Sequence
atgc intronic sequence ATGC exonic sequence...ctacttctgtagatcagactgcacaaagtgtccttttttatttctctcttgacttgtgaagataagaagtttctttttcatctttctttggcatcatcagATTAGCAAGAGGGTGTTCAATGTGATGAGGAGTGAATTCTTGGATGCATCCAAATCAGATACTGCAGATAATGAAGAAAATGCCCCTTCCCTTGTAAAAG
Basic information
species | Oryza sativa |
transcript | LOC_Os02g57400.3 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os02g57400.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G342327_T03 (Zea mays), 3'ss of exon 2
ctactt-ctgtagatcagactgcacaaagtgtccttttttatttctctcttgacttgtgaagataagaagtttctttttcatctttctttggcatcatcagATTAGCAAGAGGGTGTTCAATGTGATGAGGAGTGAATTCTTGGATGCATCCAAATCAGATACTGCAGATAATGAAGAAAATGCCCCTTCCCTTGTAAAAG
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atacctgctgctcttcagacgactatgtgaaccgctgttcctttctagactaact-atggtaataaacctttttttttctaaatccttgttgccataacagATTAGCAAGAGAGTATTCAATGTGATGAAGAGTGAATTCTTGGCCACATCAAAGTCAGATGGGGCAACCAAACAAGAAAATTATCCTGCCTTTGGCCTTG
upper sequence: LOC_Os02g57400.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G123544_T01 (Zea mays), 3'ss of exon 1
ctacttctgtagatcagactgcacaaagtgtccttt----tttatttctctcttgacttgtgaagataagaagtttctttttcatctttctt-tggcatcatcagATTAGCAAGAGGGTGTTCAATGTGATGAGGAGTGAATTCTTGGATGCATCCAAATCAGATACTGCAGATAATGAAGAAAATGCCCCTTCCCTTGTAAAAG
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-----attacaagacttgtcatacctactggtctgcagagcatgttcctttctagacttgcgttggtaataatcttttttttcccgatccttgttgccacaacagATTAGCAAGAGAGTATTCGATGTAATGAAGAGTGAATTCTTGGCTCAATCAAAGTCAGACGGGGCAGGCAAACAAGAAAATTATCCTGCTCTTGGCCTTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctcttgacttgtgaagataagaagtttctttttcatctttctttggcatcatcagATTAGCAAGAGGGTGTTCAATGTGATGAGGAGTGAATTCTTGGATGCATCCAAATCAGATACTGCAGATAATGAAGAAAATGCCCCTTCCCTTGTAAAAG
tcttgac putative branch site (score: 3)
tttctttttcatcttt putative PPT
tttcttttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ctacttctgtagatcagactgcacaaagtgtccttttttatttctctcttgacttgtgaagataagaagtttctttttcatctttctttggcatcatcagATTAGCAAGAGGGTGTTCAATGTGATGAGGAGTGAATTCTTGGATGCATCCAAATCAGATACTGCAGATAATGAAGAAAATGCCCCTTCCCTTGTAAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA