Sequence
atgc intronic sequence ATGC exonic sequencegtatgctttactcatttcagttctttgtcaggaagtaatttgcagaggcttcatgttattgtgctcccctagctttttaactaaacaagtatctccttaacagGCAATCATTGATGCTGCATCCTATGTACCTCCACCCCCTTCAGAAGAGCAAAAGAAGAAGGTTGAAAAAAT
Basic information
species | Oryza sativa |
transcript | LOC_Os03g14510.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os03g14510.2 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G170532_T01 (Zea mays), 3'ss of exon 5
gtatgctttactcatttcagttctttgtcaggaagtaatttgcagaggcttcatgttattgtgctcccctagctttttaactaaacaagtatctccttaacagGCAATCATTGATGCTGCATCCTATGTACCTCCACCCCCTTCAGAAGAGCAAAAGAAGAAGGTTGAAAAAAT
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-----------------------------gtatgcttcttcaattcagtttcattttctagggctagaccacttacattactccacaa-tttgccctgaacagGCAATCATTGATGCTGCATCATATGTTCCTCCACCCCCAACAGAAGACCAAAAGAAAAAGATTGAAAAAAT
upper sequence: LOC_Os03g14510.2 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA05G03930.1 (Glycine max), 3'ss of exon 5
-----------gtatgctttactcatttcagttctttgtcaggaagtaatttgcagaggcttcatgttattgtgctcccctagctttttaactaaacaagtatctccttaacagGCAATCATTGATGCTGCATCCTATGTACCTCCACCCCCTTCAGAAGAGCAAAAGAAGAAGGTTGAAAAAAT
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caacaacataaattgagttcattcacttcttttcttgttcctaaa--aactggcttttaccta--gcaatggtgcttttctgtttatttaatggcaaaa----------aatagGAAATCATTGATGCAGCATCTCATGTCCCACCACCTCCCTCAGAAGATCAAAAGAAGAAAATTGCAAAGAT
upper sequence: LOC_Os03g14510.2 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA17G14410.1 (Glycine max), 3'ss of exon 5
--gtatgctttactcatttcagttctttgtcaggaagtaatttgcagaggcttcatgttattgtgctcccctagctttttaactaaacaagtatctccttaacagGCAATCATTGATGCTGCATCCTATGTACCTCCACCCCCTTCAGAAGAGCAAAAGAAGAAGGTTGAAAAAAT
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caacaacataaattgagttcatttacctcttttc---ttgtttctaaaaactggcttttacttagcaatggt-gcttttctgtttatttaatggcaaaa-aatagGAAATCATTGATGCGGCATCTTATGTTCCGCCGCCTCCCTCAGAAGAGCAAAAGAAGAAAATTGCGAAGAT
upper sequence: LOC_Os03g14510.2 (Oryza sativa), 3'ss of exon 5
lower sequence: Vv02s0241g00090.t01 (Vitis vinifera), 3'ss of exon 6
-----gtat-gctttactcatt-tcagttctttgtcaggaagtaatttgcagaggcttcatgttattgt-gctcccctagctttttaactaaacaagtatctccttaacagGCAATCATTGATGCTGCATCCTATGTACCTCCACCCCCTTCAGAAGAGCAAAAGAAGAAGGTTGAAAAAAT
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tgtcattattgtgtgacttgctgttgattatttttgaagtgatgttttgttgaga-ttaattttattattgattttccattattttgaatgaataa----------aacagGCAATTATTGATGCTGCTTCATATGTCCCACCGCCCCCATCAGAAGAGCAGAAGAAAAAAATTGCCAAGTT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cttcatgttattgtgctcccctagctttttaactaaacaagtatctccttaacagGCAATCATTGATGCTGCATCCTATGTACCTCCACCCCCTTCAGAAGAGCAAAAGAAGAAGGTTGAAAAAAT
aactaaa putative branch site (score: 2)
tatctcctt putative PPT
tttttaactaaacaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgctttactcatttcagttctttgtcaggaagtaatttgcagaggcttcatgttattgtgctcccctagctttttaactaaacaagtatctccttaacagGCAATCATTGATGCTGCATCCTATGTACCTCCACCCCCTTCAGAAGAGCAAAAGAAGAAGGTTGAAAAAAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG