Sequence
atgc intronic sequence ATGC exonic sequencegtactttaaatcctgtcagcaacctcctacaagaacccacttttaatatagtagttttcctgttggattctgaagttttctgctgtttcatcagATGGTCGCAGATTGCAGCTCAATTACCGGGAAGAACGGATAATGAAATAAAAAATTTGTGGAACTCCTGCATTAAGAAGAAGCTTAGACAAAAAGGCATC
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv14s0060g00240.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA19G41250.1 (Glycine max), 3'ss of exon 2
------------------------------------------------------------------------------gtactttaaatcctgtcagcaacctcctacaagaacccacttttaatatagtagtttt-cctgttggattctgaagttttctgctg-tttcatcagATGGTCGCAGATTGCAGCTCAATTACCGGGAAGAACGGATAATGAAATAAAAAATTTGTGGAACTCCTGCATTAAGAAGAAGCTTAGACAAAAAGGCATC
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gtactactactatattgttttcaaagttgttgctagtttaattcggcttttcaccatcaattactgcaagaattttcgctattacagtgtcactcagaggctgtccgtaaaacatgttcttttgtttcatggttttgtatatgtgattttatgtgtttttgatgattgtatcagGTGGTCACAGATTGCAGCTCAGTTACCAGGAAGAACTGATAATGAGATAAAGAATCTATGGAACTCCTGTCTGAAGAAGAAGCTTAGGCAAAGAGGCATT
upper sequence: Vv14s0060g00240.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA03G38660.1 (Glycine max), 3'ss of exon 2
-----------------------------------------------------------------------gtactttaaatcctgtcagcaacctcctacaagaacccacttttaatatagtagttttcctgttg---gattctgaa-----gttttctgctgtttcatcagATGGTCGCAGATTGCAGCTCAATTACCGGGAAGAACGGATAATGAAATAAAAAATTTGTGGAACTCCTGCATTAAGAAGAAGCTTAGACAAAAAGGCATC
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gtactactatattttgttttcaaagttgttgctagtttagttcgccttttcgtcgtttagattaattgttatcactacaagtattttcgctattacggtgtctcttgaggctgtcggtaaaacatgttctttgtttcatggttttgtatatgtgtttttgatggttgtatcagGTGGTCACAGATTGCAGCTCAGTTACCAGGAAGAACTGATAATGAGATAAAGAATCTATGGAATTCCTGTCTGAAGAAGAAGCTTAGGCAAAGAGGCATT
upper sequence: Vv14s0060g00240.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA10G28250.1 (Glycine max), 3'ss of exon 2
------------------------------------------------gtactttaaatcctgtcagcaacctcctacaagaaccc--acttttaatatagtagttttcctgttg--gattctgaagttttctgctgtttcatcagATGGTCGCAGATTGCAGCTCAATTACCGGGAAGAACGGATAATGAAATAAAAAATTTGTGGAACTCCTGCATTAAGAAGAAGCTTAGACAAAAAGGCATC
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gtagttttagttatatagttatatatttatatatctcatacaaggccatttttttttttttttttttcagcgtacagttattactttgacttttgttcttgatgtatggtttttattaatttttagcttggtgggtgctttatcagGTGGTCTCAGATTGCAGCACAGTTACCAGGAAGAACAGACAATGAGATTAAGAACCTATGGAACTCGTGCCTGAAGAAGAAGCTGAGGCAAAGAGGCATT
upper sequence: Vv14s0060g00240.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA20G22230.1 (Glycine max), 3'ss of exon 2
----------------gtactt-taaatcctgtcagcaacctcctacaagaacccacttttaata-tagtagttttcctg-ttggattct-------gaagtttt------ctgctgtttcatcagATGGTCGCAGATTGCAGCTCAATTACCGGGAAGAACGGATAATGAAATAAAAAATTTGTGGAACTCCTGCATTAAGAAGAAGCTTAGACAAAAAGGCATC
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gtatagttttagttatgtagttatatatctcacacaaagccctcttttttaacgtacagttattacttttgacttttgtgcttctattctatgtatggttgttttatatattttttgctttatcagGTGGTCTCAGATTGCAGCACAGTTACCAGGAAGAACAGACAATGAGATTAAGAACCTATGGAACTCTTGCCTGAAGAAGAAGCTGAGGCAAAGAGGCATT
upper sequence: Vv14s0060g00240.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: PP1S277_14V6.1 (Physcomitrella patens), 3'ss of exon 2
-----------gtactttaaatcctgtcagcaacctcctacaagaacccacttttaatatagtagttttcctgttggattctgaagttttctgctgtttcat-cagATGGTCGCAGATTGCAGCTCAATTACCGGGAAGAACGGATAATGAAATAAAAAATTTGTGGAACTCCTGCATTAAGAAGAAGCTTAGACAAAAAGGCATC
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tcatcgatgagaggcagaagggccggattgtagtctc-tgcagctacatgtgctcc---ttgcaaatgttgagttaaagc--agaatttgatcctgtataatgcagGTGGTCACAGATTGCAACCCAGCTACCAGGCCGCACGGACAACGAAATAAAAAACTTCTGGAACTCTTGCATCAAGAAGAAGCTGCGTAACATCGGCATC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cttttaatatagtagttttcctgttggattctgaagttttctgctgtttcatcagATGGTCGCAGATTGCAGCTCAATTACCGGGAAGAACGGATAATGAAATAAAAAATTTGTGGAACTCCTGCATTAAGAAGAAGCTTAGACAAAAAGGCATC
ttttaat putative branch site (score: 3)
ttttctgctgtttc putative PPT
aatatagtagtttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtactttaaatcctgtcagcaacctcctacaagaacccacttttaatatagtagttttcctgttggattctgaagttttctgctgtttcatcagATGGTCGCAGATTGCAGCTCAATTACCGGGAAGAACGGATAATGAAATAAAAAATTTGTGGAACTCCTGCATTAAGAAGAAGCTTAGACAAAAAGGCATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC