Sequence
atgc intronic sequence ATGC exonic sequencegtaagtcccttagacctttgtgctgaattttgcaaggacttgcttcttctttttttttttttaatctattgatattattataaatttattattatgtatttttcatattgcatttctgctcctgaccatttcagGATCCAAGGTTGTTGGGCGAGATACATGTTGCTCTCCTGAGATCCATCATTAAGGATATTGAAGATGTTGCCCGAACACCCTCCATTGGGCTGGGCGCAA
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv12s0028g03090.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: LOC_Os05g48820.1 (Oryza sativa), 3'ss of exon 9
gtaagtcccttagacctttgtgctgaattttgcaaggacttgcttcttctttttttttttttaatctattgatattattataaatttattattatgtatttttcatattgcatttctgctcctgaccat--ttcagGATCCAAGGTTGTTGGGCGAGATACATGTTGCTCTCCTGAGATCCATCATTAAGGATATTGAAGATGTTGCCCGAACACCCTCCATTGGGCTGGGCGCAA
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--------------------------------cgagcatttaacttttggtacatgtat---gattcattctcacatctaatattttttagctgcttgttctatgtga-gtatgactattgatattcatgctatagGATTCAAGGTTGTTGGGAGAATTGCATGTTGCTCTGCTGAAATCCATAATAAAAGATATTGAGGATGTTGCCCGGACTCCTTCAGTTGCTTCAGGGATGA
upper sequence: Vv12s0028g03090.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: LOC_Os01g48180.1 (Oryza sativa), 3'ss of exon 8
gtaagtcccttagacctttgtgctgaattttgcaaggacttgcttcttctttttttttttttaatctattgatattattataaatttattattatgtatttttcatattgcatttctgctcctgaccatttcagGATCCAAGGTTGTTGGGCGAGATACATGTTGCTCTCCTGAGATCCATCATTAAGGATATTGAAGATGTTGCCCGAACACCCTCCATTGGGCTGGGCGCAA
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--------------------------gtcttgaaagatgtcatctttggactgctaatgttgaat-tatgtaaatttttagcagttaactatgct----tatcctgattgatcttctcatct---ctttactagGATTCAAGGTTGTTGGGGGAACTGCACATTGCTCTGCTGAAATCCATCATAAAGGATATTGAGGATGTCTCCCGAACACCATCAGTTGCATTAGCGGTGA
upper sequence: Vv12s0028g03090.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GRMZM2G159357_T01 (Zea mays), 3'ss of exon 9
gtaagtcccttagacctttgtgctgaattttgcaaggacttgcttcttctttttttttttttaatctattgatattattataaatttattattatgtatttttcatattgcatttctgctcctgaccatttcagGATCCAAGGTTGTTGGGCGAGATACATGTTGCTCTCCTGAGATCCATCATTAAGGATATTGAAGATGTTGCCCGAACACCCTCCATTGGGCTGGGCGCAA
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------------caccctcgccttaccgctt---aggcgacgcttaagcgtcgcctt----------agggacgccttaaaaactatggactaaaatgctatcactatcacatttc---------cttttatagGATTCAAGGTTGTTGGGGGAACTGCATATTGCTCTGCTGAGATCCATTATAAAGGATATTGAGGATGTTGCTAGAACTCCATCAATTGCACTGGGGGTGA
upper sequence: Vv12s0028g03090.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA06G44290.1 (Glycine max), 3'ss of exon 11
gtaagtcccttagacctttgtgctgaattttgcaaggacttgcttcttctttttttttttttaatctattgatattattataaatttattattatgtatttttcatattgcattt----ctgctc-ctgaccatttcagGATCCAAGGTTGTTGGGCGAGATACATGTTGCTCTCCTGAGATCCATCATTAAGGATATTGAAGATGTTGCCCGAACACCCTCCATTGGGCT-GGGCGCAA
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-------------------------------------atgcactgaacctagatattacaatgagcc-ttgacatacttacatgtttctaacaaagc-tttgtgatgatggatctatatttgctctcttaataatgcagGACCCAAGGTTGTTAGGTGAGATTCATATTGCACTTCTGAAATCCATTATAAAAGATATTGAAGATGTTGCAAGAACACCCTCTACTGGGTTAGGATGCA- atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ataaatttattattatgtatttttcatattgcatttctgctcctgaccatttcagGATCCAAGGTTGTTGGGCGAGATACATGTTGCTCTCCTGAGATCCATCATTAAGGATATTGAAGATGTTGCCCGAACACCCTCCATTGGGCTGGGCGCAA
tcctgac putative branch site (score: 2)
ccatttc CT-rich tract
tttattattatgtatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagtcccttagacctttgtgctgaattttgcaaggacttgcttcttctttttttttttttaatctattgatattattataaatttattattatgtatttttcatattgcatttctgctcctgaccatttcagGATCCAAGGTTGTTGGGCGAGATACATGTTGCTCTCCTGAGATCCATCATTAAGGATATTGAAGATGTTGCCCGAACACCCTCCATTGGGCTGGGCGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG