Sequence
atgc intronic sequence ATGC exonic sequence...aaagtattttattgatagtttctgttaatttgcaagtattaaacttgtcctgatctggagaagtataatgttgagaagtctatcatggaaatttacgtagGCCTTTAATGGGAAAAAGTGGGAGAAGTTCAACAGTGAAAAGGTTGCTTCACTGGCATATGCACGGATACAAGGAAAGGCTGCGCTTGTGATGCATTTCC
Basic information
species | Glycine max |
transcript | GLYMA08G42230.1 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA08G42230.1 (Glycine max), 3'ss of exon 9
lower sequence: Vv12s0142g00100.t01 (Vitis vinifera), 3'ss of exon 11
aaagtattttattgatagtttc--tgttaatttgcaagtattaaacttgtcctgatctggagaagtataatgtt---gagaagtctatcatg-gaaatttacgtagGCCTTTAATGGGAAAAAGTGGGAGAAGTTCAACAGTGAAAAGGTTGCTTCACTGGCATATGCACGGATACAAGGAAAGGCTGCGCTTGTGATGCATTTCC
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-----gacttgccaatgtgttggatattaccttaatacttgttaaggaagaataatg-ggagttctatcatattttggaaagacttataatgcggaatttgtgcagGCATTTAATGGAAAGAAGTGGGAAAAGTTCAACAGTGAAAAAGTTGCTTCATTGGCATATGCGCGAATACAAGGCAAGGCAGCCCTTGTTACACACTTCC
upper sequence: GLYMA08G42230.1 (Glycine max), 3'ss of exon 9
lower sequence: EFJ28200 (Selaginella moellendorffii), 3'ss of exon 10
aaagtattttattgatagtttctgttaatttgcaagtattaaacttgtcctgatctggagaagtataatgttgagaagtctatcatggaaatttacgtagGCCTTTAATGGGAAAAAGTGGGAGAAGTTCAACAGTGAAAAGGTTGCTTCACTGGCATATGCACGGATACAAGGAAAGGCTGCGCTTGTGATGCATTTCC
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-----------------------------gttcgatcaattctctcgctcc--tctggttgtaatccttgttggtggctctgt------gactttcagAG--TTTTAACGGCAAGAAGTGGGAGAAGTTCAACAGCGAAAAGGTTGCTTCTCTCGCCTACGCACGGATCCAGGGCAAGGCCGCGCTGGTCGCACACTTCC
upper sequence: GLYMA08G42230.1 (Glycine max), 3'ss of exon 9
lower sequence: EFJ28199 (Selaginella moellendorffii), 3'ss of exon 12
aaagtattttattgatagtttctgttaatttgcaagtattaaacttgtcctgatctggagaagtataatgttgagaagt-ctatcatggaaatttacgtagGCCTTTAATGGGAAAAAGTGGGAGAAGTTCAACAGTGAAAAGGTTGCTTCACTGGCATATGCACGGATACAAGGAAAGGCTGCGCTTGTGATGCATTTCC
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---------------------------------------------------gtttgacaccgttgttttcttcgtgcgcattctcattctcgatcttacagACCTTCAATGGAAAGAAGTGGGAGAAGTTCAACAGCGAGAAGGTTGCTTCTCTGGCTTACGCTCGAATACAAGGCAAGGTTGCCCTCGTCGCACATTTCC
upper sequence: GLYMA08G42230.1 (Glycine max), 3'ss of exon 9
lower sequence: EFJ29693 (Selaginella moellendorffii), 3'ss of exon 10
aaagtattttattgatagtttctgttaatttgcaagtattaaacttgtcctgatctggagaagtataatgttgagaagt-ctatcatggaaatttacgtagGCCTTTAATGGGAAAAAGTGGGAGAAGTTCAACAGTGAAAAGGTTGCTTCACTGGCATATGCACGGATACAAGGAAAGGCTGCGCTTGTGATGCATTTCC
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---------------------------------------------------gtttgacaccgttgttttcttcgtgcgcattctcattctcgatcttacagACCTTCAATGGAAAGAAGTGGGAGAAATTCAACAGCGAGAAGGTTGCTTCTCTGGCTTACGCTCGAATACAAGGCAAGGTTGCCCTCGTCGCACATTTCC
upper sequence: GLYMA08G42230.1 (Glycine max), 3'ss of exon 9
lower sequence: EFJ29695 (Selaginella moellendorffii), 3'ss of exon 8
aaagtattttattgatagtttctgttaatttgcaagtattaaacttgtc-ctgatctggagaagtataatgttgagaagtctatcatggaaatttacgtagGCCTTTAATGGGAAAAAGTGGGAGAAGTTCAACAGTGAAAAGGTTGCTTCACTGGCATATGCACGGATACAAGGAAAGGCTGCGCTTGTGATGCATTTCC
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---------------------------gttcg-----atcaattctctcgctcgtctgg----ttgtaatcctt-gttgttcgctctgtgacttt---cagAGTTTTAACGGCAAGAAGTGGGAGAAGTTCAACAGCGAAAAGGTTGCTTCTCTCGCCTACGCACGGATCCAAGGCAAGGCCGCGCTGGTCGCACACTTCC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgtcctgatctggagaagtataatgttgagaagtctatcatggaaatttacgtagGCCTTTAATGGGAAAAAGTGGGAGAAGTTCAACAGTGAAAAGGTTGCTTCACTGGCATATGCACGGATACAAGGAAAGGCTGCGCTTGTGATGCATTTCC
tcctgat putative branch site (score: 3)
aagtataat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
aaagtattttattgatagtttctgttaatttgcaagtattaaacttgtcctgatctggagaagtataatgttgagaagtctatcatggaaatttacgtagGCCTTTAATGGGAAAAAGTGGGAGAAGTTCAACAGTGAAAAGGTTGCTTCACTGGCATATGCACGGATACAAGGAAAGGCTGCGCTTGTGATGCATTTCC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - -gtttctg
- - - - - - - - - - - - - - - tgcaagt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgttgag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -catggaa