Sequence
atgc intronic sequence ATGC exonic sequencegtatgtgaaattttaaagcagcataccaagggattgtgttgttctgcatctgtgaatgaaattttgttcattttgatttatacattaccgtgtcgttcatgtagGTTCTGGAGTTAGGATTGAATTTTCTCACGGCTGATGATATGAGTGCTATACTTGCTGTGAAACTAAGAAAAAGGTTGGGCTTTGGAATGTGGGCAAAAC
Basic information
species | Glycine max |
transcript | GLYMA15G39380.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA15G39380.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G144403_T01 (Zea mays), 3'ss of exon 5
gtatgtgaaattttaaagcagcataccaagggattgtgttgttctgcatctgtgaatgaaattttgttcattttgatttatacattaccgtgtcgttcatgtagGTTCTGGAGTTAGGATTGAATTTTCTCACGGCTGATGATATGAGTGCTATACTTGCTGTGAAACTAAGAAAAAGGTTGGGCTTTGGAATGTGGGCAAAAC
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----gt-aggtactaccgttgtttg--atctgaatat-ttcctttacttctatgggcaa-------ttgacaataatctgcattcattttaaccttttatctagGTTCTTGAGCTGGGATTGAATTTTCTTTCTGCTGAAGATATGAGTGCTGTACTTGCTATGCAGCTGCACAAGAGTGTGGGACTTGGAATGACTGCAAAGA
upper sequence: GLYMA15G39380.1 (Glycine max), 3'ss of exon 4
lower sequence: AT3G14590.1 (Arabidopsis thaliana), 3'ss of exon 3
gtatgtgaaattttaaagcagcataccaagggattgtgttgttctgcatctgtgaatg--aaattttgttcattttgatttatacattaccgtgtcgttcatgtagGTTCTGGAGTTAGGATTGAATTTTCTCACGGCTGATGATATGAGTGCTATACTTGCTGTGAAACTAAGAAAAAGGTTGGGCTTTGGAATGTGGGCAAAAC
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---------------------------gtatagttgcacaatttcagttctataagctctaagttctatagag---aaagtataacttatattggagtgtgtacagGTACTGGAACTTGGAATGAATTTCCTCACAGCAGATGATATGAGCGCAATACTCGCTGTGAAGTTAAGAAAAAGACTTGGGTTTGGAATGTGGACAAAGT
upper sequence: GLYMA15G39380.1 (Glycine max), 3'ss of exon 4
lower sequence: AT1G53590.1 (Arabidopsis thaliana), 3'ss of exon 4
gtatgtgaaattttaaagcagcataccaagggattgtgttgttctgcatctgtgaatgaaattttgttcattttgatttatacattaccgtgtcgttcatgtagGTTCTGGAGTTAGGATTGAATTTTCTCACGGCTGATGATATGAGTGCTATACTTGCTGTGAAACTAAGAAAAAGGTTGGGCTTTGGAATGTGGGCAAAAC
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----gtatatttgtaacgcctcata-----gaacatcatactttggcctcttc--------cctccttgatctatagtagaac-ttatgctggagtttatgcagGTACTGGAACTTGGTATGAATTTTCTCGCAGCAGATGATATGAGTGCAATACTTGCTGTGAAATTAAGGAAAAGGCTTGGTTTTGGGATGTGGACAAAGT
upper sequence: GLYMA15G39380.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv19s0138g00140.t01 (Vitis vinifera), 3'ss of exon 4
gtatgtgaaattttaaagcagcataccaagggattgtgttgttctgcatctgtgaatgaaattt-tgttcattttgatttatacattaccgtgtcgttcatgtagGTTCTGGAGTTAGGATTGAATTTTCTCACGGCTGATGATATGAGTGCTATACTTGCTGTGAAACTAAGAAAAAGGTTGGGCTTTGGAATGTGGGCAAAAC
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gtatgtttgact---agccctggaatggtggaaccttactgtgttatctattgggatactattgacataagtcttcagagattcagtg--attcaattaatgcagGTTTTGGGGTTGGGAATGAATTTTCTCACTGCTGATGATATGAGTGCAATACTAGCTATAAAACTGAGGAGAAGATTGGGATTTGGAATGTGGGCAAAAT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctgtgaatgaaattttgttcattttgatttatacattaccgtgtcgttcatgtagGTTCTGGAGTTAGGATTGAATTTTCTCACGGCTGATGATATGAGTGCTATACTTGCTGTGAAACTAAGAAAAAGGTTGGGCTTTGGAATGTGGGCAAAAC
ttttgat putative branch site (score: 4)
aaattttgttcatttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgtgaaattttaaagcagcataccaagggattgtgttgttctgcatctgtgaatgaaattttgttcattttgatttatacattaccgtgtcgttcatgtagGTTCTGGAGTTAGGATTGAATTTTCTCACGGCTGATGATATGAGTGCTATACTTGCTGTGAAACTAAGAAAAAGGTTGGGCTTTGGAATGTGGGCAAAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA