Sequence
atgc intronic sequence ATGC exonic sequencegtaaattaagccagagtgtctctgctatgctctaaaactatgcaaatgaattggttatatctatgatagactttatacatgggcagGTCCTTCAGGAAAAAGGTATCCATATATGGGATGGGAATGCGTCAAGAGAGTATCTCGATGG
Basic information
species | Arabidopsis thaliana |
transcript | AT2G16370.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT2G16370.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G139880_T01 (Zea mays), 3'ss of exon 4
-------gtaaattaa-gccagagtgtctctgctatgctctaa--aactatgcaaa---tgaattggttatatctatgatagac-tttatacatgggcagGTCCTTCAGGAAAAAGGTATCCATATATGGGATGGGAATGCGTCAAGAGAGTATCTCGATGG
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tttgataaaaaataaatgtcagaattcttctccaaatcctgagtggattaaactatctcttgaaaggtcctgttttctaaacatgcccttccatttgtagGTTTTGCAAGAAAAGGGTATTCATATCTGGGATGGCAATGCTTCAAGAGAGTATCTTGACCG
upper sequence: AT2G16370.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G005990_T01 (Zea mays), 3'ss of exon 5
--------gtaaattaagccagagtgtctctgctatgctctaa--aactatgcaaatgaatt---ggttatatctatgatagactttataca-tgggcagGTCCTTCAGGAAAAAGGTATCCATATATGGGATGGGAATGCGTCAAGAGAGTATCTCGATGG
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tttgagaaaaaggaaatgtcaaaattgttctccaaatcctgagtggattaaactatttctttaaaggtcatgttttctgaacacacccttcaatttatagGTTTTGCAAGAGAAGGGTATTCATATCTGGGATGGCAATGCTTCAAGAGAGTATCTCAACAG
upper sequence: AT2G16370.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA11G12280.1 (Glycine max), 3'ss of exon 4
--------------------gtaaattaagccagagtgtctctgctatgctctaaa-actatgcaaatgaattggttatatctatgatagactttatacatgggcagGTCCTTCAGGAAAAAGGTATCCATATATGGGATGGGAATGCGTCAAGAGAGTATCTCGATGG
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cattacatgtagtttttgttgttgattca-caagaatgtcttactggttcattagatattactataatgaatt--ttat-tctggaa---acatgttatattgacagGTGCTGCAGGAAAAAGGCATTCATATATGGGATGGCAATGCATCCAGAGA------------ atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctaaaactatgcaaatgaattggttatatctatgatagactttatacatgggcagGTCCTTCAGGAAAAAGGTATCCATATATGGGATGGGAATGCGTCAAGAGAGTATCTCGATGG
ctctaaa putative branch site (score: 3)
ttatatctatgata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaattaagccagagtgtctctgctatgctctaaaactatgcaaatgaattggttatatctatgatagactttatacatgggcagGTCCTTCAGGAAAAAGGTATCCATATATGGGATGGGAATGCGTCAAGAGAGTATCTCGATGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA