Sequence
atgc intronic sequence ATGC exonic sequencegtatgtgtctttcctatatagcagatactatagcatttttaatattttttaaaggcagtatttcttatgttctacaagtgtgtaataaaactcttcatatttgtcttcttgtgtccagAAATTGTATGAGCTTGTTGTTCGCCATTTCCTTGCTTGTTGCTCCCAACCTGCAGTTGGAGCTGAAACAACTGTGGAAATTGACATTGCTGGTGAACAGT
Basic information
species | Oryza sativa |
transcript | LOC_Os03g06900.1 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os03g06900.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G470438_T05 (Zea mays), 3'ss of exon 1
-----------------------------gtatgtgtctttcctatatagcagata---ctatagcatttttaa-tattttttaaaggcagtatttcttatgttctacaagtgtgtaataaaactcttcatatttgtcttcttgtgtccagAAATTGTATGAGCTTGTTGTTCGCCATTTCCTTGCTTGTTGCTCCCAACCTGCAGTTGGAGCTGAAACAACTGTGGAAATTGACATTGCTGGTGAACAGT
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gtgaaagaaactggagtccagaccacactgtatgttgtgtttctgaacaactgagaaatcaagtgccttttcaagtgttgtttataaactttcctataca-actctaataattttttgtttatcttgttatatctg-------gcgtccagAGATTGTATGAGTTTGTTGTCCGACATTTCCTTGCATGTTGCTCTCAACCGGCCGTTGGAGCTGAAACAACTGTGGAAATTGACATAGCTGGTGAACAGT
upper sequence: LOC_Os03g06900.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G470438_T04 (Zea mays), 3'ss of exon 1
gtatgtgtctttcctatatagcagata---ctatagcatttttaa-tattttttaaaggcagtatttcttatgttctacaagtgtgtaataaaactcttcatatttgtcttcttgtgtccagAAATTGTATGAGCTTGTTGTTCGCCATTTCCTTGCTTGTTGCTCCCAACCTGCAGTTGGAGCTGAAACAACTGTGGAAATTGACATTGCTGGTGAACAGT
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gtatgttgtgtttctgaacaactgagaaatcaagtgccttttcaagtgttgtttataaactttcctataca-actctaataattttttgtttatcttgttatatctg-------gcgtccagAGATTGTATGAGTTTGTTGTCCGACATTTCCTTGCATGTTGCTCTCAACCGGCCGTTGGAGCTGAAACAACTGTGGAAATTGACATAGCTGGTGAACAGT
upper sequence: LOC_Os03g06900.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GLYMA06G16200.1 (Glycine max), 3'ss of exon 9
gtatgtgtctttcctatatagcagatactatagcatttttaatattttttaaaggcagtatttcttatgttctacaagtgtgtaataaaactcttcatatttgtcttcttgtgtccagAAATTGTATGAGCTTGTTGTTCGCCATTTCCTTGCTTGTTGCTCCCAACCTGCAGTTGGAGCTGAAACAACTGTGGAAATTGACATTGCTGGTGAACAGT
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-------------------gtcagacatgat----tccttactagtcttt-----ctacctatattgcattttgct--ttgacattcatattcatcat--ttctcaaattac-cacagAAACTGTATGAGCTTGTTGTTCGCCACTTTTTGGCATGTGTCTCAAAGCCTGCTTTAGGAGCTGAAACCACTGTTGAAATTAATATTGCTGGTGAATTAT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cttatgttctacaagtgtgtaataaaactcttcatatttgtcttcttgtgtccagAAATTGTATGAGCTTGTTGTTCGCCATTTCCTTGCTTGTTGCTCCCAACCTGCAGTTGGAGCTGAAACAACTGTGGAAATTGACATTGCTGGTGAACAGT
tttgtcttctt CT-rich tract
tgtaataaaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgtgtctttcctatatagcagatactatagcatttttaatattttttaaaggcagtatttcttatgttctacaagtgtgtaataaaactcttcatatttgtcttcttgtgtccagAAATTGTATGAGCTTGTTGTTCGCCATTTCCTTGCTTGTTGCTCCCAACCTGCAGTTGGAGCTGAAACAACTGTGGAAATTGACATTGCTGGTGAACAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA