Sequence
atgc intronic sequence ATGC exonic sequence...gattacatttgcatctcttaactcattcgtgagagcagtggcagtgtggcactctaccatattaaccgtactgttctctttctgccgctgttaatttcagGAGTCGGCAAGGACGGCCTGATCCGGCACTTCTTCCACCGCCCGTCGAAGGCGTACACGACGGGGACGCGGAAGCGGCGGAAGGTGCACACCGACGAGCA
Basic information
species | Oryza sativa |
transcript | LOC_Os01g48130.2 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g48130.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G058518_T01 (Zea mays), 3'ss of exon 2
--gattacatttg--catctcttaactcattcgtgagagcagtggcagtgtggcactctaccatattaaccgtactgttctctttctgccgctgttaatttcagGAGTCGGCAAGGACGGCCTGATCCGGCACTTCTTCCACCGCCCGTCGAAGGCGTACACGACGGGGACGCGGAAGCGGCGGAAGGTGCACACCGACGAGCA
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acaaaaaaattaagtcgtttgttgattagcacataaaaac-gtgtct-tatgcacttccatctttttgat-atatt-tgaggacggtgtcttgatcaatttcagGTGTCGGTAAGGACGGCCTCATCCGACACTTCTTCCACCGTCCGTCTAAGGCTTACACGACCGGGACGAGGAAACGACGAAAGGTCCATACCGACGAGCA
upper sequence: LOC_Os01g48130.1 (Oryza sativa), 3'ss of exon 2
lower sequence: AT4G28500.1 (Arabidopsis thaliana), 3'ss of exon 2
gattacatttgcatctcttaactcattcgtgagagcagtggcagtgtggcactcta-ccatattaaccgtactgttctctttct-gccgctgttaattt---cagGAGTCGGCAAGGACGGCCTGATCCGGCACTTCTTCCACCGCCCGTCGAAGGCGTACACGACGGGGACGCGGAAGCGGCGGAAGGTGCACACCGACGAGCA
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-----cgatggaaattgtcatatagaaaaagaaaatgtagctaatccaatttcttaattaaattaagtttgatgaatgctaattagtcgttgaatacatatatagGAGTGAACAAGGACGGGACGGTGCGTCATTTCTTCCACCGACCGTCGAAGGCATACACGACGGGAACAAGAAAGCGACGTAAAGTCCACACTGATTCTGA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtggcactctaccatattaaccgtactgttctctttctgccgctgttaatttcagGAGTCGGCAAGGACGGCCTGATCCGGCACTTCTTCCACCGCCCGTCGAAGGCGTACACGACGGGGACGCGGAAGCGGCGGAAGGTGCACACCGACGAGCA
tgttaattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gattacatttgcatctcttaactcattcgtgagagcagtggcagtgtggcactctaccatattaaccgtactgttctctttctgccgctgttaatttcagGAGTCGGCAAGGACGGCCTGATCCGGCACTTCTTCCACCGCCCGTCGAAGGCGTACACGACGGGGACGCGGAAGCGGCGGAAGGTGCACACCGACGAGCA
- - -catttgc