Sequence
atgc intronic sequence ATGC exonic sequence...gtggcacattctagttgcatgttgggtttcacttttcattagttaagatatctttggatcatcatcacttcctttgatatgaacatatattactatgcagGTTCCAAATTTGTATTGTATTGGAGATGCCAATGGCAAACTCATGCTGGCTCATGCTGCCAGTGCACAAGGAATCTCAG
Basic information
species | Oryza sativa |
transcript | LOC_Os01g23610.2 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g23610.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G145595_T02 (Zea mays), 3'ss of exon 8
gtggcacattctagttgcatgttgg-gtttcacttttcattagttaagatatctttggat-catcatcacttcctttgatatgaacatatattactatgcagGTTCCAAATTTGTATTGTATTGGAGATGCCAATGGCAAACTCATGCTGGCTCATGCTGCCAGTGCACAAGGAATCTCAG
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gtatgctaaacctgtagtgtgttactgttactcttttgttcctttacaacaatggtaggcatttcattcaagtttgctacataaacattaaccggtatgcagGTTCCTAATTTATATTGTATCGGAGATGCCAATGGTAAGCTCATGCTTGCTCATGCAGCCAGCGCACAAGGAATCTCAG
upper sequence: LOC_Os01g23610.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GLYMA15G15310.1 (Glycine max), 3'ss of exon 9
gtggcacattctagttgcatgttgggtttcacttttcattagttaagatatctttggatcatcatcacttcctttgatatgaacatatattact--atg-cagGTTCCAAATTTGTATTGTATTGGAGATGCCAATGGCAAACTCATGCTGGCTCATGCTGCCAGTGCACAAGGAATCTCAG
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--------------------gtttgtttcaaatgtttcatgaacacattattttt--ttctctgtctgacacattgttgctgatttagagtatggaatgatagGTTCCTCATTTGTATTGTATTGGTGATGCAAATGGCAAGATGATGCTTGCTCATGCTGCCAGCGCACAAGGAATTTCAG
upper sequence: LOC_Os01g23610.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GLYMA17G03560.1 (Glycine max), 3'ss of exon 9
gtggcacattctagttgcatgttgggtttcacttttcattagttaagatatctttggatcatcatcacttcctttgatatgaacatatattactatgcagGTTCCAAATTTGTATTGTATTGGAGATGCCAATGGCAAACTCATGCTGGCTCATGCTGCCAGTGCACAAGGAATCTCAG
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--------------------gtttgtctcaatttctcatgcaataat-tatccctccctgac--ttattgttactgacatagg-atgtggaatgat--agGTGCCTCATTTATATTGTATTGGTGATGCAAATGGCAAGATGATGCTTGCTCATGCTGCCAGTGCACAAGGAATTTCAG
upper sequence: LOC_Os01g23610.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GLYMA07G37050.2 (Glycine max), 3'ss of exon 9
gtggcacattctagttgcatgttgggtttcacttttcattagttaagatatctttggatcatcatcacttcctttgatatgaacatatattactatgcagGTTCCAAATTTGTATTGTATTGGAGATGCCAATGGCAAACTCATGCTGGCTCATGCTGCCAGTGCACAAGGAATCTCAG
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--------------------gtttgtctcaacttctcaagtaataat-tatccctccctgac--ttattgttactgacatagg-atgtggaatgat--agGTGCCTCATTTATACTGTATTGGTGATGCAAATGGCAAGATGATGCTTGCTCATGCTGCCAGTGCACAAGGAATTTCAG
upper sequence: LOC_Os01g23610.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GLYMA09G04270.1 (Glycine max), 3'ss of exon 4
gtggcacattctagttgcatgttgggtttcacttttcattagttaagatatctt-tggatcatcatcacttcctttgatatgaacatatattactatgcagGTTCCAAATTTGTATTGTATTGGAGATGCCAATGGCAAACTCATGCTGGCTCATGCTGCCAGTGCACAAGGAATCTCAG
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-------------------------gtttgtttcatgaatacataattttttttcttggtctgacacattgttactgatttaga-gtatggaatgat--agGTTCCTCATTTGTATTGCATTGGTGATACAAATGGCAAGATGATGCTTGCTCATGCTGCCAGTGCACAAGGAATTTCAG
upper sequence: LOC_Os01g23610.1 (Oryza sativa), 3'ss of exon 9
lower sequence: AT4G16155.1 (Arabidopsis thaliana), 3'ss of exon 9
gtggcacattctagttgcatgttgggtttcacttttcattagttaagatatctttggatcatcatcacttcctttgata-tgaacatatattactatgcagGTTCCAAATTTGTATTGTATTGGAGATGCCAATGGCAAACTCATGCTGGCTCATGCTGCCAGTGCACAAGGAATCTCAG
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----------------gttagtggagttttctttcatatagcttat--ttcttaccaaaagttatatatttttaagctactgagtcactcttggttgatagGTTCCCCACTTGTACTGCATCGGTGATGCCAATGGTAAACTGATGCTTGCTCATGCAGCTAGTGCTCAAGGAATTTCTG
upper sequence: LOC_Os01g23610.1 (Oryza sativa), 3'ss of exon 9
lower sequence: AT3G16950.2 (Arabidopsis thaliana), 3'ss of exon 9
gtggcacattctagttgcatgttgggtttcacttttcattagtta-agatatctttggatcatcatcacttcctttgatatga-acatatattactat-----gcagGTTCCAAATTTGTATTGTATTGGAGATGCCAATGGCAAACTCATGCTGGCTCATGCTGCCAGTGCACAAGGAATCTCAG
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---------------------------gtcggttttatttgcatatacataccttttccttgtcagcaattctttctatatgctaaattcatttctacttgtgatagGTTCCGAACTTGTACTGCATTGGTGATGCCAATGGTAAATTGATGCTTGCACATGCAGCCAGTGCCCAAGGAATTTCTG
upper sequence: LOC_Os01g23610.1 (Oryza sativa), 3'ss of exon 9
lower sequence: Vv14s0060g01330.t01 (Vitis vinifera), 3'ss of exon 9
gtggcacattctagttgcatgttgggtttcacttttcattagttaagatatctttggatcatcatcacttcctttgatatgaacatatat---tactatgcagGTTCCAAATTTGTATTGTATTGGAGATGCCAATGGCAAACTCATGCTGGCTCATGCTGCCAGTGCACAAGGAATCTCAG
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--------------------gttggtcattaatttcc-----ttaatgtctttgtttgttgtatttattcatcttttcattggcatgtatctttgatgaatagGTTCCTCACTTGTATTGCATTGGTGATGCAAATGGAAAAATGATGCTTGCTCATGCTGCAAGTGCCCAAGGAATCTCTG
upper sequence: LOC_Os01g23610.1 (Oryza sativa), 3'ss of exon 9
lower sequence: Vv05s0077g01210.t01 (Vitis vinifera), 3'ss of exon 9
gtggcacattctagttgcatgttgggtttcacttttcattagttaagatatctttggatcatcatcacttcct-ttgatatgaacatatattactatgcagGTTCCAAATTTGTATTGTATTGGAGATGCCAATGGCAAACTCATGCTGGCTCATGCTGCCAGTGCACAAGGAATCTCAG
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--------------------gtctgttataattctcttacaagcacactttttgtgtggcttagccgattgttactgacatggaactttttt--tat-tagGTTCCTCACTTGTATTGCATAGGTGATGCAAATGGTAAAATGATGCTTGCTCATGCAGCAAGTGCACAAGGAATTTCAG
upper sequence: LOC_Os01g23610.1 (Oryza sativa), 3'ss of exon 9
lower sequence: EFJ16882 (Selaginella moellendorffii), 3'ss of exon 9
gtggcacattctagttgcatgttgggtttcacttttcattagttaagatatctttggatcatcatcacttcctttgatatgaacatatattactatgcagGTTCCAAATTTGTATTGTATTGGAGATGCCAATGGCAAACTCATGCTGGCTCATGCTGCCAGTGCACAAGGAATCTCAG
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-----------------------------------------gttg-gttgtcttcg---tttgacaagttacat--acatga-cttttgtcttgctttagGTACCTCATTTGTACTGCATCGGCGATGCAAATGGCAAACTGATGCTTGCTCACGCTGCCAGTGCTCAGGGCATTTCAG
upper sequence: LOC_Os01g23610.1 (Oryza sativa), 3'ss of exon 9
lower sequence: EFJ06739 (Selaginella moellendorffii), 3'ss of exon 9
gtggcacattctagttgcatgttgggtttcacttttcattagttaagatatctttggatcatcatcacttcctttgatatgaacatatattactatgcagGTTCCAAATTTGTATTGTATTGGAGATGCCAATGGCAAACTCATGCTGGCTCATGCTGCCAGTGCACAAGGAATCTCAG
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-------------------------------------gttggtt--gttttcgtttgacaa--gttacatacatgact-----cttgtcttgcttt--agGTACCTCATTTGTACTGCATCGGCGATGCAAATGGCAAACTGATGCTTGCTCACGCTGCCAGTGCTCAGGGCATTTCAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.agatatctttggatcatcatcacttcctttgatatgaacatatattactatgcagGTTCCAAATTTGTATTGTATTGGAGATGCCAATGGCAAACTCATGCTGGCTCATGCTGCCAGTGCACAAGGAATCTCAG
ctttgat putative branch site (score: 5)
atatgaacatatatta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtggcacattctagttgcatgttgggtttcacttttcattagttaagatatctttggatcatcatcacttcctttgatatgaacatatattactatgcagGTTCCAAATTTGTATTGTATTGGAGATGCCAATGGCAAACTCATGCTGGCTCATGCTGCCAGTGCACAAGGAATCTCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA