTTGAAACCAGAGTGCGGATTCTGGCTGATCTAAGGGAGCTTGCTTCAGCTGAGAGTCTGGATAGTTTTACTCTCATTTATACAAATATTCTGGAAC
Basic information
species | Oryza sativa |
transcript | LOC_Os02g51430.2 |
intron # | 21 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os02g51430.1 (Oryza sativa), 3'ss of exon 22
lower sequence: GRMZM2G070045_T01 (Zea mays), 3'ss of exon 17
gtaagtatacttgcaacttccattcatgtggctttcattcaaagtccaagctacccacgataccatgtattttgtgctattgtataattaaactggattttacaattttagcatcgaacatctgtaatcctagacttttcttcacaaatgcttatttgttggttctg-taactt-taaccactctatgattttg----tgctccagAAAGTTGAAACCAGAGTGCGGATTCTGGCTGATCTAAGGGAGCTTGCTTCAGCTGAGAGTCTGGATAGTTTTACTCTCATTTATACAAATATTCTGGAAC
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----------------------------------------------------------------------------------------------------------ttggtcattgaacacccagtgtcctagaaagatatttcggagttatgatgcttctgtattactaacttgtaactgaaaagttgtctttacactgatccagAAAGTTGAAAGCAGAGTGCGGATTCTGGCAGATATGAGGGAGCTAGCTTCAGCTGAGAGTTTGGATAGCTTTACTCTCATTTACACTAATATACTGGAAC
upper sequence: LOC_Os02g51430.1 (Oryza sativa), 3'ss of exon 22
lower sequence: GRMZM2G161553_T01 (Zea mays), 3'ss of exon 4
gtaagtatacttgcaacttccattcatgtggctttcattcaaagtccaagctacccacgataccatgtattttgtgctattgtataattaaactggattttacaattttagcatcgaacatctgtaatcctagacttttcttcacaaatgcttatttgttggttctgtaactttaaccactctatgattttgtgctccagAAAGTTGAAACCAGAGTGCGGATTCTGGCTGATCTAAGGGAGCTTGCTTCAGCTGAGAGTCTGGATAGTTTTACTCTCATTTATACAAATATTCTGGAAC
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--------------------------------------------------------------------------------ggtgtccttgaac----acccattgtactagaa--agacatttcggatgtatgatgcttctgtat---tactaact---tggaactgaaaagttg-----tatttacacttat---ccagAAAGTTGAAAGTAGAGTGCGGATTCTGGCAGATATGAGAGATCTAGCTTCAGCTGGGAGTTTGGATAGCTTTACTCTCATTTTCACAAATATACTGGAAC
upper sequence: LOC_Os02g51430.1 (Oryza sativa), 3'ss of exon 22
lower sequence: GLYMA03G03120.2 (Glycine max), 3'ss of exon 23
gtaagtatacttgcaacttccattcatgtggctttcattcaaagtccaagctacccacgataccatgtattttgtgctattgtataattaaactggattttacaattttagcatcgaacatctgt-aatcctagacttttcttcacaaatgcttatttgttggttctgtaactttaaccactctatgattttgtgctccagAAAGTTGAAACCAGAGTGCGGATTCTGGCTGATCTAAGGGAGCTTGCTTCAGCTGAGAGTCTGGATAGTTTTACTCTCATTTATACAAATATTCTGGAAC
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------------------------------------------------------------------gtaagttac-cttttagacattttg--ttactgttgct-ctctaacatcgatattgtgccagttccgaatctgttaatgttggcacactctgcccaagtttcttactcgaat--ttccttcatttgga---ttagAAAGTTGAAAACAGAGTGAGTGTACTTAGCGACTTGAGGGAGCTTGCTTCAGCAGAGAGCCTGGATACCTTTACACTCATCTATACAAATATACTCGAACMapped 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|87031003|gb|CI270151.1|CI270151EST: TTGATGAAGAAGTGCTTATGGATTTTTTCAGAGAACACATTAATGTGACA AAAGTTGAAACCAGAGTGCGGATTCTGGCTGATCTAAGGGAGCTTGCTTCA
genomic: TTGATGAAGAAGTGCTTATGGATTTTTTCAGAGAACACATTAATGTGACAgtaagtatac ... tgtgctccagAAAGTTGAAACCAGAGTGCGGATTCTGGCTGATCTAAGGGAGCTTGCTTCA
EST:
gi|86482093|gb|CI124726.1|CI124726EST: TTGATGAAGAAGTGCTTATGGATTTTTTCAGAGAACACATTAATGTGACC AAAGTTGAAACCAGAGTTCGGATTCTGGCTGATCTAAGGGAGCTTGCTTCA
genomic: TTGATGAAGAAGTGCTTATGGATTTTTTCAGAGAACACATTAATGTGACAgtaagtatac ... tgtgctccagAAAGTTGAAACCAGAGTGCGGATTCTGGCTGATCTAAGGGAGCTTGCTTCA
EST:
gi|86855814|gb|CI271033.1|CI271033EST: TTGATGAAGAAGTGCTTATGGATTTTTTCAGAGAACACATTAATGTGACA AAAGTTGAAACCAGAGTGCGGATTCTGGCTGATCTAAGGGAGCTTGCTTCA
genomic: TTGATGAAGAAGTGCTTATGGATTTTTTCAGAGAACACATTAATGTGACAgtaagtatac ... tgtgctccagAAAGTTGAAACCAGAGTGCGGATTCTGGCTGATCTAAGGGAGCTTGCTTCA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aaatgcttatttgttggttctgtaactttaaccactctatgattttgtgctccagAAAGTTGAAACCAGAGTGCGGATTCTGGCTGATCTAAGGGAGCTTGCTTCAGCTGAGAGTCTGGATAGTTTTACTCTCATTTATACAAATATTCTGGAAC
ctttaac putative branch site (score: 3)
ttatttgtt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagtatacttgcaacttccattcatgtggctttcattcaaagtccaagctacccacgataccatgtattttgtgctattgtataattaaactggattttacaattttagcatcgaacatctgtaatcctagacttttcttcacaaatgcttatttgttggttctgtaactttaaccactctatgattttgtgctccagAAAGTTGAAACCAGAGTGCGGATTCTGGCTGATCTAAGGGAGCTTGCTTCAGCTGAGAGTCTGGATAGTTTTACTCTCATTTATACAAATATTCTGGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA