Sequence
atgc intronic sequence ATGC exonic sequence...acattacacttatatacattattgttagtactggaattatttctcatcacatattctttatgtgttttgcctgcttatttctgcatgcctgtcattgcagGGTGGCGATTTGAGATATTGTCAGAAATGTTCCCATTATAAGCCTCCCCGTGCTCATCATTGTCGTGTCTGCAAGAGATGTGTTCTAAGAATG
Basic information
species | Oryza sativa |
transcript | LOC_Os01g62620.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g62620.2 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G064853_T02 (Zea mays), 3'ss of exon 1
acattacacttatata--cattattgttagtactggaattatttctcatca-catattctttatgtgttttgcctgcttatttctgcatgcctgtcattgcagGGTGGCGATTTGAGATATTGTCAGAAATGTTCCCATTATAAGCCTCCCCGTGCTCATCATTGTCGTGTCTGCAAGAGATGTGTTCTAAGAATG
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gtagtaattttattttgtcaggaatgttaaaaaggaatctatatgactaaatcagactaatacaggggactatgtgctaacttacaccag---aacattgcagGGTGGTGATTTGAGATACTGCCAGAAATGTTCGCATTATAAACCTCCTCGAGCGCACCATTGTCGTGCCTGCAAAAGATGTGTTCTAAGAATG
upper sequence: LOC_Os01g62620.2 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA01G24430.1 (Glycine max), 3'ss of exon 1
acattacacttatatacattattgttagtactggaattat-ttctcatcacatattctttatgtgttttgcctgcttatttctgcatgcctgtcattgcagGGTGGCGATTTGAGATATTGTCAGAAATGTTCCCATTATAAGCCTCCCCGTGCTCATCATTGTCGTGTCTGCAAGAGATGTGTTCTAAGAATG
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agaagatccgca-aaatattcccataaatgtttggtttatgttaatatcaagcataatggaaattaactttcaagtaatgtttttttgggtctgccagcagGGTGGAGATTTGCGATATTGCCAAAAGTGTTCTCACTATAAGCCTCCTCGTGCACATCATTGTCGGGTTTGTAAAAGATGTGTTCTACGAATG
upper sequence: LOC_Os01g62620.2 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA03G12460.1 (Glycine max), 3'ss of exon 1
acattacacttatatacattattgttagtactggaattat-ttctcatcacatattctttatgtgttttgcctgcttat-ttctgcatgcctgtcattgcagGGTGGCGATTTGAGATATTGTCAGAAATGTTCCCATTATAAGCCTCCCCGTGCTCATCATTGTCGTGTCTGCAAGAGATGTGTTCTAAGAATG
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tctgtgatctgcaaaagattcccataaatatttggtttatattaatattaagcatcatggaaattaactttcaagtaatgttttttggatctgcaa--gcagGGTGGAGATTTGCGATATTGCCAAAAGTGTTCTCACTATAAGCCTCCCCGTGCACATCATTGCCGGGTTTGTAAAAGATGTGTTCTACGAATG
upper sequence: LOC_Os01g62620.2 (Oryza sativa), 3'ss of exon 1
lower sequence: Vv08s0007g00620.t01 (Vitis vinifera), 3'ss of exon 1
acattacacttatatacattattgttagtactggaattatttctcatcac----atattctttatgtgttttgcctgctta-tttctgcatgcctgtcattgcagGGTGGCGATTTGAGATATTGTCAGAAATGTTCCCATTATAAGCCTCCCCGTGCTCATCATTGTCGTGTCTGCAAGAGATGTGTTCTAAGAATG
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--ttggaacctgttt---tttctaaaaaggttgaaattgctctgaatactgagaaaaatgagtatggcttctaaggtttgactttctattgagatgtttttgcagGGTGGAGATCTGAGATACTGCCAGAAGTGTGCCCACTATAAACCTGCCCGTGCACACCATTGTCGTGTTTGCAGAAGATGTGTTTTGCGAATG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atcacatattctttatgtgttttgcctgcttatttctgcatgcctgtcattgcagGGTGGCGATTTGAGATATTGTCAGAAATGTTCCCATTATAAGCCTCCCCGTGCTCATCATTGTCGTGTCTGCAAGAGATGTGTTCTAAGAATG
atattctttat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
acattacacttatatacattattgttagtactggaattatttctcatcacatattctttatgtgttttgcctgcttatttctgcatgcctgtcattgcagGGTGGCGATTTGAGATATTGTCAGAAATGTTCCCATTATAAGCCTCCCCGTGCTCATCATTGTCGTGTCTGCAAGAGATGTGTTCTAAGAATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ttgcctg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gcatgcc