Sequence
atgc intronic sequence ATGC exonic sequencegtgagttcttttacgcttccttccttttaattatttttaatatagacttatgctaaaaaatttaaagttagtgtaagcgtgtaactgttgtacttctttgttttaatgtttttttttaagtcaaatcttctttctttgcgcaattgatctttcctcccctttattatttgtaaagGTGGTGTCATGACATTGGTCGCGAACAAGCTGCAAATAAGCCGCTTTTAAAAACTGTGTTTCAG
Basic information
species | Glycine max |
transcript | GLYMA15G02780.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA15G02780.1 (Glycine max), 3'ss of exon 5
lower sequence: AC196426.3_FGT007 (Zea mays), 3'ss of exon 3
gtgagttcttttacgcttccttccttttaattatttttaatatagacttatgctaaaaaatttaaagttagtgtaagcgtgtaactgttgtacttctttgttttaatgtttttttttaagtcaaatcttctttctttgcgcaattgatctttcctcccctttattatttgtaaagGTGGTGTCATGACATTGGTCGCGAACAAGCTGCAAATAAGCCGCTTTTAAAAACTGTGTTTCAG----
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------------------------------------------------------------------------gtaagtttgtt-tagtgaagcgatcgttgttggacttggaatcttggaccta---ttatccccttgtgcaactcaaaattcttttgtttt----cctgtatagGTGGTGTCATGACATTGGCAGAGAACAGGCTGCAAACAAGCCTCTTTTGAAGACTGTTTTCCAGGCAA
upper sequence: GLYMA15G02780.1 (Glycine max), 3'ss of exon 5
lower sequence: AT3G13870.2 (Arabidopsis thaliana), 3'ss of exon 5
gtgagttcttttacgcttccttccttttaattatttttaatatagacttatgctaaaaaatttaaagttagtgtaagcgtgtaactgttgtactt--ctttgttttaatgtttttttttaagtcaaatcttctttctttgcgcaattgatctttcctccccttt-attatttgtaaagGTGGTGTCATGACATTGGTCGCGAACAAGCTGCAAATAAGCCGCTTTTAAAAACTGTGTTTCAG
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--------------------------------------------------------------------------------gtaagtggtgttctttactttgttttctttgatattaatagataacagga-cttcttttgccgtctttatcttatatcttctcggatttgtaatgcagGTGGTGTCATGATATTGGTCGGGAACAAGCAGCAAATAAACCTCTTTTAAAGACTGTGTTCCAG
upper sequence: GLYMA15G02780.1 (Glycine max), 3'ss of exon 5
lower sequence: AT1G72960.1 (Arabidopsis thaliana), 3'ss of exon 5
gtgagttcttttacgcttccttccttttaattatttttaatatagacttatgctaaaaaatttaaagttagtgtaagcgtgtaactgttgtacttctttgttttaatgtttttttttaagtcaaatcttctttctttgcgcaattgatctttcctcccctttattatttgtaaagGTGGTGTCATGACATTGGTCGCGAACAAGCTGCAAATAAGCCGCTTTTAAAAACTGTGTTTCAG
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-----------------------------------------------------------gtaagattgtagtggaaacatcaaaatat-gcagctttcggttttggtg---------aaaggaaag--tgtttcgttacaaa------ttctcaatgcttgtgctttt-----agGTGGTGTCACGACATTGGCCGTGAACAAGCTGCTAATAAACCTCTCTTGAAAACTGTCTTTCAG
upper sequence: GLYMA15G02780.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv09s0002g02200.t01 (Vitis vinifera), 3'ss of exon 5
gtgagttcttttacgcttccttccttttaattatttttaatatagacttatgctaaaaaatttaaagttagtgtaagcgtgtaactgttgtacttctttgttttaatgtttttttttaagtcaaatcttctttctttgcgcaattgatctttcctcccctttattatttgtaaagGTGGTGTCATGACATTGGTCGCGAACAAGCTGCAAATAAGCCGCTTTTAAAAACTGTGTTTCAG
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-----------------------------gtaagttttattacaaaacaaggc-atataacttggattctaca-gattatgtttcagttaaacat----gttttgaggtatctctttaa------------tggtttatgcgagtaatatcttgaagcgaattttgttt----agGTGGTGTCATGATATTGGTCGTGAGCAGGCTGCAAATAAGCCTCTTCTGAAAACTGTATTCCAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcaaatcttctttctttgcgcaattgatctttcctcccctttattatttgtaaagGTGGTGTCATGACATTGGTCGCGAACAAGCTGCAAATAAGCCGCTTTTAAAAACTGTGTTTCAG
aattgat putative branch site (score: 4)
tctttcctccccttta CT-rich tract
tttattatttgtaaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgagttcttttacgcttccttccttttaattatttttaatatagacttatgctaaaaaatttaaagttagtgtaagcgtgtaactgttgtacttctttgttttaatgtttttttttaagtcaaatcttctttctttgcgcaattgatctttcctcccctttattatttgtaaagGTGGTGTCATGACATTGGTCGCGAACAAGCTGCAAATAAGCCGCTTTTAAAAACTGTGTTTCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC