Sequence
atgc intronic sequence ATGC exonic sequencegtttgtactgcctttcttgcatatgatgaatgtatttcatgcttacaaatacacattaaaaatattattagtttctctattttctcggcaaaatttctataaattgcaattgtactgatttgtcagtttaaaatatgagttcgtacttaagacattttgtgaatccctgcagCCAAGGAACACAAAGTATATGTCATTAGGGGATGGACGCAGCTTGTGCATGGAATGCCTGGATTCTGCAATCATGGACACCGGTGAATGTCAACCGCTAT
Basic information
species | Oryza sativa |
transcript | LOC_Os03g16090.2 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os03g16090.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G151934_T02 (Zea mays), 3'ss of exon 7
gtttgtactgcctttcttgcatatgatgaatgtatttcatgc-ttacaaatacacattaa---aaatattattagtttctctattttctcggcaaaatttctataaatt-gcaattgtactgatttgtcagtttaaaatatgagttcgtacttaagacattttgt------gaatccctgcagCCAAGGAACACAAAGTATATGTCATTAGGGGATGGACGCAGCTTGTGCATGGAATGCCTGGATTCTGCAATCATGGACACCGGTGAATGTCAACCGCTAT
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----gtataa--atactaggaaaaaaataatatttatcatacgctgtgcactattatgaatccacacgaaaatggttcgcatgcagttctggctacttgttttcaaactagtccttccattgactgat---tcaaaggcatttcttcaccacaagttctttttttccggttgtaattctgcagCCAAGGAACACAAAGTACATGTCACTGGGAGACGGCCGCAGCCTGTGCATGGAATGCCTGGGGTCTGCGGTCATGGACACCGGTGAATGCCAGCCCCTGT
upper sequence: LOC_Os03g16090.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G160198_T01 (Zea mays), 3'ss of exon 7
gtttgtactgcctttcttgcatatgatgaatgtatttcatgcttacaaatac-acattaaaaatattattagtttctctattttctcggcaaaatttctataaattgcaattgtactgatttgtcagtttaaaatatgagttcgtacttaagacattttgtgaatccctgcagCCAAGGAACACAAAGTATATGTCATTAGGGGATGGACGCAGCTTGTGCATGGAATGCCTGGATTCTGCAATCATGGACACCGGTGAATGTCAACCGCTAT
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------------------------------------------gtacagatactagatagaaaatgtggtcg--cagtccgatcactcg-------ttttcaaactaggttgtacattgcctgatcatattcaag---ggcatcacttttcgg-----ttgtgatt--gtgcagCCAAGGAACACGAAGTACATGTCGCTGGGAGACGGACGCGGCCTGTGCATGGAATGCCTGGGATCTGCAGTGATGGACACGAGCGAGTGCCAGCCTCTGT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atttgtcagtttaaaatatgagttcgtacttaagacattttgtgaatccctgcagCCAAGGAACACAAAGTATATGTCATTAGGGGATGGACGCAGCTTGTGCATGGAATGCCTGGATTCTGCAATCATGGACACCGGTGAATGTCAACCGCTAT
tactgat putative branch site (score: 2)
tccctgc putative PPT
tttaaaatatgagtt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtttgtactgcctttcttgcatatgatgaatgtatttcatgcttacaaatacacattaaaaatattattagtttctctattttctcggcaaaatttctataaattgcaattgtactgatttgtcagtttaaaatatgagttcgtacttaagacattttgtgaatccctgcagCCAAGGAACACAAAGTATATGTCATTAGGGGATGGACGCAGCTTGTGCATGGAATGCCTGGATTCTGCAATCATGGACACCGGTGAATGTCAACCGCTAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA