Sequence
atgc intronic sequence ATGC exonic sequencegtaattagctcttctctctctctctctctctctcttctctgttttgtacttacacatgcaaattcattccatgcgcatctatgcagcagaaagaatgtttcagagatgcaccctaacacaaaatatgcttggttattttgaccatagtttagatgcatgagtagttaatgaaaattttccatatgcagGGAGAACTCTTTGAGATTCTTGAGGATGACAAGTGCCTTCCTGAAGAACAAGTTCAAGCAATTGCAAAGCAGTTG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv16s0039g02400.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: LOC_Os12g24550.1 (Oryza sativa), 3'ss of exon 4
gtaattagctcttctctctctctctctctctctcttctctgttttgtacttacacatgcaaattcattccatgcgcatctatgcagcagaaagaatgtttcagagatgcaccctaacacaaaatatgcttggttattttgaccatagtttagatgcatgagtagttaatgaaaattttccatatgcagGGAGAACTCTTTGAGATTCTTGAGGATGACAAGTGCCTTCCTGAAGAACAAGTTCAAGCAATTGCAAAGCAGTTG
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---------------------------------------------------------------------------------------gtacaggttgatttttcagtgtagtttt-caccaacaat---tggtt--ttgcagtggaatttagttggttaaac--ttcatatataatggttgtct-cagGGAGAGCTGTTTGAGGTGCTTGAGGATGATAAGTGCCTTCCAGAAGAACAGGTTCAAGCAATTGCTAAGCAGCTG
upper sequence: Vv16s0039g02400.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GRMZM2G062524_T02 (Zea mays), 3'ss of exon 3
gtaattagctcttctctctctctctctctctctcttctctgttttgtacttacacatgcaaattcattccatgcgcatctatgcagcagaaagaatgtttcagagatgcaccctaacacaaaatatgcttggttattttgaccatagtttagatgcatgagtagttaatgaaaattttccatatgcagGGAGAACTCTTTGAGATTCTTGAGGATGACAAGTGCCTTCCTGAAGAACAAGTTCAAGCAATTGCAAAGCAGTTG
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--------------------------------------------------------------------------------gtacacaagaactca-gttt----gat-taccttgtcctttctcatctttgactggtttcaattgtttgcagctggctaact--ctaatgaaaatgctt-gtct-cagGGAGAACTGTTTGAGGTGCTCGAGGATGATAAATGCCTTCCAGAAGAACAAGTTCAGGCAATTGCTAAGCAGCTG
upper sequence: Vv16s0039g02400.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA10G22860.1 (Glycine max), 3'ss of exon 3
gtaattagctcttctctctctctctctctctctcttctctgttttgtacttacacatgcaaattcattccatgcgcatctatgcagcagaaagaatgtttcagagatgcacc-ctaacacaaaatatgcttggttattttgaccatagtttagatgcatgagtagttaatgaaaattttccatatgcagGGAGAACTCTTTGAGATTCTTGAGGATGACAAGTGCCTTCCTGAAGAACAAGTTCAAGCAATTGCAAAGCAGTTG
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gtaatcatctgtattttcagt-tgacggtttgactgttac-ttctatatttgaaagttaacacttacccctt-----------------aataggtgatccaattatactcagctatctgatagtgaaacaggaaactgtgaat-tattagagatgc-tgtcaagctgattatattttttattttacagGGTGAGCTATTTGAGATTCTTGAGGATGATAAGTGCCTTCCGGAAGAGCAAGTTCAAGCAATTGCAAAGCAATTG
upper sequence: Vv16s0039g02400.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA20G16860.1 (Glycine max), 3'ss of exon 3
gtaattagctcttctctctctctctctctctctcttctctgttttgtacttacacatgcaaattcattccatgcgcatctatgcagcagaaagaatgt-ttcagagatgc-accctaacacaaaatatgcttggttattttgaccatagtttagatgcatgagtagttaatgaaaattttccatatgcagGGAGAACTCTTTGAGATTCTTGAGGATGACAAGTGCCTTCCTGAAGAACAAGTTCAAGCAATTGCAAAGCAGTTG
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---------------gtaatcatctgcattttcagttgacggtttg-attgatacttgaaagtt-accacttaccccttaat-tggtgatctaagtatactcagctatctgattgtggaacaggaca--ctgaattatt--------ag---agatgc-tgttgagctgattatattttttattttgcagGGTGAGCTATTTGAGATTCTTGAGGATGATAAGTGCCTTCCGGAAGAGCAAGTTCAAGCAATTGCAAAACAATTG
upper sequence: Vv16s0039g02400.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: AT1G50240.2 (Arabidopsis thaliana), 3'ss of exon 3
gtaattagctcttctctctctctctctctctctcttctctgttttgtacttacacatgcaaattcattccatgcgcatctatgcagcagaaagaatgtttcagagatgcaccctaacacaaaatatgcttggttattttgaccatagtttagatgcatgagtagttaatgaaaattttccatatgcagGGAGAACTCTTTGAGATTCTTGAGGATGACAAGTGCCTTCCTGAAGAACAAGTTCAAGCAATTGCAAAGCAGTTG
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----------------------------------------------------------------------gtacttttct-cactgtagattgtagaatctaaag---tactgatttatgaagcata------tagctagact-tatatgaaataaagaatcacc--atggaacacccaattttacagGGTGAATTGTTTGAGATTCTTGAAGATGACAAGTGCCTTCCCGAAGAGCAAGTTCAAGCAATCGCAAAGCAATTG
upper sequence: Vv16s0039g02400.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: EFJ33693 (Selaginella moellendorffii), 3'ss of exon 3
gtaattagctcttctctctctctctctctctctcttctctgttttgtacttacacatgcaaattcattccatgcgcatctatgcagcagaaagaatgtttcagagatgcaccctaacacaaaatatgcttggttattttgaccatagtttagatgcatgagtagttaatgaaaattttccatatgcagGGAGAACTCTTTGAGATTCTTGAGGATGACAAGTGCCTTCCTGAAGAACAAGTTCAAGCAATTGCAAAGCAGTTG
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-------------------------------------------------------------------------------------------gtaacattttcttgttgt-ttctagtgt---attttttcatttttcttttctagtgtgtggttactcacatttttatcattgttctttc-----tagGGAGAATTGTTTGAGATTCTTGAAGACGACAAGTGCCTCCCCGAAGCTCAAGTCCAGGCGATAGCAAAGCAACTG
upper sequence: Vv16s0039g02400.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: EFJ37043 (Selaginella moellendorffii), 3'ss of exon 3
gtaattagctcttctctctctctctctctctctcttctctgttttgtacttacacatgcaaattcattccatgcgcatctatgcagcagaaagaatgtttcagagatgcaccctaacacaaaatatgcttggttattttgaccatagtttagatgcatgagtagttaatgaaaattttccatatgcagGGAGAACTCTTTGAGATTCTTGAGGATGACAAGTGCCTTCCTGAAGAACAAGTTCAAGCAATTGCAAAGCAGTTG---------------------
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-------------------------------------------------------------------------------------gcaagtgtaacattttctttttgt-ttctggtgt---attttttcatttttcttttctagtgtgtggttactcacatttttatcattgttctttc-----tagGGAGAATTGTTTGAGATTCTTGAAGACGACAAGTGCCTCCCCGAAGCTCAAGTCCAGGCGATAGCAAAGCAACTGGTATGTATGTTAAGCCATCTT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tattttgaccatagtttagatgcatgagtagttaatgaaaattttccatatgcagGGAGAACTCTTTGAGATTCTTGAGGATGACAAGTGCCTTCCTGAAGAACAAGTTCAAGCAATTGCAAAGCAGTTG
ttttccat CT-rich tract
tagttaatgaaaattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaattagctcttctctctctctctctctctctcttctctgttttgtacttacacatgcaaattcattccatgcgcatctatgcagcagaaagaatgtttcagagatgcaccctaacacaaaatatgcttggttattttgaccatagtttagatgcatgagtagttaatgaaaattttccatatgcagGGAGAACTCTTTGAGATTCTTGAGGATGACAAGTGCCTTCCTGAAGAACAAGTTCAAGCAATTGCAAAGCAGTTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG