Sequence
atgc intronic sequence ATGC exonic sequencegtaaaacctctaattctgatgtttttgcttgttaatactttctaaatttaatgatttaattgtgtttgttttctgtacagaaatgaatgctataatttgcatgccacaattcatgaacttgttaattttattgtttttcacagATTGTATCAAAAGATTTATCAGATCCAGTACGTTCTCATAAAGATCTTGATAAGGATGCAGCACCATATTTTAAGAAAGCAGTCCAATTTTATGAAAATA
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv05s0062g00130.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: LOC_Os11g24560.1 (Oryza sativa), 3'ss of exon 2
gtaaaacctctaattctgatgtttttgcttgttaatactt-tctaaatttaatgatttaattgtgtttgttttctgtacagaaatgaatgctataatttgcatgccacaattcatgaacttgttaattttattgtttttcacagATTGTATCAAAAGATTTATCAGATCCAGTACGTTCTCATAAAGATCTTGATAAGGATGCAGCACCATATTTTAAGAAAGCAGTCCAATTTTATGAAAATA
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--------------------------gtttgttattctttgtccccctctaatattttctccatgcttctgttc--------atttttcatgatgctttgaa-gtcccaatttaata---------ctttactgggcaatgcagATTGTGTCGAAAGATTTGTCAGAGCCAGTTAGATCACATAAGGATCTTGATAAGGATGCAGCTCCTCACTTCCAGAAAGCTGTCAAATTTTACGATGGCC
upper sequence: Vv05s0062g00130.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G045987_T01 (Zea mays), 3'ss of exon 2
gtaaaacctctaattctgatgtttttgcttgttaatactttctaaatttaatgatttaattgtgtttgttt-tctgta-cagaaatgaatgctataatttgcatgccacaattc-atgaacttgttaat--tttattgtttttcacagATTGTATCAAAAGATTTATCAGATCCAGTACGTTCTCATAAAGATCTTGATAAGGATGCAGCACCATATTTTAAGAAAGCAGTCCAATTTTATGAAAATA
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------------------------------------------------tatggaatttatcatgctcctctgttcatagcagaatttttctctatttattgttcataattcttttaaagtctttctaatactgtattcgtgagtgcagATTGTTTCAAAAGATTTGTCAGAACCAGTTAGATCACATAAGGATCTTGACAAGGATGCAGCTCCTCACTTCCAGAAAGCAGTTAAATTTTATGATGGTC
upper sequence: Vv05s0062g00130.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA18G00670.1 (Glycine max), 3'ss of exon 2
gtaaaacctctaattctgatgtttttgcttgttaatactttctaaatttaatgattt-aattgtgtttgttttctgtacagaaatgaatgctataatttgcatgccacaattcatgaacttgttaattttattgtttttcacagATTGTATCAAAAGATTTATCAGATCCAGTACGTTCTCATAAAGATCTTGATAAGGATGCAGCACCATATTTTAAGAAAGCAGTCCAATTTTATGAAAATA
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-------------------------------------------gaattcggggaagggaatcgtggtcaatgattctatgcttactcttgtc-tatattgaatgtttctggtgccaaagatttagatttcaaatttctttgcagATTGTGTCAAAAGATTTATCTGACCCAGTGCGTTCTCATAAAGATCTTGATAAAGATGCAGCACCATTCTTCAAGAAAGCAGTCAAATTTTATGAGGGTC
upper sequence: Vv05s0062g00130.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA11G36760.1 (Glycine max), 3'ss of exon 2
gtaaaacctctaattctgatgtttttgcttgttaatactttctaaatttaatgatttaattgtgtttgttttctgtacagaaatgaatgctataatttgcatgccacaattcatgaacttgttaattttattgtttttcacagATTGTATCAAAAGATTTATCAGATCCAGTACGTTCTCATAAAGATCTTGATAAGGATGCAGCACCATATTTTAAGAAAGCAGTCCAATTTTATGAAAATA
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------------------------gtatacggggaagggaattgaggtcaatgat---gctatgcttgctct-tgt-ctgtattaaatgtt----tctgt-tgccaaagatt---------tagatttcaaatttctttgcagATTGTGTCAAAAGATCTATCTGACCCGGTGCGTTCTCATAAAGATCTTGATAAAGATGCAGCACCATTCTTCAAGAAAGCAGTCAAATTTTATGAGGGTC
upper sequence: Vv05s0062g00130.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: AT1G05520.1 (Arabidopsis thaliana), 3'ss of exon 2
gtaaaacctctaattctgatgtttttgcttgttaatactttctaaatttaatgatttaattgtgtttgttttctgtacagaaatgaatgctataatttgcatgccacaattcatgaacttgttaattttattgtttttcacagATTGTATCAAAAGATTTATCAGATCCAGTACGTTCTCATAAAGATCTTGATAAGGATGCAGCACCATATTTTAAGAAAGCAGTCCAATTTTATGAAAATA
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------------------gtgtttaggagaag-agcacactctgaactttccttgttaattgt--ttggcctc-----------aaatacaaagtttt-----------tcctttgagttagtactacctctggcttctgcagATTGTGTCAAAGGATCTATCAGAACCTTTGCGTTCACATAAAGATCTTGATAAAGATGCGGCTCCGTTCTATAAGAAAGCGGAGAAATTTTATGATGCGC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gctataatttgcatgccacaattcatgaacttgttaattttattgtttttcacagATTGTATCAAAAGATTTATCAGATCCAGTACGTTCTCATAAAGATCTTGATAAGGATGCAGCACCATATTTTAAGAAAGCAGTCCAATTTTATGAAAATA
tgttaat putative branch site (score: 3)
ttttattgtttttc CT-rich tract
aacttgttaattttat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaaacctctaattctgatgtttttgcttgttaatactttctaaatttaatgatttaattgtgtttgttttctgtacagaaatgaatgctataatttgcatgccacaattcatgaacttgttaattttattgtttttcacagATTGTATCAAAAGATTTATCAGATCCAGTACGTTCTCATAAAGATCTTGATAAGGATGCAGCACCATATTTTAAGAAAGCAGTCCAATTTTATGAAAATA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA