Sequence
atgc intronic sequence ATGC exonic sequence...aaatgttgctacttaattttatttttggtcgtttcccaacttatttttaaacttgatactgtttgaaattaaattgtggtgattattaatttattatcagGTGGATATGACAAGGAAGATAAGGCTGCGAGGGCTTATGATTTAGCAGCTCTAAA
Basic information
species | Glycine max |
transcript | GLYMA08G38190.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA08G38190.1 (Glycine max), 3'ss of exon 3
lower sequence: AT5G10510.2 (Arabidopsis thaliana), 3'ss of exon 3
aaatgttgctacttaattttatttttggtcgtttcccaacttatttttaaacttgatactgtttgaaattaaattgtggtgatta--ttaatttattat-cagGTGGATATGACAAGGAAGATAAGGCTGCGAGGGCTTATGATTTAGCAGCTCTAAA----------------------------------
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---aatcaacagtatacttgggtaagaacaaatatcttaatcagtcagcatgtgaataatgttgaatatgtatctgtggtgtctaactttgttaatgattcagGTGGATATGACAAAGAAGATAAGGCAGCTCGAGCTTACGATTTAGCAGCTCTGAAATACTGGAATGCTACTGCTACCACCAATTTCCCT
upper sequence: GLYMA08G38190.1 (Glycine max), 3'ss of exon 3
lower sequence: AT5G10510.1 (Arabidopsis thaliana), 3'ss of exon 4
aaatgttgctacttaattttatttttggtcgtttcccaacttatttttaaacttgatactgtttgaaattaaattgtggtgatta--ttaatttattat-cagGTGGATATGACAAGGAAGATAAGGCTGCGAGGGCTTATGATTTAGCAGCTCTAAA----------------------------------
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---------------------gtaagaacaaatatcttaatcagtcagcatgtgaataatgttgaatatgtatctgtggtgtctaactttgttaatgattcagGTGGATATGACAAAGAAGATAAGGCAGCTCGAGCTTACGATTTAGCAGCTCTGAAATACTGGAATGCTACTGCTACCACCAATTTCCCT
upper sequence: GLYMA08G38190.1 (Glycine max), 3'ss of exon 3
lower sequence: AT5G10510.3 (Arabidopsis thaliana), 3'ss of exon 4
aaatgttgctacttaattttatttttggtcgtttcccaacttatttttaaacttgatactgtttgaaattaaattgtggtgatta--ttaatttattat-cagGTGGATATGACAAGGAAGATAAGGCTGCGAGGGCTTATGATTTAGCAGCTCTAAA----------------------------------
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-----------gtatacttgggtaagaacaaatatcttaatcagtcagcatgtgaataatgttgaatatgtatctgtggtgtctaactttgttaatgattcagGTGGATATGACAAAGAAGATAAGGCAGCTCGAGCTTACGATTTAGCAGCTCTGAAATACTGGAATGCTACTGCTACCACCAATTTCCCT
upper sequence: GLYMA08G38190.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv00s1291g00010.t01 (Vitis vinifera), 3'ss of exon 3
aaatgtt-gctacttaattttatttttggtcgtttcccaacttatttttaaact---tgatactgtttgaaattaaattgtggtgattattaatttattatcagGTGGATATGACAAGGAAGATAAGGCTGCGAGGGCTTATGATTTAGCAGCTCTAAA----------------------------------
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---cgttcgcttcctttgttctttctaacaaatcctctaatactgggttgaacagtattacagagtattaaattaa-ttatgatggacttgtgtaaattatcagGTGGGTATGACAAGGAAGAAAAGGCAGCAAGGGCCTATGATTTAGCAGCTCTAAAGTACTGGGGTGCTTCTGCAACTACCAATTTCCCT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttaaacttgatactgtttgaaattaaattgtggtgattattaatttattatcagGTGGATATGACAAGGAAGATAAGGCTGCGAGGGCTTATGATTTAGCAGCTCTAAA
tattaat putative branch site (score: 2)
tttgaaattaaattgt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
aaatgttgctacttaattttatttttggtcgtttcccaacttatttttaaacttgatactgtttgaaattaaattgtggtgattattaatttattatcagGTGGATATGACAAGGAAGATAAGGCTGCGAGGGCTTATGATTTAGCAGCTCTAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC
- -tgttgct
- - - - - - - - - - - - - - - - -tcccaac
- - - - - - - - - - - - - - - - - - - - - - - - - - - gatactg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaattaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgtggtg