Sequence
atgc intronic sequence ATGC exonic sequencegtaagacatttgatgattccctcataaatcttgtatcttaatttcatgccaccctgtaactccttgatgctttcagGTACAAAAATGATCCTGAGATCCTCGCCATGACAAACTTGATTGCAGCATATCAGAAGAATGACATCATGGAATTTGAAAAGATTCTAAAG
Basic information
species | Oryza sativa |
transcript | LOC_Os01g17180.2 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g17180.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G079196_T01 (Zea mays), 3'ss of exon 8
gtaagacatttgatgattccctcataaatcttgtatcttaatttca-tgccaccctgtaactccttgatgctttcagGTACAAAAATGATCCTGAGATCCTCGCCATGACAAACTTGATTGCAGCATATCAGAAGAATGACATCATGGAATTTGAAAAGATTCTAAAG
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gtaagacaatttatgatccccgcataaatatggtagcttgatttccctcccaccctgaaaattct-aatgtttgcagGTACAAGAATGATCCTGAAATCCTTGCAATGACAAACCTGATTGCAGCGTACCAGAAGAATGACATCATGGAATTTGAAAAGATCCTGAAG
upper sequence: LOC_Os01g17180.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G132804_T01 (Zea mays), 3'ss of exon 8
gtaagacatttgatgattccctcataaatcttgtatcttaattt-catgccaccctgtaactccttgatgctttcagGTACAAAAATGATCCTGAGATCCTCGCCATGACAAACTTGATTGCAGCATATCAGAAGAATGACATCATGGAATTTGAAAAGATTCTAAAG
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gtaagacaactgatgat-cccgcataaatcttgtagcttgatttacctcccaccctgaaaa-ctcaaatgcttgcagGTACAAGAACGATAGTGAAATCCTTGCAATGACAAACCTGATTGCAGCGTACCAGAAGAACGACATCATGGAGTTTGAAAAGATCCTGAAG
upper sequence: LOC_Os01g17180.1 (Oryza sativa), 3'ss of exon 8
lower sequence: AT2G26990.1 (Arabidopsis thaliana), 3'ss of exon 8
gtaagacatttgatgattccctcataaatcttgtatcttaatttcatgccaccctgtaactccttgat--gctttc---agGTACAAAAATGATCCTGAGATCCTCGCCATGACAAACTTGATTGCAGCATATCAGAAGAATGACATCATGGAATTTGAAAAGATTCTAAAG
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--------gtaagtcatttccgtatatattttttgttgaacactcgttttggttcgttgcttcatagttggctctctgcagGTACAAAAACGACCCTGAGATTTTGGCAATGACAAATTTGATCGCAGCATATCAACGAAATGAGATCATAGAGTTTGAGAGAATACTAAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcataaatcttgtatcttaatttcatgccaccctgtaactccttgatgctttcagGTACAAAAATGATCCTGAGATCCTCGCCATGACAAACTTGATTGCAGCATATCAGAAGAATGACATCATGGAATTTGAAAAGATTCTAAAG
tgctttc CT-rich tract
ttgtatcttaattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagacatttgatgattccctcataaatcttgtatcttaatttcatgccaccctgtaactccttgatgctttcagGTACAAAAATGATCCTGAGATCCTCGCCATGACAAACTTGATTGCAGCATATCAGAAGAATGACATCATGGAATTTGAAAAGATTCTAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA