Sequence
atgc intronic sequence ATGC exonic sequencegtcagttgttaaagcaatcggttccttcctttctccacttctgctttttcataatggataaaataacttgtgaaacaacattatcattccagGTTAGGTTGGATCCTTCTAGGCCCTTGAGCAAGCACAAGCATTGGGTTGTTGCTGAAATTCTGAAGAAAGCTCGAATCTATGTGCCACCTGAACCTATTG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv09s0070g00270.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: LOC_Os08g27090.1 (Oryza sativa), 3'ss of exon 1
--------gtcagttgttaaagcaatcggttccttcctttctccacttctgctttttcataatggataaaataacttgtgaaacaacattatcattccagGTTAGGTTGGATCCTTCTAGGCCCTTGAGCAAGCACAAGCATTGGGTTGTTGCTGAAATTCTGAAGAAAGCTCGAATCTATGTGCCACCTGAACCTATTG
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tctcccccttttgtagttcacaaagtgcgacctaagagcgcattaattttttatctccaagaaaaacctttttgatgatgactggataatttctctccagGTTAAGCTTGATCCTTCTAGGCCCTTGAGCAAAAGGAAGCACTGGGTTGTTGCCGAGATTCTTCGTAGAGCTAAGGTGTATTCTCCATCAGCTGCTGCAG
upper sequence: Vv09s0070g00270.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GRMZM2G177654_T01 (Zea mays), 3'ss of exon 1
-----gtcagttgttaaagcaatcggttccttcctttctccacttctgctttttcataatggataaaataacttgtgaaac---aacattatcattccagGTTAGGTTGGATCCTTCTAGGCCCTTGAGCAAGCACAAGCATTGGGTTGTTGCTGAAATTCTGAAGAAAGCTCGAATCTATGTGCCACCTGAACCTATTG
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ctacgtttctttgtactatggttctgttgaagcccattcacggtaaactagttttctgcgcaaagaacccttttatgatggctggataatgttctttcagGTTAGGCTGGATCCTTCTAGGCCCTTGAGCAGACACAAGCACTGGGTTGTTGCTGAAATTCTCCGCAGAGCTAAGGTGTACGTTCCACCAGCTGCAACAG
upper sequence: Vv09s0070g00270.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GRMZM2G108008_T01 (Zea mays), 3'ss of exon 1
--gtcagttgttaaagcaatcggttcctt-----cctttctccactt-ctgctttttcataatggataaaataacttgtgaaacaacattatcattccagGTTAGGTTGGATCCTTCTAGGCCCTTGAGCAAGCACAAGCATTGGGTTGTTGCTGAAATTCTGAAGAAAGCTCGAATCTATGTGCCACCTGAACCTATTG
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ctagcgttcctttgaactaaggttctgttgaagtccattcacgataaattagttttcctctcagaactctttttatgatggctgtatactgttctttcagGTTAGGCTGGACCCTTCTAGGCCCTTGAGCAGATATAAGCACTGGGTTGTTGCTGAAATTCTTCGCAGAGCTAAGGTATATGTTCCACCAGCTGCAACAG
upper sequence: Vv09s0070g00270.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA07G19190.1 (Glycine max), 3'ss of exon 2
----------------------------------------------------------gtcagttgttaaagcaatcggttccttcctttctccacttctgctttttcataatggataaaataacttgtgaaacaacattatcattccagGTTAGGTTGGATCCTTCTAGGCCCTTGAGCAAGCACAAGCATTGGGTTGTTGCTGAAATTCTGAAGAAAGCTCGAATCTATGTGCCACCTGAACCTATTG
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gttagtagcatggacttaccaatttaattggtttattgttcatcacttaagttcttgtgcatgttattcttatgatcttatcacttaatt-tgtactcttggttttgcccaaaagttaataaatctatcaattttgccatgttgttt-agGTTCGACTGGATCCTTCTAGACCTTTGAGCAAGCATAAACATTGGGTTGTTGCTGAAATTCTTAAGAAGGCACAGATATACGTTCCACCCTCCACCCCTG
upper sequence: Vv09s0070g00270.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA18G43720.1 (Glycine max), 3'ss of exon 1
--------------------------------------gtcagttgttaaagcaatcggttccttcctttctccactt---ctgctttttcataatgg---ataaaataacttgtgaaacaacattatcat----tccagGTTAGGTTGGATCCTTCTAGGCCCTTGAGCAAGCACAAGCATTGGGTTGTTGCTGAAATTCTGAAGAAAGCTCGAATCTATGTGCCACCTGAACCTATTG-
||| ||||| | | || | | ||||| || | | | | | | || ||| | | ||| || |||| | ||||| | |||||||||||||||| ||||||||||| || || |||||||||||||||||||| ||||| || | || ||||| |||| || |
gttagtagcatgaacttacaattttatttggtttattcttcatcacttaaattcttgtgcatgttattcttatcacttgatttgtactctaacttttgcccaaaagttaatgaatctatcaattttgtcatgttgtttagGTTCGACTGGATCCTTCTAGGCCTTTGAGCAAGCATAAACACTGGGTTGTTGCTGAAATTCTTAAGAAGGCACAGATATATGTTCCAC-TGTCCACGCCAG
upper sequence: Vv09s0070g00270.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA01G31470.1 (Glycine max), 3'ss of exon 2
gtcagtt--gttaaagcaatcg-gttccttcctttctccacttctgctt---tttcataatggataaaataacttgtgaaacaac----------attatcattccagGTTAGGTTGGATCCTTCTAGGCCCTTGAGCAAGCACAAGCATTGGGTTGTTGCTGAAATTCTGAAGAAAGCTCGAATCTATGTGCCACCTGAACCTATTG
|| |||| || | | | | || | |||| || || || | | || || ||| | | | ||| | || |||||| || |||||||||||||||| ||||| ||||| || ||||||| |||||||||||||| |||||||| || || ||||| || || | |
gttagtttcattgattcttttgtgtattgtgcttttggcatgattggttctactctgggttttgcaagatggcttattgagtggctgcttttgtgattgttgttgcagGTTCGGCTGGATCCTTCTAGGCCTTTGAGTAAGCATAAACATTGGGCAGTTGCTGAAATTCTCAAGAAAGCACGTATATATGTTCCGCCCTCAATGCCAG
upper sequence: Vv09s0070g00270.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: AT3G18880.1 (Arabidopsis thaliana), 3'ss of exon 1
------------------------------------------------------------gtcagttgttaaagcaatcggttccttcctttc----tccactt--ctgctttttcataa------tggataaaataacttgtgaaacaacattatcattccagGTTAGGTTGGATCCTTCTAGGCCCTTGAGCAAGCACAAGCATTGGGTTGTTGCTGAAATTCTGAAGAAAGCTCGAATCTATGTGCCACCTGAACCTATTG
| || | | | | | | | || || | |||| ||| || || || | | || |||||| || || |||| | ||||||||||| ||||| ||||||||||| ||||||||| ||||| | ||||| | |||||||| || || ||| |||| | || ||
gtattttccccttcattttttgaatttgatatacatttgatcaagagctcgaaaatttagggaagctctaggaatatttgaactcaaccattggaagtagacttgcctgtttgttattaggctgctttggaaatgaaacttgatttggttgtttgaaatattagGTGAAATTGGATCCTTCAAGGCCTTTGAGCAAGCATAAGCATTGGATTGTTTCAGAAATCATAAAGAAAGCACGCATTTATTCTCCACAAGCTGCTGCTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cttctgctttttcataatggataaaataacttgtgaaacaacattatcattccagGTTAGGTTGGATCCTTCTAGGCCCTTGAGCAAGCACAAGCATTGGGTTGTTGCTGAAATTCTGAAGAAAGCTCGAATCTATGTGCCACCTGAACCTATTG
aaataac putative branch site (score: 2)
tcattcc putative PPT
tttttcataatggata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtcagttgttaaagcaatcggttccttcctttctccacttctgctttttcataatggataaaataacttgtgaaacaacattatcattccagGTTAGGTTGGATCCTTCTAGGCCCTTGAGCAAGCACAAGCATTGGGTTGTTGCTGAAATTCTGAAGAAAGCTCGAATCTATGTGCCACCTGAACCTATTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA