Sequence
atgc intronic sequence ATGC exonic sequence...atttggtatctgttcatttgcatatattgctgtgtcaaaaattctttccgtcatactgttttatctcaaggtttgatactgttttctataattcgaacagGGAAGAGCACACTATTAAATCATTTGTTTGGTACCAACTTCAGGGAGATGGATGCTTTTAGAGGAAG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv09s0002g02200.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA07G01230.1 (Glycine max), 3'ss of exon 2
atttggtatctgttc--atttgcatatattgctgtgtcaaaaattctttccgtcatactgttttatctcaaggtttgatact--gttttctataattcgaacagGGAAGAGCACACTATTAAATCATTTGTTTGGTACCAACTTCAGGGAGATGGATGCTTTTAGAGGAAG
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--tttgcgtttgtttaaatttgttagcataa-tgagatgattactattcccaataaaaggatctttat-attatctagttctttgttttctttgctctggacagGCAAGAGCACACTGTTAAATCATTTGTTTGGTACCAACTTCAGAGAGATGGATGCTTTTAAGGGAAG
upper sequence: Vv09s0002g02200.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA08G20610.1 (Glycine max), 3'ss of exon 2
atttggtatctgttcatttgcatatat-tgctgtgtcaaaaattctttccgtcatactgttttatctcaaggtttgatact--gttttctataattcgaacagGGAAGAGCACACTATTAAATCATTTGTTTGGTACCAACTTCAGGGAGATGGATGCTTTTAGAGGAAG
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--tttgcatttgtttaaatttatttgcataacgagatgattactattcccaataaaaggatctttat-attatctagttctttgttttctttgctctgggcagGCAAGAGCACGCTATTAAATAATTTGTTTGGTACCAACTTCAGAGAGATGGATGCTTTTAAGGGAAG
upper sequence: Vv09s0002g02200.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: AT3G13870.1 (Arabidopsis thaliana), 3'ss of exon 2
--atttggtatctgttcatttgcatatattg-ctgtgtcaaaaattctttccgtcatactgttttatctcaaggtttgatactgttttctataattcgaacagGGAAGAGCACACTATTAAATCATTTGTTTGGTACCAACTTCAGGGAGATGGATGCTTTTAGAGGAAG
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gtatgtatcaaatccttgaatgtaaaaagtggcttctttggaatctattttttgtatattggctgattttatg---tcattctggttg----aatttg--cagGGAAGAGTACGCTCTTGAATCATTTGTTTGGAACCAACTTTAGAGAAATGGATGCATTTAGAGGAAG
upper sequence: Vv09s0002g02200.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: AT3G13870.2 (Arabidopsis thaliana), 3'ss of exon 2
--atttggtatctgttcatttgcatatattg-ctgtgtcaaaaattctttccgtcatactgttttatctcaaggtttgatactgttttctataattcgaacagGGAAGAGCACACTATTAAATCATTTGTTTGGTACCAACTTCAGGGAGATGGATGCTTTTAGAGGAAG----
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gtatgtatcaaatccttgaatgtaaaaagtggcttctttggaatctattttttgtatattggctgattttatg---tcattctggttg----aatttg--cagGGAAGAGTACGCTCTTGAATCATTTGTTTGGAACCAACTTTAGAGAAATGGATGCATTTAGAGGAAGGCAT
upper sequence: Vv09s0002g02200.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: AT1G72960.1 (Arabidopsis thaliana), 3'ss of exon 2
atttggtatctgttcatttgcatatattg---ctgtgtcaaaaattctttccgtcatactgtt-ttatctcaaggtttgatactgttttctataattcgaacagGGAAGAGCACACTATTAAATCATTTGTTTGGTACCAACTTCAGGGAGATGGATGCTTTTAGAGGAAG
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-----gtatgcattcctttagagaagatggacttttgtaataatcagaatttgtttgaatgtagttagttca---tttacagaaatgttttgtgatttga-cagGGAAAAGTACACTATTGAACCATTTGTTTGGAACAAACTTTATGGAGATGGATGCATTCAAGGGAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttccgtcatactgttttatctcaaggtttgatactgttttctataattcgaacagGGAAGAGCACACTATTAAATCATTTGTTTGGTACCAACTTCAGGGAGATGGATGCTTTTAGAGGAAG
gtttgat putative branch site (score: 5)
tgttttctataatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
atttggtatctgttcatttgcatatattgctgtgtcaaaaattctttccgtcatactgttttatctcaaggtttgatactgttttctataattcgaacagGGAAGAGCACACTATTAAATCATTTGTTTGGTACCAACTTCAGGGAGATGGATGCTTTTAGAGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - catttgc
- - - - - - - - - - - - - ttgctgt
- - - - - - - - - - - - - - - - - tcaaaaa