Sequence
atgc intronic sequence ATGC exonic sequence...ctttgtacctcaataagggtctcttcctctccccccttccttgcatccctctctctgctttgaattaaccttgcttaatggccttctgggtatatggcagAGGACCGAGTTGTATGAATACTCAAAGGTGCTTGGAAACTCTCAGTTTGTTCTGCTACCATTTCAGCCATATAAGCTTATATATGCACACATGTTGGCTG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv00s0229g00030.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: LOC_Os02g01490.1 (Oryza sativa), 3'ss of exon 7
ctttgtacctcaataagggtctcttcctctccccccttccttgcatccctct---ctctgctttgaattaaccttgcttaatggccttctgggtatatggcagAGGACCGAGTTGTATGAATACTCAAAGGTGCTTGGAAACTCTCAGTTTGTTCTGCTACCATTTCAGCCATATAAGCTTATATATGCACACATGTTGGCTG
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-ctggaaatgcaagattgtgtgtaaccgctaacctgttgctt-catctttttttactctgctgtccactgttctgaactaatattttgaaatgcg-ataacagAGGACAGAGATTTATGAATATGCGAAGGTGCTTGGTAATTCTCAATATATCCTGCTACCCTTTCAGCCATATAAGCTGATATATGCATACATGCTTGCGG
upper sequence: Vv00s0229g00030.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GRMZM2G163277_T01 (Zea mays), 3'ss of exon 7
----ctttgtacctcaataagggtctcttcctctccccccttccttgcatccctctctctgctttgaattaaccttgcttaatggccttctgggtatatggcagAGGACCGAGTTGTATGAATACTCAAAGGTGCTTGGAAACTCTCAGTTTGTTCTGCTACCATTTCAGCCATATAAGCTTATATATGCACACATGTTGGCTG
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aacaattaatatacggatatcaggat-tacgcgtagttatttattagcttattttctgtagctgttcactg-tctggactaatg--tttttaaattgcaaacagAGGACAGAGGTTTATGAATACGCGAAGGTGCTTGGTAATTCTCAGTATATCCTACTACCCTTTCAGCCATATAAGCTGATATATGCATACATGCTTGTTG
upper sequence: Vv00s0229g00030.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GRMZM2G429241_T01 (Zea mays), 3'ss of exon 7
-ctttgtacctcaataagggtctcttcctctccccccttccttgcatccctctctctgctttgaattaaccttgcttaatggccttctgggtatatggcagAGGACCGAGTTGTATGAATACTCAAAGGTGCTTGGAAACTCTCAGTTTGTTCTGCTACCATTTCAGCCATATAAGCTTATATATGCACACATGTTGGCTG
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tacagatacattggcagcactatgcatagttttttgttattttatttctgttgctattcactgtctggactctggactaatatcttcaaaatgca-aacagAGGACAGAGGTTTATGAATATGCGAAGGTGCTTGGTAATTCTCAATATATCCTACTATCCTTTCAGCCATATAAGCTGATATATGCATACATGCTTGTGG
upper sequence: Vv00s0229g00030.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GRMZM2G442742_T01 (Zea mays), 3'ss of exon 3
ctttgtacctcaataagggtctcttcctctccccccttccttgcatccctctctctgctttgaattaaccttgcttaatggccttctgggtatatggcagAGGACCGAGTTGTATGAATACTCAAAGGTGCTTGGAAACTCTCAGTTTGTTCTGCTACCATTTCAGCCATATAAGCTTATATATGCACACATGTTGGCTG----------------------------
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----------------------------------------------------------------ggactctggactaata-tcttcaaaatgca-aatagaggacagaggtttatgaatatgcgaaggtgcttggtaattctcaatatatcctactatcctttcagCCATATAAGCTGATATATGCATACATGCTTGTGGAAGTGGGGAAAGTTTCTGCTTCTTTGAG
upper sequence: Vv00s0229g00030.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GRMZM2G107218_T02 (Zea mays), 3'ss of exon 2
ctttgtacctcaataagggtctcttcctctccccccttccttgcatccctctctctgctttgaattaaccttgcttaatggccttctgggtatatggcagAGGACCGAGTTGTATGAATACTCAAAGGTGCTTGGAAACTCTCAGTTTGTTCTGCTACCATTTCAGCCATATAAGCTTATATATGCACACATGTTGGCTG----------------------------
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----------------------------------------------------------------ggactctggactaata-tcttcaaaatgca-aacagaggacagaggttaatgaatatgcgaaggtgcttggtaattctcaatatatcctactatcctttcagCCATATAAGCTGATATATGCATACATGCTTGTGGAAGTGGGGAAAGTTTCTGATTCTTTGAG
upper sequence: Vv00s0229g00030.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GRMZM2G107218_T01 (Zea mays), 3'ss of exon 2
-ctttgtacctcaataagggtctcttcctctccccccttccttgcatccctctctctgctttgaattaaccttgcttaatggccttctgggtatatggcagAGGACCGAGTTGTATGAATACTCAAAGGTGCTTGGAAACTCTCAGTTTGTTCTGCTACCATTTCAGCCATATAAGCTTATATATGCACACATGTTGGCTG
||| | | | | | | || || | || | | || | || || | |||| | | |||||||| ||| | ||||||| | ||||||||||| || ||||| | | | || ||| | ||||||||||||||||| ||||||||| ||||| | | |
tacagttacattggcagcactatgcatagttttttgttattttatttctgttgctattcactgtctggactctggactaatatcttcaaaatgca-aacagAGGACAGAGGTTAATGAATATGCGAAGGTGCTTGGTAATTCTCAATATATCCTACTATCCTTTCAGCCATATAAGCTGATATATGCATACATGCTTGTGG
upper sequence: Vv00s0229g00030.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GRMZM2G480185_T01 (Zea mays), 3'ss of exon 2
-ctttgtacctcaataagggtctcttcctctccccccttccttgcatccctctctctgctttgaattaaccttgcttaatggccttctgggtatatggcagAGGACCGAGTTGTATGAATACTCAAAGGTGCTTGGAAACTCTCAGTTTGTTCTGCTACCATTTCAGCCATATAAGCTTATATATGCACACATGTTGGCTG
| ||| | | | | | | || || | || | | || | || || | |||| | | ||||||| ||| | || ||||| | ||||||||||| || ||||| | | | || ||| | ||||||||||||||||| ||||||||| ||||| | | |
tatagatacattggcagcactatgcatagttttttgttattttatttctgttgctattcactgtctggactctggactaatatcttcaaaatgca-aacagAGGATAGAGGTTTACGAATATGCGAAGGTGCTTGGTAATTCTCAATATATCCTACTATCCTTTCAGCCATATAAGCTGATATATGCATACATGCTTGTGG
upper sequence: Vv00s0229g00030.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GLYMA11G03590.1 (Glycine max), 3'ss of exon 12
ctttgtacctcaataagggtctcttcctctccccccttccttgcatccctctctctgctttgaattaaccttgcttaatggccttctgggtatatgg-cagAGGACCGAGTTGTATGAATACTCAAAGGTGCTTGGAAACTCTCAGTTTGTTCTGCTACCATTTCAGCCATATAAGCTTATATATGCACACATGTTGGCTG
|||| || | | ||| ||| || || || || | || | || | | | || | |||| ||| |||||||||||||| |||||||| ||||||||| ||||||||||||||||| | ||| |||||||||||||||||||||||||||||| ||| | ||||
acttgtgccacc-tcaggatctgttgctttcttaaaagaacatgttcaaatatgattctgtatgttgctttcatattcttatctgattggtacttggacagAGGACCGAGTTATATGAATATTCAAAGGTGGTTGGAAACTCTCAGTTTACTTTGCATCCATTTCAGCCATATAAGCTTATATATGCATTTATGCTAGCTG
upper sequence: Vv00s0229g00030.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GLYMA01G41790.1 (Glycine max), 3'ss of exon 11
ctttgtacctcaataagggtctcttcctctccccccttccttgcatccctctctctgctttgaattaaccttgcttaatggccttctgggtatatgg-cagAGGACCGAGTTGTATGAATACTCAAAGGTGCTTGGAAACTCTCAGTTTGTTCTGCTACCATTTCAGCCATATAAGCTTATATATGCACACATGTTGGCTG
|||| | | | ||| ||| || || || || | | | || | | | ||| | |||| ||| |||||||||||||| |||||||| ||||||||| ||||||||||||||||| | ||| |||||||||||||||||||||||||||||| ||| | ||||
acttgtgcaacc-tcaggatctgttgctttcttaaaagaacatattcaaatatgattcagtatgttgctttcatattcttacctgattggtacttggacagAGGACCGAGTTATATGAATATTCAAAGGTGGTTGGAAACTCTCAGTTTACTTTGCATCCATTTCAGCCATATAAGCTTATATATGCATTTATGCTAGCTG
upper sequence: Vv00s0229g00030.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GLYMA01G41800.1 (Glycine max), 3'ss of exon 9
ctttgtacctcaataagggtctcttcctctccccccttccttgcatccctctctctgctttgaattaaccttgcttaa-tggccttctgggtatat-ggcagAGGACCGAGTTGTATGAATACTCAAAGGTGCTTGGAAACTCTCAGTTTGTTCTGCTACCATTTCAGCCATATAAGCTTATATATGCACACATGTTGGCTG
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-tctgttgctttctaaaaacatgttcaatatgattcagcat-gttgcatgatgtgtttattaaataactcaaacatatcttacctgattggtatttcgacagAGGACCGAGTTATATGAATATTCAAAGGTGGTTGGAAACTCTCAGTTTACTTTGCATCCATTTCAGCCATATAAGCTTATATATGCATTTATGCTAGCTG
upper sequence: Vv00s0229g00030.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GLYMA11G03580.1 (Glycine max), 3'ss of exon 12
ctttgtacctcaataagggtctcttcctctccccccttccttgcatccctctctctgctt-tgaattaaccttgcttaatggccttctgggtatatgg-cagAGGACCGAGTTGTATGAATACTCAAAGGTGCTTGGAAACTCTCAGTTTGTTCTGCTACCATTTCAGCCATATAAGCTTATATATGCACACATGTTGGCTG
||| || ||| | | || ||| | | | || || | | |||| | ||| | ||||| ||| |||||||||||||| |||||||| ||||||||| ||||||||||||||||| | ||| ||||||||||| |||||||||||||||||| || | ||||
--ctgttgctttctaaacacaacatgttcaatatgattcagcatgttgcatgatgtggttattgaataactcgaacatcttacctgattggtatttggacagAGGACCGAGTTATATGAATATTCAAAGGTGGTTGGAAACTCTCAGTTTACTTTGCATCCATTTCAGCCGTATAAGCTTATATATGCATTTTTGCTAGCTG
upper sequence: Vv00s0229g00030.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: AT5G47480.1 (Arabidopsis thaliana), 3'ss of exon 6
------------------------------------------------------------------------------ctttgtacctcaataagggtctcttc---ctctccccccttccttg--------catccctctctctgc---tttgaattaaccttgcttaatggccttctgggtatatgg-cagAGGACCGAGTTGTATGAATACTCAAAGGTGCTTGGAAACTCTCAGTTTGTTCTGCTACCATTTCAGCCATATAAGCTTATATATGCACACATGTTGGCTG
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gtgaatttttatcacagtgttttagttattataatactagacgtaagattctattttgaggctttttatgaatactctccatgtttctcaaatatgttgtatagaaactctgacgaaattcatggaggacgccattttttttcttacttatttgaaattctcttgatttgtcggttgatctttgcatgggcagAGAACAGAGTTATATGAATACTCTAAGACGCTGGGAAACTCTCAGTATATCCTGTTACCGTTTCAACCATATAAAATCATATATGCTCATATGCTGGCTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tccctctctctgctttgaattaaccttgcttaatggccttctgggtatatggcagAGGACCGAGTTGTATGAATACTCAAAGGTGCTTGGAAACTCTCAGTTTGTTCTGCTACCATTTCAGCCATATAAGCTTATATATGCACACATGTTGGCTG
tttgaattaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ctttgtacctcaataagggtctcttcctctccccccttccttgcatccctctctctgctttgaattaaccttgcttaatggccttctgggtatatggcagAGGACCGAGTTGTATGAATACTCAAAGGTGCTTGGAAACTCTCAGTTTGTTCTGCTACCATTTCAGCCATATAAGCTTATATATGCACACATGTTGGCTG
- - - acctcaa
- - - - - - - - - -tctcttc
- - - - - - - - - - - - - ctctccc
- - - - - - - - - - - - - - - - -cccttcc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -accttgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ggccttc