Sequence
atgc intronic sequence ATGC exonic sequencegtattaaagatgcatatagaattcacttgtcatttgttgtaatgttttaattgtaaaatgtaataataagcgtattggtatatcatgtatccataataatatgctccctttacagACTTGGATTTCTCATTTCTCGAGATGAACCCATTTACCATCGTGAATGGAGAGCCGTATCCTCTGGACATGAGAGGAGAATTAGATGACACAGCAGCTTT
Basic information
species | Oryza sativa |
transcript | LOC_Os11g47120.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os11g47120.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G340672_T01 (Zea mays), 3'ss of exon 3
gtattaaagatgcatatagaattcacttgtcatttgttgtaatgttttaattgtaaaatgtaataataa-gcgtattggtatatcatgtatccataataat-atgctccctttacagACTTGGATTTCTCATTTCTCGAGATGAACCCATTTACCATCGTGAATGGAGAGCCGTATCCTCTGGACATGAGAGGAGAATTAGATGACACAGCAGCTTT---------------
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-----------------------------------gctgtagtgaattaa---gaaattttcatgtcactatattttcttattttccatgtttataataattatgctccatctccatac--ggatttctcatttcttgagATGAATCCGTTCGCCATGGTCAACGGGGAGCCATATCCTCTGGACATCAGAGGAGAACTAGATGACACAACAGCCTTCAAAAACTTCAAGAA
upper sequence: LOC_Os11g47120.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G072216_T01 (Zea mays), 3'ss of exon 3
gtattaaagatgcatatagaattcacttgtcatttgttgtaatgttttaattgtaaaatgtaataataagcgtattggtatatcatgtatccataataat-atgctccctttacagACTTGGATTTCTCATTTCTCGAGATGAACCCATTTACCATCGTGAATGGAGAGCCGTATCCTCTGGACATGAGAGGAGAATTAGATGACACAGCAGCTTT------
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---------------ggaatgtttatttgcctgctgtagtgaattaagaaatttttcatgtcactata----ttttcttatttgccatgtttataataattatgctccatctccatac--ggATTTCTCATTTCTTGAGATGAATCCGTTCGCCATGGTCAACGGGGAGCCATATCCTCTGGACATCAGAGGAGAACTAGATGACACAACAGCCTTCAAAAA
upper sequence: LOC_Os11g47120.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G107082_T01 (Zea mays), 3'ss of exon 4
gtattaaagatgcatatagaattcacttgtcatttgttgtaatgttttaattgtaaaatgtaataataagcgtattggtatatcatgtatccataataatatgctccctttacagACTTGGATTTCTCATTTCTCGAGATGAACCCATTTACCATCGTGAATGGAGAGCCGTATCCTCTGGACATGAGAGGAGAATTAGATGACACAGCAGCTTT
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gtaccgcagatttgggaattttttatttgcca---gctgtagtgaattaagaattgctcatgtcgctatatctcctgagttgccatgttgataaga-aatatgctccatctccagACTTGGATTTCTCATTTCTTGAGATGAATCCGTTCACCATGGTCAATGGGGAGCCATATCCTCTGGACATGAGAGGAGAACTAGATGACACAGCAGCTTT
upper sequence: LOC_Os11g47120.1 (Oryza sativa), 3'ss of exon 4
lower sequence: AT1G09430.1 (Arabidopsis thaliana), 3'ss of exon 5
gtattaaagatgcatatagaattcacttgtcatttgttgtaatgttttaattgtaaaatgtaataataagcgtattggtatatcatgtatccataataatatgctccctttacagACTTGGATTTCTCATTTCTCGAGATGAACCCATTTACCATCGTGAATGGAGAGCCGTATCCTCTGGACATGAGAGGAGAATTAGATGACACAGCAGCTTT
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-----gtatgagtatattagattaggccacttcttgactt--tgctctgatt-cgagatctctcaagga-catcttcttat------tatc--tacttgtgtgtttc-tttaaagATTTGGATTTCAGTTTTATGGAGATGAATCCTTTTACACTAGTCGATGGAGAACCATTCCCTCTGGATATGAGAGGAGAATTAGATGACACTGCTGCCTT
upper sequence: LOC_Os11g47120.1 (Oryza sativa), 3'ss of exon 4
lower sequence: Vv14s0060g00550.t01 (Vitis vinifera), 3'ss of exon 5
gtattaaagatgcatatagaattcacttgtcatttgttgtaatgttttaattgtaaaatgtaataataagcgtattggtatatcatgtatccataataatatgctccctttacagACTTGGATTTCTCATTTCTCGAGATGAACCCATTTACCATCGTGAATGGAGAGCCGTATCCTCTGGACATGAGAGGAGAATTAGATGACACAGCAGCTTT
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------------tgtgtataattt--ttgtt-ttcattcttctattttttgtttaacattttgttgagaacattgtcattgttcacttctaactgttgtaccattctctccacagATCTTGACTTCAGTTTCCTAGAGATGAACCCATTTACCCTGGTGAATGGGGAACCATACCCACTGGATATGAGGGGAGAATTGGATGATACTGCTGCTTT
upper sequence: LOC_Os11g47120.1 (Oryza sativa), 3'ss of exon 4
lower sequence: EFJ27687 (Selaginella moellendorffii), 3'ss of exon 5
gtattaaagatgcatatagaattcacttgtcatttgttgtaatgttttaattgtaaaatgtaataataagcgtattggtatatcatgtatccataataatatgctccctttacagACTTGGATTTCTCATTTCTCGAGATGAACCCATTTACCATCGTGAATGGAGAGCCGTATCCTCTGGACATGAGAGGAGAATTAGATGACACAGCAGCTTT
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----------------------------------------------------gtgcactgccttacgaaacagcctgcattcttattta--caaggcga-atttttctttttcagACTTGGACTTCTCTCTGATCGAGATGAATCCCTTCACTTTGGTGAATGGCGAACCGTATCCTCTGGACATGCGTGGAGAGTTGGATGACACAGCTCTCTT
upper sequence: LOC_Os11g47120.1 (Oryza sativa), 3'ss of exon 4
lower sequence: EFJ37257 (Selaginella moellendorffii), 3'ss of exon 5
gtattaaagatgcatatagaattcacttgtcatttgttgtaatgttttaattgtaaaatgtaataataagcgtattggtatatcatgtatccataataatatgctccctttacagACTTGGATTTCTCATTTCTCGAGATGAACCCATTTACCATCGTGAATGGAGAGCCGTATCCTCTGGACATGAGAGGAGAATTAGATGACACAGCAGCTTT
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----------------------------------------------------gtgcactgccttatgaaacagcctgcattcttattta--caaggcga-atttttctttttcagACTTGGACTTCTCTCTGATCGAGATGAATCCCTTCACTTTGGTGAATGGCGAACCGTATCCTCTGGACATGCGTGGAGAGTTGGATGACACAGCTCTCTT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.taataataagcgtattggtatatcatgtatccataataatatgctccctttacagACTTGGATTTCTCATTTCTCGAGATGAACCCATTTACCATCGTGAATGGAGAGCCGTATCCTCTGGACATGAGAGGAGAATTAGATGACACAGCAGCTTT
tgctcccttt CT-rich tract
tatccataataatat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtattaaagatgcatatagaattcacttgtcatttgttgtaatgttttaattgtaaaatgtaataataagcgtattggtatatcatgtatccataataatatgctccctttacagACTTGGATTTCTCATTTCTCGAGATGAACCCATTTACCATCGTGAATGGAGAGCCGTATCCTCTGGACATGAGAGGAGAATTAGATGACACAGCAGCTTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT