Sequence
atgc intronic sequence ATGC exonic sequencegtaaactttatttacatttaagagtacttcaaaagtcctttttaggctgatcaattagatctgtgattatatcatttttctacttaaaaatatctcatttgcagGTAAAATGGTTCTACTGGATAAGTTACTTCCTAAACTAAAAGAACGTGATTCTAGGGTCCTTATATTTTCACAG
Basic information
species | Glycine max |
transcript | GLYMA07G38050.2 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA07G38050.2 (Glycine max), 3'ss of exon 9
lower sequence: LOC_Os05g05780.1 (Oryza sativa), 3'ss of exon 9
gtaaactttatttacatttaagagtacttcaaaagtcctttttaggctgatcaattagatctgtgattatatcatttttctacttaaaaatatctcatttgcagGTAAAATGGTTCTACTGGATAAGTTACTTCCTAAACTAAAAGAACGTGATTCTAGGGTCCTTATATTTTCACAG
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-------------gtactattcatccactctagtatttgtcataatttggt--actatttctgcaat---actgcacatatgatcatgcactcttattttacagGAAAAATGGTTCTGTTAGATAAATTACTTCCCAAGCTAAAGGAACGTGATTCCAGAGTACTTATTTTCTCACAG
upper sequence: GLYMA07G38050.2 (Glycine max), 3'ss of exon 9
lower sequence: GRMZM2G010085_T01 (Zea mays), 3'ss of exon 6
gtaa----actttatttacatttaagagtacttcaaaagtcctttttaggctgatcaattagatctgtgattatatcatttttctacttaaaaatatctcatttgcagGTAAAATGGTTCTACTGGATAAGTTACTTCCTAAACTAAAAGAACGTGATTCTAGGGTCCTTATATTTTCACAG
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gtaacaccatgttattttgttttcataatagt---aacatattttactacataatttatatgaatgcttattg-acagtttttttg-------atattta---catagGAAAAATGGTTCTACTTGATAAATTGCTGCCCAAGCTAAAGGAGCGTGATTCCAGAGTCCTTATTTTTTCACAG
upper sequence: GLYMA07G38050.2 (Glycine max), 3'ss of exon 9
lower sequence: AT3G06400.1 (Arabidopsis thaliana), 3'ss of exon 9
gtaaactttatttacatttaagagtacttcaaaagtcctttttaggct-gatcaattagatctgtgattatatcatttttcta-cttaaaaatatctcatttgcagGTAAAATGGTTCTACTGGATAAGTTACTTCCTAAACTAAAAGAACGTGATTCTAGGGTCCTTATATTTTCACAG
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-----------------------------gtaaggctagaaataaactagatccttcagatttctgtggaagttttttatgaagcatctctatattgttattttagGTAAGATGGTTCTCTTGGATAAATTGCTTCCTAAGTTGAAAGAACGTGATTCAAGGGTGCTGATATTTTCTCAG
upper sequence: GLYMA07G38050.2 (Glycine max), 3'ss of exon 9
lower sequence: Vv05s0020g01780.t01 (Vitis vinifera), 3'ss of exon 9
gtaaactttatttacatttaagagtact---tcaaaagtcc--tttttaggctgatcaattagatctgtgattatatcatttttctacttaaaaatatctcatttgcagGTAAAATGGTTCTACTGGATAAGTTACTTCCTAAACTAAAAGAACGTGATTCTAGGGTCCTTATATTTTCACAG
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gtaagctctgccttc-tctaaatatattgagttaagcattgggttttatggttaatcaa--agacgatcaaccctatctcttttgtacttata----------tggcagGTAAGATGGTTCTTTTGGATAAGCTACTTCCAAAGCTAAAAGAGCGTGATTCTAGGGTTCTAATATTTTCACAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atcaattagatctgtgattatatcatttttctacttaaaaatatctcatttgcagGTAAAATGGTTCTACTGGATAAGTTACTTCCTAAACTAAAAGAACGTGATTCTAGGGTCCTTATATTTTCACAG
ggctgat putative branch site (score: 4)
tctcattt putative PPT
attatatcatttttct 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaactttatttacatttaagagtacttcaaaagtcctttttaggctgatcaattagatctgtgattatatcatttttctacttaaaaatatctcatttgcagGTAAAATGGTTCTACTGGATAAGTTACTTCCTAAACTAAAAGAACGTGATTCTAGGGTCCTTATATTTTCACAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC