Sequence
atgc intronic sequence ATGC exonic sequencegttatcttactttttaaataatcaattattaactctctgtcttgtaatgtctcttctgagttgcataagattgcaatccaaatgctatgaaggtacttgcatcttacatatgttgtttgtttttcctccagTCATTCGCCCGGATGAACAAGAAAGATTCATGGCTTTTCTGGTGAACGCTTTACCTTACAGTAAGAAAACATCGATTGGTTACACATTAGAGCAT
Basic information
species | Glycine max |
transcript | GLYMA03G38940.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA03G38940.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G048117_T01 (Zea mays), 3'ss of exon 3
gttatcttactttttaaataatcaattattaactctctgtcttgtaatgtctct-tctgagttgcataagattgcaatccaaatgctatg-aaggtacttgcatcttacatatgttgtttgtttttcctccagTCATTCGCCCGGATGAACAAGAAAGATTCATGGCTTTTCTGGTGAACGCTTTACCTTACAGTAAGAAAACATCGATTGGTTACACATTAGAGCAT
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------------------------------------------------gtctgtgcctgctttgcctgtgatgttaattgtattcgtgtgtgaaattgttgcaggttg--taacttgaatgttc--cctgcagTCTCTCGCTCGGATGAACAAGAAGGATTCATGGCTGTTCTGGTGGACTCTTTACTTGACT-----------------------------------
upper sequence: GLYMA03G38940.1 (Glycine max), 3'ss of exon 3
lower sequence: AT1G09330.1 (Arabidopsis thaliana), 3'ss of exon 3
gttatcttactttttaaataatcaattattaactctctgtcttgtaatgtctcttctgagttgcataagattgcaatccaaatgctatgaaggtacttgcat-cttacatatgttgtttgtttttcc-tccagTCATTCGCCCGGATGAACAAGAAAGATTCATGGCTTTTCTGGTGAACGCTTTACCTTACAGTAAGAAAACATCGATTGGTTACACATTAGAGCAT
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-----gttagcttttcttcacttattcacaag------gatatgggttcagcctgtcgagaaatgtggggttgtgtttccctttccgttttttt-tttgtatactcatgtgttttcatcatttttctatacagTCTTTGGCTCGGATGAACAAGAAAGACTCATGGCTTTTCTGGTGGACACTTTACCTTGCA-----------------------------------
upper sequence: GLYMA03G38940.1 (Glycine max), 3'ss of exon 3
lower sequence: PP1S6_365V6.1 (Physcomitrella patens), 3'ss of exon 3
gttatcttactttttaaataatcaattattaactctctgtcttgtaatgtctcttctgagttgcataagattgcaatccaaatgctatgaaggtacttgcatcttacatatgttgtttgtttttcctccagTCATTCGCCCGGATGAACAAGAAAGATTCATGGCTTTTCTGGTGAACGCTTTACCTTACAGTAAGAAAACATCGATTGGTTACACATTAGAGCAT
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-------------------tccaagttattgagggattga--tgtagtttctattcaaa-----atgaattcgtagt--aagagat-tgcagatgttg--acttaagattggttatggatgacgtctgcagACCTTGGAGACATTGAACAAGAAAGATGCTTGGCTATTCTGGTGGACGCTGTACCTTACT----------------------------------- atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tccaaatgctatgaaggtacttgcatcttacatatgttgtttgtttttcctccagTCATTCGCCCGGATGAACAAGAAAGATTCATGGCTTTTCTGGTGAACGCTTTACCTTACAGTAAGAAAACATCGATTGGTTACACATTAGAGCAT
atcttac putative branch site (score: 3)
ttgtttgtttttcctc putative PPT
tttgttttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttatcttactttttaaataatcaattattaactctctgtcttgtaatgtctcttctgagttgcataagattgcaatccaaatgctatgaaggtacttgcatcttacatatgttgtttgtttttcctccagTCATTCGCCCGGATGAACAAGAAAGATTCATGGCTTTTCTGGTGAACGCTTTACCTTACAGTAAGAAAACATCGATTGGTTACACATTAGAGCAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA