Sequence
atgc intronic sequence ATGC exonic sequence...atttatatggcaaaaagaattctatttgcgctatatttgtgtcatgaaatgtgtaatttgttagtcaaaaagaagctgatctttcttcccttgggggcagAGATGATGGTAGGGAGATGCAGCTCAAATGGCATGTGTATGTGACTGGTCATAGTTTAGGTGGTGCATTAGCCACCCTTCTTGCGCTTGAGCTTTCATCA
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv05s0077g00480.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: LOC_Os04g43030.1 (Oryza sativa), 3'ss of exon 11
------atttatatggcaaaaagaattctatttgcgctatatttgtgtcatgaaatgtgtaatttgttagtcaaaaagaagctgatctttcttcccttgggggcagAGATGATGGTAGGGAGATGCAGCTCAAATGGCATGTGTATGTGACTGGTCATAGTTTAGGTGGTGCATTAGCCACCCTTCTTGCGCTTGAGCTTTCATCA
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gtaagtatttctataatgaaacagtttctaccacaaacatatatctcctgccaagtat-taagtaatctttcttt--gtttctattcatttttccactgcagGGATGAA-GAAGACGGAGAAAACATACCTAAGTGGCATGTCTATGTGACTGGACATAGTTTAGGTGGAGCACTAGCAACCCTTCTTGCTCTTGAACTTTCA---
upper sequence: Vv05s0077g00480.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GRMZM2G377641_T01 (Zea mays), 3'ss of exon 11
-------atttatatggcaaaaagaattctatttgcgctatatttgtgtcatg-aaatgtgtaatttgttagtcaaaaagaagctgatctttcttcccttgggggcagAGATGATGGTAGGGAGATGCAGCTCAAATGGCATGTGTATGTGACTGGTCATAGTTTAGGTGGTGCATTAGCCACCCTTCTTGCGCTTGAGCTTTCATCA
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tttacacatttattgtgtgtgtgtatatatatatata-tatatcttcaccaagtaactatctaaaactttattgacaaagcatttaattattccactgc-agTGATGAAGAAGATGCAGAAAACATAC---CTAGGTGGCATGTTTATGTGACTGGACACAGTTTAGGTGGAGCACTAGCGACTCTTCTTGCTCTTGAACTTTCA---
upper sequence: Vv05s0077g00480.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA20G20890.1 (Glycine max), 3'ss of exon 9
-----atttatatggcaaaaa---gaattctat-ttgcgctatatttgtgtcatgaaatgtgtaatttgttagtcaaaaagaagctgatctttcttcccttgggggcagAGATGATGGTAGGGAGATGCAGCTCAAATGGCATGTGTATGTGACTGGTCATAGTTTAGGTGGTGCATTAGCCACCCTTCTTGCGCTTGAGCTTTCATCA
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tactgttttgtgtctctaattcttgagtccaacactatgccaatagtacatctcaaaatttgatttcgcattgacaaacagaaggtattttttgtgcc---------agAGATGATCATTCTGAGTCGCTCCACAAATGGCATGTTTATGTGACTGGTCATAGTTTGGGTGGTGCATTGGCAACCTTGCTTGCTCTTGAACTTTCATCT
upper sequence: Vv05s0077g00480.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA10G26510.1 (Glycine max), 3'ss of exon 3
------atttatatggcaaaaagaattctatttg-cgctatatttgtg--tcatgaaatgtgtaatttgttagtcaaaaagaagctgatctttcttcccttgggggcagAGATGATGGTAGGGAGATGCAGCTCAAATGGCATGTGTATGTGACTGGTCATAGTTTAGGTGGTGCATTAGCCACCCTTCTTGCGCTTGAGCTTTCATCA
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aattactgttttgtgtctctaattcttgagtccaacactatgccaacagtacatctcaaatttgatttcgcattgacaaacaaggtattttttgtgcc---------agAGATGATCATTCTGAGTCGCTCCACAAATGGCATGTTTATGTGACTGGTCATAGTTTGGGTGGTGCACTGGCAACCTTGCTTGCTCTTGAACTTTCATCT
upper sequence: Vv05s0077g00480.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: AT4G13550.1 (Arabidopsis thaliana), 3'ss of exon 11
atttatatggcaaaaagaattctattt-gcgctatatttgtgtcatgaaatgtgtaatttgttagtcaaaaagaagctga-tctttct-tcccttgggggcagAGATGATGGTAGGGAGATGCAGCTCAAATGGCATGTGTATGTGACTGGTCATAGTTTAGGTGGTGCATTAGCCACCCTTCTTGCGCTTGAGCTTTCATCA
|| | | || | |||| || | |||| | |||| | || || | | ||| | ||| ||| ||| || | |||||||| |||| || ||| | ||||||||||| ||||||||||||||||| || ||||| |||||||| || || | || || || ||||| ||
--cagtacaatatagtgattgaaattttacgtcttcgaggtgtgctaaaatcttacatcaattc-taataaacatgctctctctctctctcaccccttggcagAGACGATGTTACTGAGCGTGAAGATAAATGGCATGTTTATGTGACTGGTCATAGCTTGGGTGGCGCATTAGCTACACTCTTGGCTCTCGAACTTTCGTCC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gaaatgtgtaatttgttagtcaaaaagaagctgatctttcttcccttgggggcagAGATGATGGTAGGGAGATGCAGCTCAAATGGCATGTGTATGTGACTGGTCATAGTTTAGGTGGTGCATTAGCCACCCTTCTTGCGCTTGAGCTTTCATCA
agctgat putative branch site (score: 4)
ctgatctttcttccct CT-rich tract
taatttgtta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
atttatatggcaaaaagaattctatttgcgctatatttgtgtcatgaaatgtgtaatttgttagtcaaaaagaagctgatctttcttcccttgggggcagAGATGATGGTAGGGAGATGCAGCTCAAATGGCATGTGTATGTGACTGGTCATAGTTTAGGTGGTGCATTAGCCACCCTTCTTGCGCTTGAGCTTTCATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT
- - -tatggca
- - - - - - aaaagaa
- - - - - - - - - - - - - - - - - - - - - catgaaa