Sequence
atgc intronic sequence ATGC exonic sequencegtaagaaagtcaacctgcatgagctttgatattattgtgacgttttcacttttacacaataagcaagtctttgctcctccagGTCTAAATTTGTCAACTGAGTACACTGTACCAGAAGAAGTTAAAACTGCAGGCTTTGAAATTTGTGCTGATGAGCTGGGATCAATTGTTGAGGGACGTGA
Basic information
species | Glycine max |
transcript | GLYMA04G04810.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA04G04810.1 (Glycine max), 3'ss of exon 2
lower sequence: AT1G27770.1 (Arabidopsis thaliana), 3'ss of exon 2
gtaagaa-agtcaacctgcatgagctttgatattattgtgacgttttcacttttacacaataagcaagtctt-tgctcctccagGTCTAAATTTGTCAACTGAGTACACTGTACCAGAAGAAGTTAAAACTGCAGGCTTTGAAATTTGTGCTGATGAGCTGGGATCAATTGTTGAGGGACGTGA
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gtgagaatagactactcccttgtgttattcaat-------atgtatttgatttc-cttaacgagaaggtattgcgtgcttacagGTTTAAAGTTGTCCAGTGAGTATACACTACCTGAAGAAGTAAGAAAAGCAGGGTTTGAGATTTGTCCTGATGAGTTGGGATCAATTGTAGAAGGTCATGA
upper sequence: GLYMA04G04810.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv18s0001g09150.t01 (Vitis vinifera), 3'ss of exon 2
gtaagaaagtc---aacctgcatgagctttgatattattgtgacgttttcacttttacacaataagcaagtctttgctcctccagGTCTAAATTTGTCAACTGAGTACACTGTACCAGAAGAAGTTAAAACTGCAGGCTTTGAAATTTGTGCTGATGAGCTGGGATCAATTGTTGAGGGACGTGA------
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gtaagaacatcttcagtcttctccaactcaaaggttctgatagtgaggtgtgccttttttattgga-----tttcccttcaatgccttcagGTTTGTCCAGTGACTACGTTGCACCTGAGGAAGTAACAGCTGCAGGTTTTCAAATTTGTGCTGATGAGTTGGGATCAATTGTGGAAGGCCATGACTTAAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gatattattgtgacgttttcacttttacacaataagcaagtctttgctcctccagGTCTAAATTTGTCAACTGAGTACACTGTACCAGAAGAAGTTAAAACTGCAGGCTTTGAAATTTGTGCTGATGAGCTGGGATCAATTGTTGAGGGACGTGA
ctttgat putative branch site (score: 5)
tctttgctcctcc putative PPT
actttta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagaaagtcaacctgcatgagctttgatattattgtgacgttttcacttttacacaataagcaagtctttgctcctccagGTCTAAATTTGTCAACTGAGTACACTGTACCAGAAGAAGTTAAAACTGCAGGCTTTGAAATTTGTGCTGATGAGCTGGGATCAATTGTTGAGGGACGTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT