Sequence
atgc intronic sequence ATGC exonic sequence...tcgctgcagtgcatctagaaagttttactcaacacacccaaaatgtttggctagatttcaattcaatgttgtttgcttggttttggttgcaacttgcaagGATCCACGAACGGAGAACGACCCGTACATGGGGTTCATCTACACGACGTTCCAGGAGCGCGCCACCTCCATCTCCCACGGCAACACGGCGCGCCACGCGG
Basic information
species | Oryza sativa |
transcript | LOC_Os02g30200.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os02g30200.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G027673_T02 (Zea mays), 3'ss of exon 2
tcgctgcagtgcatctagaaagttttactcaacacacccaaaatgtttggctagatttcaattcaatgt-tgtttgcttggttttggttgcaacttgca-agGATCCACGAACGGAGAACGACCCGTACATGGGGTTCATCTACACGACGTTCCAGGAGCGCGCCACCTCCATCTCCCACGGCAACACGGCGCGCCACGCGG
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-----------------gtgagtaattatttac---ctttaaatgatggg-tggttgatgcatgaacgtacgcacgcatgacgtacgtacaaacaaatgcagGATCCCAAGACGGAGACGAACCCGTACATGGGCTTCGTCTACACGTCGTTCCAGGAGCGCGCCACCTTCATCTCCCACGGCAACACGGCGCGCCACGCCA
upper sequence: LOC_Os02g30200.1 (Oryza sativa), 3'ss of exon 3
lower sequence: EFJ20422 (Selaginella moellendorffii), 3'ss of exon 6
tcgctgcagtgcatctagaaagttttactcaacacacccaaaatgtttggctagatttcaattcaatgttgtttgcttggttttggttgcaacttgcaagGATCCACGAACGGAGAACGACCCGTACATGGGGTTCATCTACACGACGTTCCAGGAGCGCGCCACCTCCATCTCCCACGGCAACACGGCGCGCCACGCGG
| | | ||| | | | | | || |||| | | ||||| | |||||| |||||| | || |||||| | || || | |||||||||||||| ||||||||||| |||||| ||||||| ||||||||||| || |||||| ||
-----------------------------gtaaagagccagagtttcttctttctcgggaactcaaaa------gttcggtttccatc----cttgca-gGATCCCCAGACCGAGAACAATCCATATCTCGGGTTCATCTACACCTTCTTCCAGGAGCGAGCCACCGCCATCTCTCACGGCAACACTGCTCGCCACACGA
upper sequence: LOC_Os02g30200.1 (Oryza sativa), 3'ss of exon 3
lower sequence: EFJ20426 (Selaginella moellendorffii), 3'ss of exon 6
tcgctgcagtgcatctagaaagttttactcaacacacccaaaatgtttggctagatttcaattcaatgttgtttgcttggttttggttgcaacttgcaagGATCCACGAACGGAGAACGACCCGTACATGGGGTTCATCTACACGACGTTCCAGGAGCGCGCCACCTCCATCTCCCACGGCAACACGGCGCGCCACGCGG
| | | ||| | | | | | || |||| | | ||||| | |||||| ||||| | || |||||| | || || | |||||||||||||| ||||||||||| |||||| ||||||| ||||||||||| || |||||| ||
-----------------------------gtaaagagccagagtttcttctttctcgggaactcaaaa------gttcggtttccatc----cttgca-gGATCTCCAGACCGAGAACAATCCATATCTCGGGTTCATCTACACCTTCTTCCAGGAGCGAGCCACCGCCATCTCTCACGGCAACACTGCTCGCCACACGA
upper sequence: LOC_Os02g30200.1 (Oryza sativa), 3'ss of exon 3
lower sequence: EFJ09930 (Selaginella moellendorffii), 3'ss of exon 2
tcgctgcagtgcatctagaaagttttactcaacacacccaaaatgtttggctagatttcaattcaatgttgtttgcttggttttggttgcaacttgcaagGATCCACGAACGGAGAACGACCCGTACATGGGGTTCATCTACACGACGTTCCAGGAGCGCGCCACCTCCATCTCCCACGGCAACACGGCGCGCCACGCGG
| | |||| |||||| | | || | ||| | | ||||| ||| || | | || || || | || |||| ||||||||| ||| |||||| | || ||| ||||||||||||||||| | ||||||||||| ||||| | |||||| ||||||||||| || ||||||||
-----gtacgtagtctataaagttct-----aaacttctaaagttct---ctagagttct-ctcgagttgattgaagtgtttcttttttcaacc----agGATCCACAAACCGAGAACAATCCTTACCTGGGGTTCATCTACACGTCCTTCCAGGAGCGGGCCACTTTCATCTCGCACGGCAACACCGCCCGCCACGCCA
upper sequence: LOC_Os02g30200.1 (Oryza sativa), 3'ss of exon 3
lower sequence: EFJ20423 (Selaginella moellendorffii), 3'ss of exon 5
tcgctgcagtgcatctagaaagttttactcaacacacccaaaatgtttggctagatttcaattcaatgttgtttgcttggttttggttgcaacttgcaagGATCCACGAACGGAGAACGACCCGTACATGGGGTTCATCTACACGACGTTCCAGGAGCGCGCCACCTCCATCTCCCACGGCAACACGGCGCGCCACGCGG
| | | ||| | | | | | || |||| | | || ||| | || ||| ||||||| | || |||||| | || || | ||||||||||||||| | ||||||||||| ||||| ||||||| ||||||||||| || ||||||||
-----------------------------gtaaagagccagagtttcttctttctcgggaactcaaaa------gttcgggttt---tccatctttgcagGATCCCCAGACCGAGAACAATCCATATCTCGGGTTCATCTACACGTCCTTCCAGGAGCGAGCCACTGCCATCTCTCACGGCAACACTGCTCGCCACGCCA
upper sequence: LOC_Os02g30200.1 (Oryza sativa), 3'ss of exon 3
lower sequence: EFJ22568 (Selaginella moellendorffii), 3'ss of exon 1
-----------------------tcgctgcagtgcatctagaaagttttactcaacacacccaaaatgtttggctagatttcaattcaatgttgtttgctt----ggtttt----ggttgcaacttgcaagGATCCACGAACGGAGAACGACCCGTACATGGGGTTCATCTACACGACGTTCCAGGAGCGCGCCACCTCCATCTCCCACGGCAACACGGCGCGCCACGCGG--------
||| | ||| | || | | || || | | ||| | | | || ||| || || || | ||| || | | | | || |||||| | || ||| | |||||||||||| | | ||||||||| |||||||||||||| ||||||||||| || ||||| ||
gtatctctagctcactggacgagtcgatatgaagcaaatcgagaagacgatccagtac-ttgatcggttctggaatggtaaagagccagagtttcttctttctcgggaactcaaaagttcgggttttccatccttgcagGACCGAGAACAATCCATACCTCAGGTTCATCTACAAGTCCTTCCAGGAGGAAGCCACCTCCATCTCTCACGGCAACACTGCTCGCCATGCCAAGGAGCAC
upper sequence: LOC_Os02g30200.1 (Oryza sativa), 3'ss of exon 3
lower sequence: EFJ20424 (Selaginella moellendorffii), 3'ss of exon 1
tcgctgcagtgcatctagaaagttt--tactcaacacacccaaaatgtttg---gctagatttcaattcaatgttgtttgcttg---gttttggttgcaacttgcaagGATCCACGAACGGAGAACGACCCGTACATGGGGTTCATCTACACGACGTTCCAGGAGCGCGCCACCTCCATCTCCCACGGCAACACGGCGCGCCACGCGG
| | ||| | |||| | | || |||| | || ||| || ||| | | | || ||| | || || | | ||||||| | || |||||| | || || | |||||||||||||| ||||||||||| |||||| ||||||| ||||||||||| || |||||| ||
-------aaatcgagaagacgatccagtacttatcggtcctggaatggtaaagagccagagtttc-ttctttctcgggaactcaaaagttcggtttccatccttgcagGATCCCCAGACCGAGAACAATCCATATCTCGGGTTCATCTACACCTTCTTCCAGGAGCGAGCCACCGCCATCTCTCACGGCAACACTGCTCGCCACACGA
upper sequence: LOC_Os02g30200.1 (Oryza sativa), 3'ss of exon 3
lower sequence: EFJ20436 (Selaginella moellendorffii), 3'ss of exon 1
tcgctgcagtgcatctagaaagttttactcaacacacccaaaatgtttggctagatttcaattcaatgttgtttgcttggttttggttgcaacttgcaagGATCCACGAACGGAGAACGACCCGTACATGGGGTTCATCTACACGACGTTCCAGGAGCGCGCCACCTCCATCTCCCACGGCAACACGGCGCGCCACGCGG
| || | | | | | || |||| || | || || || |||||| |||||| | || |||||| | || || | ||||||||||||||| | ||||||||||| |||||| ||||||| || |||||||| || ||||||||
-------------------------------gtaagagcagagtttcttctttctcgggaactcaaaa--gtcggttt---ttccatt----cttgca-gGATCCCCAGACCGAGAACAATCCATATCTCGGGTTCATCTACACGTCCTTCCAGGAGCGAGCCACCGCCATCTCTCATGGCAACACTGCTCGCCACGCCA
upper sequence: LOC_Os02g30200.1 (Oryza sativa), 3'ss of exon 3
lower sequence: EFJ28408 (Selaginella moellendorffii), 3'ss of exon 1
tcgctgcagtgcatctagaaagttttactcaacacacccaaaatgtttggctagatttcaattcaatgttgtttgcttggttttggttgcaacttgcaagGATCCACGAACGGAGAACGACCCGTACATGGGGTTCATCTACACGACGTTCCAGGAGCGCGCCACCTCCATCTCCCACGGCAACACGGCGCGCCACGCGG------------------------------------------------------
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gtacttgatcggttctggaatggt-------aaagagccagagtttcttctttctcaggaactccaaa--gttcgc---gtttccatc----cttgca-ggatcctcagaccgagaacaatccatatctcgggttcgtctacacgtccttccagGAGCGAGCCACCACCATCTCTCACGGCAACACTGCTCGCCACGCCAAGGAGCACGGAGACCACAAGCTCGCGTGTTTGCGGCCTCATCGCAGCCGACGAG
upper sequence: LOC_Os02g30200.1 (Oryza sativa), 3'ss of exon 3
lower sequence: EFJ28417 (Selaginella moellendorffii), 3'ss of exon 1
tcgctgcagtgcatctagaaagttttactcaacacacccaaaatgtttggctagatttcaattcaatgttgtttgcttggttttggttgcaacttgcaagGATCCACGAACGGAGAACGACCCGTACATGGGGTTCATCTACACGACGTTCCAGGAGCGCGCCACCTCCATCTCCCACGGCAACACGGCGCGCCACGCGG
|| | |||| | | | | | || |||| | | |||||| | || | | ||||||| | || |||||| | || || | ||||||||||||||| | ||||||||||| |||||| ||||||| || |||||||| || ||||||||
----------------------------gtaaga-gcccagagtttcttctttctcgggaactcaaaa------gttcggtttt---tccattcttccagGATCCCCAGACCGAGAACAATCCATATCTCGGGTTCATCTACACGTCCTTCCAGGAGCGAGCCACCGCCATCTCTCATGGCAACACTGCTCGCCACGCCA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttggctagatttcaattcaatgttgtttgcttggttttggttgcaacttgcaagGATCCACGAACGGAGAACGACCCGTACATGGGGTTCATCTACACGACGTTCCAGGAGCGCGCCACCTCCATCTCCCACGGCAACACGGCGCGCCACGCGG
atttcaatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tcgctgcagtgcatctagaaagttttactcaacacacccaaaatgtttggctagatttcaattcaatgttgtttgcttggttttggttgcaacttgcaagGATCCACGAACGGAGAACGACCCGTACATGGGGTTCATCTACACGACGTTCCAGGAGCGCGCCACCTCCATCTCCCACGGCAACACGGCGCGCCACGCGG
- gctgcag
- - - - -tgcatct
- - - - - - - - - - - - - - -caacaca
- - - - - - - - - - - - - - - - - - - - - atgtttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aatgttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tggttgc