Sequence
atgc intronic sequence ATGC exonic sequence...ttctgataaaatattgaactaccactcaccatcagctcttatgtttttggtatcagctttttgacttatttgttgtttcccctgtttgttctctttgcagATTCTCAACCCAAATCCTGATGCAATGTCTAAGATGATTACAGAAAATGCCAGCGAGGAATTTCTATATTCACTGAGTAATTATTGTGCACTTCAG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv12s0035g01920.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: LOC_Os05g01470.1 (Oryza sativa), 3'ss of exon 3
ttctgataaaatattgaactaccactcaccatcagctcttatgtttttggtatcagctttttgacttatttgttgtttcccctgtttgttctctttgcagATTCTCAACCCAAATCCTGATGCAATGTCTAAGATGATTACAGAAAATGCCAGCGAGGAATTTCTATATTCACTGAGTAATTATTGTGCACTTCAG
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-----gtacagtcatgctaatatattcttttttgaaaggaaattatagtaaaccagacggaaggaaaactc-ttactccccaaatcc--tcccttttcagATTCTTAACCCAAATCCAGAAGCAATGTCAAAGATCGTAACTGAAAATTCCAGTGAGGAGTTCTTGTATTCATTGAGTAACTACTGTGCTCTTCAG
upper sequence: Vv12s0035g01920.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA16G00210.1 (Glycine max), 3'ss of exon 3
-ttctgataaaatattgaactaccactcacca-tcagctcttatgt-ttttggtatcagctttttgacttatttgt-tgtttcccctgtttgttctctttgcagATTCTCAACCCAAATCCTGATGCAATGTCTAAGATGATTACAGAAAATGCCAGCGAGGAATTTCTATATTCACTGAGTAATTATTGTGCACTTCAG
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cttttagcag--tcatgagtcttaatgaattggtttatccttgggtgttttgacatcatcgttt-gattaatacaaatttttctattgattggt-tccctgtagATTCTTAATCCAAATCCAGATGCAATGTCTAAGATGATAACAGAAAATGCAAGCGAGGAATTCCTGCATTCATTGAGTAATTATTGTGCACTTCAG
upper sequence: Vv12s0035g01920.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA12G28490.1 (Glycine max), 3'ss of exon 3
ttctgataaaatattgaactaccactcaccatcagctcttatgt-ttttggtatcagctttttgacttatttgt-tgtttcccctgtttgttctctttgcagATTCTCAACCCAAATCCTGATGCAATGTCTAAGATGATTACAGAAAATGCCAGCGAGGAATTTCTATATTCACTGAGTAATTATTGTGCACTTCAG
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ttttagcagtcatgagttttaatgaatttggtttatccttgggtgttttggcatcatcattt-gattaatacaaatttttctattggttgg-ctccctgcagATTCTTAATCCAAATCCAGATGCAATGTCTAAGATGATAACAGAAAACGCAAGCGAGGAATTCCTGCATTCATTGAGTAATTATTGTTCACTTCAG
upper sequence: Vv12s0035g01920.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: AT5G49810.1 (Arabidopsis thaliana), 3'ss of exon 3
------ttctgataaaatattgaactaccactcaccatcagctcttatgtttttggtatcagctttttgacttatttgttgtttcccctgt-----ttgttctctttgcagATTCTCAACCCAAATCCTGATGCAATGTCTAAGATGATTACAGAAAATGCCAGCGAGGAATTTCTATATTCACTGAGTAATTATTGTGCACTTCAG
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gtagtttgtccttctggtctctaataacttatatgtgtaggatttcaatctccgaaaaactgacgttttccttttatgcatgcttccttgtatcttatgctcttgtggcagATTCTTAATCCAAACCCAGAAGCTATGTCTAAGCTGATCACAGAAAATGCAAGTGAGGAATTTCTCCATTCGCTGAGTAACTATTGTGCCCTTCAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttggtatcagctttttgacttatttgttgtttcccctgtttgttctctttgcagATTCTCAACCCAAATCCTGATGCAATGTCTAAGATGATTACAGAAAATGCCAGCGAGGAATTTCTATATTCACTGAGTAATTATTGTGCACTTCAG
ttttgac putative branch site (score: 3)
tttgttgtttcccctg putative PPT
tttttgacttattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttctgataaaatattgaactaccactcaccatcagctcttatgtttttggtatcagctttttgacttatttgttgtttcccctgtttgttctctttgcagATTCTCAACCCAAATCCTGATGCAATGTCTAAGATGATTACAGAAAATGCCAGCGAGGAATTTCTATATTCACTGAGTAATTATTGTGCACTTCAG
- - gataaaa
- - - - - - - - - - -ccactca
- - - - - - - - - - - - - - -catcagc