Sequence
atgc intronic sequence ATGC exonic sequencegtagttttgttttctctgtttcagatctgactattttgattcctcaaattgcatcatgaaatcttccctgattgttatttcctactcttgtgttgctaaaataaaaacccaacatttaaccaaaacatcagtttggtgatttgttgctgacatattttttcataccgcagTTGTTAGTGTGGGCGCAGCTATGTTCTTGTTCCAACAGCTTGCCGGTATAAATGCTGTTGTATATTACTCTACATCGGTGTTCCGCAGTGCAGGCATTGC
Basic information
species | Oryza sativa |
transcript | LOC_Os01g04190.4 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g04190.4 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G153704_T01 (Zea mays), 3'ss of exon 13
gtagttttgttttctctgtttcagatctgactattttgattcctcaaattgcatcatgaaatcttccctgattgttatttcctactcttgtgttgctaaaataaaaacccaacatt-taaccaaaacatcagtttggtgatttgttgctgacatattttttcataccgcagTTGTTAGTGTGGGCGCAGCTATGTTCTTGTTCCAACAGCTTGCCGGTATAAATGCTGTTGTATATTACTCTACATCGGTGTTCCGCAGTGCAGGCATTGC
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----------------------------------------------------------------gttttgata--tgtgaattgcattcaacctaaaacgtcaatgaatcgatactgtggtggagacccta---caatacatgttttctgatatatgtct-cat-ttgcagTTGTGAGTGTGGGGGCAGCACTGTTTTTGTTCCAGCAGCTTGCTGGTATAAACGCTGTTGTATATTACTCTACATCGGTGTTCCGTAGTGCAGGCATTGC
upper sequence: LOC_Os01g04190.4 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G098011_T02 (Zea mays), 3'ss of exon 9
gtagttttgttttctctgtttcagatctgactattttgattcctcaaattgcatcatgaaatcttccctgattgttatttcctactcttgtgttgctaaaataaaaacccaacatt-taaccaaaacatcagtttggtgatttgttgctgacatattttttcataccgcagTTGTTAGTGTGGGCGCAGCTATGTTCTTGTTCCAACAGCTTGCCGGTATAAATGCTGTTGTATATTACTCTACATCGGTGTTCCGCAGTGCAGGCATTGC
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----------------------------------------------------------------gttttgata--tgttgattgcaaacaacctaaaacgtcaaagaattgatactatggtggagacgcca--caagacatgt-tttctgatatatcttt-cat-ttgcagTTGTGAGTGTGGGGGCAGCACTGTTTTTGTTCCAGCAGCTTGCTGGTATAAACGCTGTTGTATATTACTCTACATCGGTGTTCCGTAATGCAGGCATTAC
upper sequence: LOC_Os01g04190.4 (Oryza sativa), 3'ss of exon 9
lower sequence: Vv14s0006g02720.t01 (Vitis vinifera), 3'ss of exon 9
gtagttttgttttctctgtttcagatctgactattttgattcctcaaattgcatcatgaaatcttccctgattgttatttcctactcttgtgttgctaaaataaaaacccaacatttaaccaaaacatcagtttggtgatttgttgctgacatattttttcataccgcagTTGTTAGTGTGGGCGCAGCTATGTTCTTGTTCCAACAGCTTGCCGGTATAAATGCTGTTGTATATTACTCTACATCGGTGTTCCGCAGTGCAGGCATTGC
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---------------------------------------------------------------------aggttcaattcccttgcaagttgctgctatacttgcagtcatgctttctggtgcaattatgttgaaagcagatttttatgacacatgcatct-tgctgcagTTGTGAGTGTTGGCGCAGCACTTTTCTTGTTCCAACAGTTGGCCGGCATAAATGCTGTGGTGTACTATTCAACATCTGTGTTCCGCAGTGCTGGAATTGC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttaaccaaaacatcagtttggtgatttgttgctgacatattttttcataccgcagTTGTTAGTGTGGGCGCAGCTATGTTCTTGTTCCAACAGCTTGCCGGTATAAATGCTGTTGTATATTACTCTACATCGGTGTTCCGCAGTGCAGGCATTGC
tgctgac putative branch site (score: 2)
tattttttc CT-rich tract
acatattttttcata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtagttttgttttctctgtttcagatctgactattttgattcctcaaattgcatcatgaaatcttccctgattgttatttcctactcttgtgttgctaaaataaaaacccaacatttaaccaaaacatcagtttggtgatttgttgctgacatattttttcataccgcagTTGTTAGTGTGGGCGCAGCTATGTTCTTGTTCCAACAGCTTGCCGGTATAAATGCTGTTGTATATTACTCTACATCGGTGTTCCGCAGTGCAGGCATTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT