Sequence
atgc intronic sequence ATGC exonic sequencegcatgtaacttgagatactgacgtactgtactactatggctacaaatttagtggttgtatatctgccatgattactagtcaatctttctctctaatgcatgcatttgtgtagGACGTGGAGCGAAGGAGGCGAATCTTTACACTGAGATAGCTGAAGGCATCCATGCTTATGGAATAAAAGGCCACCGTCATG
Basic information
species | Oryza sativa |
transcript | LOC_Os10g35170.1 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os10g35170.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G038848_T02 (Zea mays), 3'ss of exon 9
gcatgtaacttgagatactgacgtactgtactactatggctacaaatttagtggttgtatatctgccatgattactagtcaatctttctctctaatgcatgcatttgtgtagGACGTGGAGCGAAGGAGGCGAATCTTTACACTGAGATAGCTGAAGGCATCCATGCTTATGGAATAAAAGGCCACCGTCATG
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------------------gttcgtatttatttgagatta--atcgattcatt--ttatatatctgtttcaacatcaaatga--tttggtctctaaaacatgcatcattgtagGACGTGGGGCTAAGGAAGCAAATCTTTACACTGAAATCGCTGAGGGTATCCATGCTTATGGGATAACAAGCCATCGGCATG
upper sequence: LOC_Os10g35170.1 (Oryza sativa), 3'ss of exon 9
lower sequence: AT2G19940.1 (Arabidopsis thaliana), 3'ss of exon 9
gcatgtaacttgagatactgacgtactgtactactatggctacaaatttagtggttgtatatctgccatgatt--actagtcaatctttctctctaatgcatgcatttgtgtagGACGTGGAGCGAAGGAGGCGAATCTTTACACTGAGATAGCTGAAGGCATCCATGCTTATGGAATAAAAGGCCACCGTCATG
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--------------------------------------gtttgagcttactccgtgatcaatgaacaatgatgcaatgtttctagtttcttgactgatatgaaattttcatcagGACGTGGTGCTAAGGAGGCAAATCTTTACTCTGAGATAGCTGAAGGCATTTCTTCTTATGGTGTCACCCGTCATCGCCATG
upper sequence: LOC_Os10g35170.1 (Oryza sativa), 3'ss of exon 9
lower sequence: Vv03s0063g01110.t01 (Vitis vinifera), 3'ss of exon 8
gcatgtaacttgagatactgacgtactgtactactatggctacaaatttagtggttgtatatctgccatgattactagtcaatctttctctctaatgcatgcatttgtgtagGACGTGGAGCGAAGGAGGCGAATCTTTACACTGAGATAGCTGAAGGCATCCATGCTTATGGAATAAAAGGCCACCGTCATG
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gttaggattttttattttttatttttaatgcaa--attcttagcagtata-tattcttgattccacttgcagcacatttcagcagcttttggtatttggtgcattt-tgcagGTCGTGGTGCCAAGGAGGCAAATCTGTACACTGAAATAGCTGAAGGCATTCATTCTTATGGTATTACAAGGCATCGCCATG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tatatctgccatgattactagtcaatctttctctctaatgcatgcatttgtgtagGACGTGGAGCGAAGGAGGCGAATCTTTACACTGAGATAGCTGAAGGCATCCATGCTTATGGAATAAAAGGCCACCGTCATG
ctctaat putative branch site (score: 3)
atgatta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gcatgtaacttgagatactgacgtactgtactactatggctacaaatttagtggttgtatatctgccatgattactagtcaatctttctctctaatgcatgcatttgtgtagGACGTGGAGCGAAGGAGGCGAATCTTTACACTGAGATAGCTGAAGGCATCCATGCTTATGGAATAAAAGGCCACCGTCATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG