Sequence
atgc intronic sequence ATGC exonic sequencegtttgatcctcgacgagctgagctcgcgacatggtggcgagagatgagactagagtgctaaataatatatgtgcagGTGGTCCAAGATCGCGTCGCACCTGCCGGGCAGGACGGACAACGAGATCAAGAACCACTGGAACACGCACATCAAGAAGAAGCTCCGGAAGATGGGGATC
Basic information
species | Oryza sativa |
transcript | LOC_Os09g23620.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os09g23620.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA11G33620.1 (Glycine max), 3'ss of exon 2
----------------------gtttgatcctcgacgagctgagctcgcgacatggtggcgagaga-tgaga-ctagagtgctaaataatatatgtgcagGTGGTCCAAGATCGCGTCGCACCTGCCGGGCAGGACGGACAACGAGATCAAGAACCACTGGAACACGCACATCAAGAAGAAGCTCCGGAAGATGGGGATC
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cctagtatggaccttttgttggaatcatttttttaataataataattgtgattcctttactaattactgatatcttgtatttttttcctcccttatgcagATGGTCTAAGATTGCTTCTCATCTCCCAGGAAGAACTGATAATGAGATCAAGAATCACTGGAACACCCACATAAAGAAAAAGCTCAAGAAAATGGGAATT
upper sequence: LOC_Os09g23620.1 (Oryza sativa), 3'ss of exon 2
lower sequence: AT1G66230.1 (Arabidopsis thaliana), 3'ss of exon 1
gtt--tgatcctcgacgagctgagctcgcgacatggtggcgagagatgagactagagtgctaaataatatatgtgcagGTGGTCCAAGATCGCGTCGCACCTGCCGGGCAGGACGGACAACGAGATCAAGAACCACTGGAACACGCACATCAAGAAGAAGCTCCGGAAGATGGGGATC
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gttaacaaacgtttcttacttgtgctt--taagtttcgatatgttctgtttttgagattttgttttttgtatgtaaagGTGGTCAAAGATAGCTTCTCATTTACCAGGAAGAACAGACAACGAAATCAAGAATCATTGGAACACTCACATCAAGAAGAAGTTGAGGAAAATGGGGATT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gctcgcgacatggtggcgagagatgagactagagtgctaaataatatatgtgcagGTGGTCCAAGATCGCGTCGCACCTGCCGGGCAGGACGGACAACGAGATCAAGAACCACTGGAACACGCACATCAAGAAGAAGCTCCGGAAGATGGGGATC
tgctaaa putative branch site (score: 2)
taaataatatatgt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtttgatcctcgacgagctgagctcgcgacatggtggcgagagatgagactagagtgctaaataatatatgtgcagGTGGTCCAAGATCGCGTCGCACCTGCCGGGCAGGACGGACAACGAGATCAAGAACCACTGGAACACGCACATCAAGAAGAAGCTCCGGAAGATGGGGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG