Sequence
atgc intronic sequence ATGC exonic sequence...gcactagttccatgttgctctagtttcctttcttccttttatttattgacttttttggttcagtcatgaactttaaaattattgtaattgtaatctgcagATTAGTAGTCGTAATTTGGACAGAGTTCGTAAACTGAAGAGTGCAATGACAAGGCTGACTGCTAGGGTTCAAAAG
Basic information
species | Glycine max |
transcript | GLYMA20G35260.2 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA20G35260.2 (Glycine max), 3'ss of exon 4
lower sequence: AT5G64560.1 (Arabidopsis thaliana), 3'ss of exon 5
gcactagttccatgttgctctagtttcctttcttccttttatttattgacttttttggttcagtcatgaactttaaaattattgtaattgtaatctgcagATTAGTAGTCGTAATTTGGACAGAGTTCGTAAACTGAAGAGTGCAATGACAAGGCTGACTGCTAGGGTTCAAAAG
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-------------------gtaggtacct------caatgatttattatcaccagtgatccagttttcaact---acatttttacattcgt--cttgtagATTAGTAGCCGTAATTTGGATAGAGTTCGGAAATTGAAGAGTGCCATGACTCGGTTGACAGCTCGGGTTCAAAAG
upper sequence: GLYMA20G35260.2 (Glycine max), 3'ss of exon 4
lower sequence: AT5G09690.1 (Arabidopsis thaliana), 3'ss of exon 4
gcactagttccatgttgctctagtttcctttcttccttttatttattgacttttttggttcagtcatgaactttaaaattattgtaattgt---aatctgcagATTAGTAGTCGTAATTTGGACAGAGTTCGTAAACTGAAGAGTGCAATGACAAGGCTGACTGCTAGGGTTCAAAAG
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-------------gtagctaactcagcaattattgtcatcactgatctaattcca-acttcatttaactccattcagtcgatgagaaccgtttcattttgtagATAAGTAGCCGTAACTTGGAAAGAGTTCGTAAATTGAAGAGTGCCATGACCCGTTTGACAGCTCGGGTCCAAAAG
upper sequence: GLYMA20G35260.2 (Glycine max), 3'ss of exon 4
lower sequence: Vv05s0020g04720.t01 (Vitis vinifera), 3'ss of exon 4
gcactagttccatgttgctctagtt-tcctttcttccttttatttattgactttt----ttggttcagtcatgaactttaaa-attat-tgtaat-tgtaatctgcagATTAGTAGTCGTAATTTGGACAGAGTTCGTAAACTGAAGAGTGCAATGACAAGGCTGACTGCTAGGGTTCAAAAG
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--------cctatattgtttcagatatgcctctttctttttgttttttttcttctgagcttgctgcttttgtcatctttgatcattatgtgtcttctgtaaactgcagATTAGTAGCCTTAATTTGGATCGGGTTCGTAAATTGAAGAGTGCAATGACGAGATTGACTGCTCGGGTTCAAAAG
upper sequence: GLYMA20G35260.2 (Glycine max), 3'ss of exon 4
lower sequence: PP1S76_98V6.2 (Physcomitrella patens), 3'ss of exon 5
gcactagtt---ccatgttgctctagtttcctttcttccttttatttattgacttttttggttcagtcatgaactttaaaattattgta-attgtaatctgcagATTAGTAGTCGTAATTTGGACAGAGTTCGTAAACTGAAGAGTGCAATGACAAGGCTGACTGCTAGGGTTCAAAAG
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taatttgcttagccagcctaaattggtttcccttgtaccctt-attt-tttactgaat--gttgggttgttttctatgatgcttttgtgtgtcgctgagtacagATTAGTAGTCGTAATTTGGACCGCGTACGTAAGTTGAAGAGTAGCATGACAAGGCTTAATGCCCGAGTTCAGAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttgacttttttggttcagtcatgaactttaaaattattgtaattgtaatctgcagATTAGTAGTCGTAATTTGGACAGAGTTCGTAAACTGAAGAGTGCAATGACAAGGCTGACTGCTAGGGTTCAAAAG
tattgac putative branch site (score: 2)
atgaactttaaaatta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gcactagttccatgttgctctagtttcctttcttccttttatttattgacttttttggttcagtcatgaactttaaaattattgtaattgtaatctgcagATTAGTAGTCGTAATTTGGACAGAGTTCGTAAACTGAAGAGTGCAATGACAAGGCTGACTGCTAGGGTTCAAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA