Sequence
atgc intronic sequence ATGC exonic sequencegtacatggcacactaggccaacaatatatctttaaccgagcaaacaggaagctaataaattgatgtaccttttcgtgtttgcagAGCTGTACAGTATTGTTGGAAGACCTAATATATTCAGTTATGGTGAACTAAGGTCCGCAACTGAAAATTTTAGTTCCAGCAACCGTCTTGGTGAAGGAGG
Basic information
species | Oryza sativa |
transcript | LOC_Os04g52640.3 |
intron # | 19 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os04g52640.2 (Oryza sativa), 3'ss of exon 18
lower sequence: GRMZM2G155837_T01 (Zea mays), 3'ss of exon 15
gtacatggcacacta-ggcca-----acaatatatctttaaccgagc--aaacaggaagctaataaattgatgtaccttttcgtgtttgcagAGCTGTACAGTATTGTTGGAAGACCTAATATATTCAGTTATGGTGAACTAAGGTCCGCAACTGAAAATTTTAGTTCCAGCAACCGTCTTGGTGAAGGAGG
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gtaaatgagataccatgatcacaagtacaatatattatgaatcaagcttagatattgtgtttataaact--tatcttttgtgatgttttcagAGCTTTACAGTATTGTTGGAAGACCCAATGTATTTGTTTATGGTGAGCTAAGGACCGCTACTGAAAATTTTAGTTCCAATAACCTTCTTGGTGAAGGAGG
upper sequence: LOC_Os04g52640.2 (Oryza sativa), 3'ss of exon 18
lower sequence: GRMZM2G031536_T01 (Zea mays), 3'ss of exon 4
gtacatggcacacta-ggcca------acaatatatctttaaccgagcaaacaggaagctaataaattgatgtaccttttcgtgtttgcagAGCTGTACAGTATTGTTGGAAGACCTAATATATTCAGTTATGGTGAACTAAGGTCCGCAACTGAAAATTTTAGTTCCAGCAACCGTCTTGGTGAAGGAGG
||| ||| | || | | || ||||| ||| | | | |||| || || | || | | | | || | ||||| ||| || |||||||||||||||||||||||| |||||| |||||||||||||||| | | ||||||||||||||||||| |||| ||| |||||||||||
gtaaatgagataccatgatcataagttacaatgtat-tgtgaatgagctaagagattgtgtttataaagttatcttttgtgttgtttttagAACTTTACAGTATTGTTGGAAGACCTAATGTATTCACTTATGGTGAACTAAGGACGTCTACTGAAAATTTTAGTTCCAATAACCTTCTGGGTGAAGGAGG
upper sequence: LOC_Os04g52640.2 (Oryza sativa), 3'ss of exon 18
lower sequence: GRMZM2G126858_T02 (Zea mays), 3'ss of exon 17
--------gtaca-tggcacactaggccaacaatatatctttaaccgagcaaacaggaag---ctaataaattgatgtaccttttcgtgtttgcagAGCTGTACAGTATTGTTGGAAGACCTAATATATTCAGTTA------TGGTGAACTAAGGTCCGCAACTGAAAATTTTAGTTCCAGCAACCGTCTTGGTGAAGGAGG
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gtaaaatgatatgctagattgctaggctaacgcaat-ccttaaactcagcaaataggttttttcttacaaactaac--agtatgtggtgtttgcagAGCTCTACAATATTGTTCGAATACCTAATGTATTCTGTTACACTTATGGTGAACTAAGGACCGCTACTGAAAATTTTAGTTCTGCTAATCTTCTTGGTGA------Mapped 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|29632427|gb|CB637436.1|CB637436EST: TATCACTGGAGCAACAAA AGCTGTACAGTATTGTTGGAAGACCTAATATATTCAGTTATGGTGAACTAA
genomic: TATCACTGGAGCAACAAGgtacatggca ... gtgtttgcagAGCTGTACAGTATTGTTGGAAGACCTAATATATTCAGTTATGGTGAACTAA
EST:
gi|29634408|gb|CB639417.1|CB639417EST: AATCTTTCTTTGGAGAAAGAAAAGGAGAAAGCTATCACTGGAGCAACAAG AGCTGTACAGTATTGTTGGAAGACCTAATATATTCAGTTATGGTGAACTAA
genomic: AATCTTTCTTTGGAGAAAGAAAAGGAGAAAGCTATCACTGGAGCAACAAGgtacatggca ... gtgtttgcagAGCTGTACAGTATTGTTGGAAGACCTAATATATTCAGTTATGGTGAACTAA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctttaaccgagcaaacaggaagctaataaattgatgtaccttttcgtgtttgcagAGCTGTACAGTATTGTTGGAAGACCTAATATATTCAGTTATGGTGAACTAAGGTCCGCAACTGAAAATTTTAGTTCCAGCAACCGTCTTGGTGAAGGAGG
ccttttcgt CT-rich tract
taataaattgatgta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtacatggcacactaggccaacaatatatctttaaccgagcaaacaggaagctaataaattgatgtaccttttcgtgtttgcagAGCTGTACAGTATTGTTGGAAGACCTAATATATTCAGTTATGGTGAACTAAGGTCCGCAACTGAAAATTTTAGTTCCAGCAACCGTCTTGGTGAAGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG