Sequence
atgc intronic sequence ATGC exonic sequence...aacactgaactcccggcatattgcttgcttgtgttgttcataatgagtaccagaaatccagaattgtatttctttcttaccagtacatctgggcttgcagATATATTAGTTCAGTCATTCCAATCGGAGCAATGTTTGCAATGACACTCTGGCTAGGGAACAGTGCTTACCTCTATATATCTGTTGCATTTGCACAGATG
Basic information
species | Oryza sativa |
transcript | LOC_Os08g04110.2 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os08g04110.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G022793_T01 (Zea mays), 3'ss of exon 3
aacact-gaactcccggcatattgcttgcttgtgttgttcataatgagtaccagaaatcca-gaattgtatttctttc-ttaccagtacatctgggcttgcagATATATTAGTTCAGTCATTCCAATCGGAGCAATGTTTGCAATGACACTCTGGCTAGGGAACAGTGCTTACCTCTATATATCTGTTGCATTTGCACAGATG
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ttcatttgtgcttgtactatgatgtt--cctgaactcattgttttatttactttaagtacaagaactgtctttttttccttactagttc-cctgaactttcagATATATTACTTCAGTCATTCCAATTGGAGGAATGTTTGCAATGACACTTTGGCTAGGGAACAGTGCGTACCTCTACATATCTGTCGCATTTGCACAGATG
upper sequence: LOC_Os08g04110.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA15G40160.1 (Glycine max), 3'ss of exon 3
--aacactgaactcccggc--atattgcttgcttgtgttgttcataatgagtaccagaaatccagaattgtatttctttcttaccagtacatctgggcttgcagATATATTAGTTCAGTCATTCCAATCGGAGCAATGTTTGCAATGACACTCTGGCTAGGGAACAGTGCTTACCTCTATATATCTGTTGCATTTGCACAGATG
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aaaattattaacttcaagtctatgttccttaatattttattgcattaaatgcataagatgtttccaa----attccagttgtaattataccttgattgtttcagATACGCTACTTCAGTAGTGCCAATTGGGGCCATGTTTGCAATGACTCTTTGGCTGGGAAATACTGCCTACCTGTATATTTCTGTTGCTTTTGCACAAATG
upper sequence: LOC_Os08g04110.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA08G18730.1 (Glycine max), 3'ss of exon 4
--aacactgaactcccggc--atattgcttgcttgtgttgttcataatgagtaccagaaatccagaattgtatttctttcttaccagtacatctgggcttgcagATATATTAGTTCAGTCATTCCAATCGGAGCAATGTTTGCAATGACACTCTGGCTAGGGAACAGTGCTTACCTCTATATATCTGTTGCATTTGCACAGATG
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aaattttttaacttcaagtctatgtaccttaatagtttattgcattaaatgcataagatgtttccaa----attccagttgtaattataccttgattgtttcagATACGCTACTTCGGTAGTGCCAATTGGGGCCATGTTTGCAATGACTCTTTGGCTGGGAAATACTGCCTACCTGTATATTTCTGTTGCTTTTGCACAAATG
upper sequence: LOC_Os08g04110.2 (Oryza sativa), 3'ss of exon 3
lower sequence: AT1G53660.1 (Arabidopsis thaliana), 3'ss of exon 3
aacactgaactcccggcatattgcttgcttgtgttgttcataatgagtaccagaaatccagaattgtatttctttctta-ccagtacatc----tgggcttgcagATATATTAGTTCAGTCATTCCAATCGGAGCAATGTTTGCAATGACACTCTGGCTAGGGAACAGTGCTTACCTCTATATATCTGTTGCATTTGCACAGATG
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-----------------gtaa-gaaagaaagtgtt-tctgtaagcaatttatttatttttgagttgtaaataccgtttagctaaaacatcactctatgtactcagATATGTTACATCAGTTATTCCAATAGGTGCAATGTTTGCAATGACTCTATGGTTAGGAAACACTGCTTATCTCTACATAACTGTTGCATTTTCCCAAATG
upper sequence: LOC_Os08g04110.2 (Oryza sativa), 3'ss of exon 3
lower sequence: AT3G14410.1 (Arabidopsis thaliana), 3'ss of exon 3
--------aacactgaactcccggcatattgcttgcttgtgttgttcataatgagtac----cagaaatccagaattgtatttctttcttaccagtaca-------tctgggcttgcagATATATTAGTTCAGTCATTCCAATCGGAGCAATGTTTGCAATGACACTCTGGCTAGGGAACAGTGCTTACCTCTATATATCTGTTGCATTTGCACAGATG
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gtaaggaagaaagagacttcgtaaggaatttgattttggagtagtcgaaaatacccataacataaatatctttactaattttatcaatgtagcagtattaactcactttatgtactcagATATGTTACGTCAGTTATTCCAATAGGTGCAATGTTTGCAATGACCCTCTGGTTGGGAAACACTGCCTACCTCTACATATCAGTTGCATTTGCGCAGATG
upper sequence: LOC_Os08g04110.2 (Oryza sativa), 3'ss of exon 3
lower sequence: Vv15s0046g00460.t01 (Vitis vinifera), 3'ss of exon 3
aacactgaactcccggcatattgcttgcttgtgttgttcataatgagtaccagaaatccagaattgtatttctttcttaccagtacatctgggcttgca-------gATATATTAGTTCAGTCATTCCAATCGGAGCAATGTTTGCAATGACACTCTGGCTAGGGAACAGTGCTTACCTCTATATATCTGTTGCATTTGCACAGATG
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ctctctctctcttgcacatgtggatagcatgt-ttattc-tattgcatacttgat-----gatgttccttcctttagaacaaatataattaaattttcaatgttcagATATACTACATCTGTGATCCCTATTGGTGCAACATTTGCAATGACTCTTTGGCTGGGAAACACTGCTTACCTGTATATTTCTGTTGCATTTGCACAAATGMapped EST sequences
Showing partial alignments of ESTs and genomic sequences. See full alignments
ATGC EST sequence
ATGC genomic sequence (exon)
ATGC genomic sequence (truncated intron)
EST:
gi|58598476|gb|CK009004.1|CK009004EST: ATTGTAAAGATTGAGGAGGGAATGACTACCGATAT ATATATTAGTTCAGTCATTCCAATCGGAGCAATGTTTGCAATGACACTCTG
genomic: ATTGTAAAGATTGAGGAGGGAATGACTACCGATATgtgagtcatg ... gggcttgcagATATATTAGTTCAGTCATTCCAATCGGAGCAATGTTTGCAATGACACTCTG
EST:
gi|58600548|gb|CK011076.1|CK011076EST: AGATTGTAAAGATTGAGGAGGGAATGACTACCGATAT ATATATTAGTTCAGTCATTCCAATCGGAGCAATGTTTGCAATGACACTCTG
genomic: AGATTGTAAAGATTGAGGAGGGAATGACTACCGATATgtgagtcatg ... gggcttgcagATATATTAGTTCAGTCATTCCAATCGGAGCAATGTTTGCAATGACACTCTG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.agtaccagaaatccagaattgtatttctttcttaccagtacatctgggcttgcagATATATTAGTTCAGTCATTCCAATCGGAGCAATGTTTGCAATGACACTCTGGCTAGGGAACAGTGCTTACCTCTATATATCTGTTGCATTTGCACAGATG
ttcttac putative branch site (score: 2)
aattgtatttcttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
aacactgaactcccggcatattgcttgcttgtgttgttcataatgagtaccagaaatccagaattgtatttctttcttaccagtacatctgggcttgcagATATATTAGTTCAGTCATTCCAATCGGAGCAATGTTTGCAATGACACTCTGGCTAGGGAACAGTGCTTACCTCTATATATCTGTTGCATTTGCACAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG