Sequence
atgc intronic sequence ATGC exonic sequence...gataacatgcccttgggcatctttctgtaatagattgtttgacgatcaagattgtatatattgtggtttattaattgagatccacttgtttataattcagCCAGGAGTAACTCTGAAACATGCTAAAGAAGGAACTGAGAGCTCGGCCTTTTGGTTTGCGCTTGGAGGAAAACAGAATTACACAAGCAAAAAAGCGTCCC
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv08s0007g08690.t01 (Vitis vinifera), 3'ss of exon 14
lower sequence: LOC_Os03g24220.2 (Oryza sativa), 3'ss of exon 15
gataacatgcccttgggcatctttctgtaatagattgtttgacgatcaagattgtatatattgtggtttattaattgagatccact--tgtttataa---ttcagCCAGGAGTAACTCTGAAACATGCTAAAGAAGGAACTGAGAGCTCGGCCTTTTGGTTTGCGCTTGGAGGAAAACAGAATTACACAAGCAAAAAAGCGTCCC
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-agaatgttttgttctgaataaaccgaaagcat-ttgatattttcttgaattcctagctatttc---tcactcaatacgattatctgatgtttccaaacttgcagCCTGGTGTTGCTGTCAAACATTGCAAGGAGGGAACTGAGAGCTCTGCCTTTTGGTTTGCTCTTGGTGGAAAGCAGAATTACACAAGCAGAAATGCCACAC
upper sequence: Vv08s0007g08690.t01 (Vitis vinifera), 3'ss of exon 14
lower sequence: GLYMA10G21350.2 (Glycine max), 3'ss of exon 14
gataacatgcccttgggcatcttt-ctgtaatagattgtttgacgatcaagattgtatatattgtggtttatt-aattgagatccacttgtttataattcagCCAGGAGTAACTCTGAAACATGCTAAAGAAGGAACTGAGAGCTCGGCCTTTTGGTTTGCGCTTGGAGGAAAACAGAATTACACAAGCAAAAAAGCGTCCC
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tcttacctccatccaaacaaagtgattttagcatgaagttaaaataatagtagttt-tgctctatacattatttgcttatgagatacatgtccatg-ttcagCCAGGAGCTACTTTAAAGCATGCTAAAGAAGGAACAGAAAGCTCAGCTTTCTGGTCTGCACTAGGAGGAAAACAAAGTTACACCAGCAAGAAAGTTGTTA
upper sequence: Vv08s0007g08690.t01 (Vitis vinifera), 3'ss of exon 14
lower sequence: GLYMA02G32100.1 (Glycine max), 3'ss of exon 13
gataacatgcccttgggcatc-tttctgtaatagattgtttgacgatcaagattgtatatattgtggtttatt-aattgagatccacttgtttataattcagCCAGGAGTAACTCTGAAACATGCTAAAGAAGGAACTGAGAGCTCGGCCTTTTGGTTTGCGCTTGGAGGAAAACAGAATTACACAAGCAAAAAAGCGTCCC
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-cttacctccatccaaacaaagtgattttaactcgaagttaaaaattgtagtagttttgctctatgcattatttgcttatgagatacatgtccatg-ttcagCCAGGAGCTACTTTAAAGCATGCTAAAGAAGGAACAGAAAGCTCAGCTTTCTGGTCTGCACTAGGAGGAAAACAAAGTTACACCAGCAAGAAAGTTGTTA
upper sequence: Vv08s0007g08690.t01 (Vitis vinifera), 3'ss of exon 14
lower sequence: GLYMA19G32010.1 (Glycine max), 3'ss of exon 15
gataacatgcccttgggcatctttctg-taatagattgtttgacgatcaagattgtatatattg--tggtttattaattgagat-ccacttgtttataattcagCCAGGAGTAACTCTGAAACATGCTAAAGAAGGAACTGAGAGCTCGGCCTTTTGGTTTGCGCTTGGAGGAAAACAGAATTACACAAGCAAAAAAGCGTCCC
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---acctatttctttttcaccagtatactaatgatttttttaacatttaggttaattcatactagttaaattatatgttaacatattacacatctatg-tccagCCAGGAGTTTCTTTAAAGCTTGCTAAAGAAGGAACAGAAACCTCAACTTTCTGGTTTGCACTTGGAGGAAAACAAAGTTACACCAGCAAAAATGTCACTA
upper sequence: Vv08s0007g08690.t01 (Vitis vinifera), 3'ss of exon 14
lower sequence: AT2G41740.1 (Arabidopsis thaliana), 3'ss of exon 15
----------gataacatgcccttgggcatctttctgtaatagattgtttgacgatcaagattgtata----tattgtggtttattaattgagatccacttgtttataattcagCCAGGAGTAACTCTGAAACATGCTAAAGAAGGAACTGAGAGCTCGGCCTTTTGGTTTGCGCTTGGAGGAAAACAGAATTACACAAGCAAAAAAGCGTCCC
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gttagtttctggttgtactgtgttgttt-tcagtttatcttaaatctttcca-aataggtgctttacagttttacacggaactcataatagaaaatgtctt-tttgttaatcagCCCGGGATTACTCTCAAGCATGCCAAAGAAGGAACAGAGAGCTCAACCTTTTGGTTTGCACTTGGGGGAAAACAGAATTTCACCAGCAAGAAGGCTTCCT
upper sequence: Vv08s0007g08690.t01 (Vitis vinifera), 3'ss of exon 14
lower sequence: AT3G57410.1 (Arabidopsis thaliana), 3'ss of exon 16
--------------------------------------------------------gataacatgcccttgggcatctttctgta-atagattgtttgacgatcaagattgtatatattgtggtttattaattgag--atccacttgttta-taattcagCCAGGAGTAACTCTGAAACATGCTAAAGAAGGAACTGAGAGCTCGGCCTTTTGGTTTGCGCTTGGAGGAAAACAGAATTACACAAGCAAAAAAGCGTCCC
|| || || | || | | | | | | | | || | | ||| | | || | | ||| ||| || ||| |||||| || ||| | || || || ||||| ||||| |||||||| ||||||||||||| ||||| ||||||||||| | ||| ||||| |||| |||
gtagtttctaatggtgttatctttgattttaatttagctgaaattgtccaagtaggaatggtataatttttattaagcttttaaataaaaactcactcgtacttcttatcactttt-ctgtaactggtaaacttaatcatcttctttcttgctaagtcagCCTGGGACTACTATCAAGCACGCAAAAGAGGGAACAGAGAGCTCATCCTTTTGGTTTGCACTTGGGGGAAAACAGAACTTCACCAGCAAGAAAGTTTCCT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcaagattgtatatattgtggtttattaattgagatccacttgtttataattcagCCAGGAGTAACTCTGAAACATGCTAAAGAAGGAACTGAGAGCTCGGCCTTTTGGTTTGCGCTTGGAGGAAAACAGAATTACACAAGCAAAAAAGCGTCCC
tattaat putative branch site (score: 2)
cttgttt putative PPT
tatatattgtggttta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gataacatgcccttgggcatctttctgtaatagattgtttgacgatcaagattgtatatattgtggtttattaattgagatccacttgtttataattcagCCAGGAGTAACTCTGAAACATGCTAAAGAAGGAACTGAGAGCTCGGCCTTTTGGTTTGCGCTTGGAGGAAAACAGAATTACACAAGCAAAAAAGCGTCCC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - -catgccc
- - - - - - - - - - ctttctg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ttgtggt