Sequence
atgc intronic sequence ATGC exonic sequence...tccattagcattccccttcatatgaatgttcaaaataaatataaattttgtttatttgtcatgtctctagctcattttctacatgtatctttcttcatagGTTACAGTAAATTCTGGAGGAGTTGTTTTCATTGCATTATTCAAAACATCTGAATATGATGACCTTCCGTCCAAGGAGACTGCAGCGGTCATTAAAATAG
Basic information
species | Oryza sativa |
transcript | LOC_Os01g24470.2 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g24470.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G061684_T01 (Zea mays), 3'ss of exon 3
-----tccattagcattccccttcatatgaatgttcaaaataaatataaattttgtttatttgtcatgtctctagctcattttc-tacatgtatctttcttcatagGTTACAGTAAATTCTGGAGGAGTTGTTTTCATTGCATTATTCAAAACATCTGAATATGATGACCTTCCGTCCAAGGAGACTGCAGCGGTCATTAAAATAG
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ggtaatagaggtgtagctatcttc-tacgaatatgtatattag-----aattaactttacaaaccatatttctaggtccttctaataactgtactattttgctcagGTGACAGTAAATTCTGGGGGCATTGTTTTTATTGCATTATTCAAAGCTATTGAAAATGTTGATCTTCCGTCCAAGGAAACAGCTGCAGTAATTAAAATAG
upper sequence: LOC_Os01g24470.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA05G38500.1 (Glycine max), 3'ss of exon 2
tccattagcattccccttc-atatgaatgttcaaaataaatataaattt--tgtttatttgtcatgtctctagctcattttctacatgtatctttcttcatagGTTACAGTAAATTCTGGAGGAGTTGTTTTCATTGCATTATTCAAAACATCTGAATATGATGACCTTCCGTCCAAGGAGACTGCAGCGGTCATTAAAATAG
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tgtgttttctttgtaattccgtattagag---aaagtaagtatacatcaaatgtgtattttcttaatttatgtcgtaatatctcttcagttgtgtccacatagGTAACTGTAAATTCTGGAGGAGTTGTCTTCTTTGCCTTTTTCAATATCTCTGGAAATGCTGATGCTTGCCCAAAAGAAGCAGCAGCTGTTATAAAGATAG
upper sequence: LOC_Os01g24470.2 (Oryza sativa), 3'ss of exon 3
lower sequence: AT5G23720.2 (Arabidopsis thaliana), 3'ss of exon 4
tccattagcattccccttcatatgaatgttcaaaataaatataaattttgtttatttgtcatgtctctagc-tcattttctacatgtatctttcttcatagGTTACAGTAAATTCTGGAGGAGTTGTTTTCATTGCATTATTCAAAACATCTGAATATGATGACCTTCCGTCCAAGGAGACTGCAGCGGTCATTAAAATAG
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-----------------------gtatat---atatcattatgatcttgg---actggtgatgctaggaggatcttttgacactattagatgtctgtacagGTTACTGTGAATTCTGGAGGAGTTGTTTTCTTTGCCCTGTTCAATAGTTCCAGCTCTGAAGATGCCTCTCGTAAGGAAGAAGCAGCAGTTATTAAATTTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttttgtttatttgtcatgtctctagctcattttctacatgtatctttcttcatagGTTACAGTAAATTCTGGAGGAGTTGTTTTCATTGCATTATTCAAAACATCTGAATATGATGACCTTCCGTCCAAGGAGACTGCAGCGGTCATTAAAATAG
tatctttcttc CT-rich tract
tttatttgt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tccattagcattccccttcatatgaatgttcaaaataaatataaattttgtttatttgtcatgtctctagctcattttctacatgtatctttcttcatagGTTACAGTAAATTCTGGAGGAGTTGTTTTCATTGCATTATTCAAAACATCTGAATATGATGACCTTCCGTCCAAGGAGACTGCAGCGGTCATTAAAATAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG