Sequence
atgc intronic sequence ATGC exonic sequencegttggattttctgcaatctgttccctagtacctggtgtctttgctattattgtaatgtaaagcaacaggaatcattttaaatttttaatagGTACTTTTGGGCGTGTTTTGGAATGCTGGGACCGTGAAACACATGAATATGTCGCAATAAAAGTTGTTCGTAGCATCCGCAAGTACAGGGATGCTGCAAT
Basic information
species | Oryza sativa |
transcript | LOC_Os01g40840.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g40840.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G366935_T09 (Zea mays), 3'ss of exon 3
-gttggattttctgcaatctgtt-----ccctagtacctggtgtctttgctattattgtaatgtaaagcaacaggaatcattttaaatttttaatagGTACTTTTGGGCGTGTTTTGGAATGCTGGGACCGTGAAACACATGAATATGTCGCAATAAAAGTTGTTCGTAGCATCCGCAAGTACAGGGATGCTGCAAT
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gttcgggttttctgcaatctgtcgtctcctcttctggtgggtatcctcgttattattctaatgaagagggctacgagttg------ggttttcgtagGTACATTTGGGCGTGTTTTGGAATGCTGGGACCGTGAAACACGTGAATATGTTGCCATAAAAGTTGTTCGCAGTATCCGCAAGTACCGTGATGCTGCAAT
upper sequence: LOC_Os01g40840.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G094039_T03 (Zea mays), 3'ss of exon 3
-gttggattttctgcaatctgtt-----ccctagtacctggtgtctttgctattattgtaatgtaaagcaacaggaatcattttaaatttttaatagGTACTTTTGGGCGTGTTTTGGAATGCTGGGACCGTGAAACACATGAATATGTCGCAATAAAAGTTGTTCGTAGCATCCGCAAGTACAGGGATGCTGCAAT
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gtttgggttttctgcaatctgtcgtctcctcttctgctgggtatctccgttattattctaatgaagagggctacgagt-----tggattttcg-tagGTACATTTGGGCGTGTTTTGGAATGCTGGGACCGTGAAACACATGAATATGTTGCCATAAAAGTTGTTCGCAGTATCCGCAAGTACCGTGATGCTGCAAT
upper sequence: LOC_Os01g40840.2 (Oryza sativa), 3'ss of exon 3
lower sequence: Vv04s0008g04220.t01 (Vitis vinifera), 3'ss of exon 3
gttggattttctgcaatctgttccct--agtacctggtgtctttgctattattgtaatgtaaagcaacaggaatcattttaaatttttaatagGTACTTTTGGGCGTGTTTTGGAATGCTGGGACCGTGAAACACATGAATATGTCGCAATAAAAGTTGTTCGTAGCATCCGCAAGTACAGGGATGCTGCAAT
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gttagctgtcaagtgctctgctgtctgcaagatcttatatttttgtgattctgct--tctatgatctcagcaa--attgctagtact--gtagGCACTTTTGGCCGGGTTTTGGAATGTTGGGATCGTGATACACGGGAATATGTTGCAATCAAGGTAGTTCGAAGCATAAGCAAGTACCGTGATGCAGCAAT
upper sequence: LOC_Os01g40840.2 (Oryza sativa), 3'ss of exon 3
lower sequence: EFJ20930 (Selaginella moellendorffii), 3'ss of exon 1
gttggattttctgcaatctgttccctagtacctggtgtctttgctattattgtaatgtaaagcaacaggaatcattttaaatttttaatagGTACTTTTGGGCGTGTTTTGGAATGCTGGGACCGTGAAACACATGAATATGTCGCAATAAAAGTTGTTCGTAGCATCCGCAAGTACAGGGATGCTGCAAT
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----------------------------------------gtgcttatagtttagtttcctttctcgttgtttac--cagagtaaatgcagGTACTTTTGGTCGCGTTTTGGAATGCTGGGACCGGAAGTATCAGGAGTTTGTGGCCGTTAAAGTTATAAGAAACGTCCCAAAATACAGAGAAGCCGCTCT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtctttgctattattgtaatgtaaagcaacaggaatcattttaaatttttaatagGTACTTTTGGGCGTGTTTTGGAATGCTGGGACCGTGAAACACATGAATATGTCGCAATAAAAGTTGTTCGTAGCATCCGCAAGTACAGGGATGCTGCAAT
ttttt CT-rich tract
aacaggaatcatttta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttggattttctgcaatctgttccctagtacctggtgtctttgctattattgtaatgtaaagcaacaggaatcattttaaatttttaatagGTACTTTTGGGCGTGTTTTGGAATGCTGGGACCGTGAAACACATGAATATGTCGCAATAAAAGTTGTTCGTAGCATCCGCAAGTACAGGGATGCTGCAAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC