Sequence
atgc intronic sequence ATGC exonic sequencegtatgaacccaggacttcattttgtttctttctcctaatttttactgtttccagagctttaggttttctgtatgttaaagtttttgcaaatgctgaatagcttcccttttttattttagctcattcttgcttttacctccatcaagttttttcccttagcaccatacatgtgtttgttagGAACATGCAAAAGGTGGAAAATGTATTGTTTTCACTCAAACAAAACGCGATGCTGATCGATTGGCATATGCTATGGCAAGAAACTTCAGATGTGAGGCTC
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv12s0142g00670.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: LOC_Os07g05050.1 (Oryza sativa), 3'ss of exon 4
gtatgaacccaggacttcattttgtttctttctcctaatttttactgtttccagagctttaggttttctgtatgttaaagtttttgcaaatgctgaatagcttcccttttttattttagctcattcttgcttttacctccatcaagttttttcccttagcaccatacatgtgtttgttagGAACATGCAAAAGGTGGAAAATGTATTGTTTTCACTCAAACAAAACGCGATGCTGATCGATTGGCATATGCTATGGCAAGAAACTTCAGATGTGAGGCTC
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--------------------------------------------------------------------------------------------gtgagcactcttctgaatgtatgatgtgtt-ttatagtttgcaccgttaacgactcttttctct--acac----------ttccacagGAGCATGCTAATGGTGGAAAATGTATTGTGTTTACTCAAACTAAACGAGAGGCAGATAGATTAGCATATGCTATGGGCAGGAGCTATGCATGTCAGGCGC
upper sequence: Vv12s0142g00670.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: LOC_Os07g05050.2 (Oryza sativa), 3'ss of exon 4
gtatgaacccaggacttcattttgtttctttctcctaatttttactgtttccagagctttaggttttctgtatgttaaagtttttgcaaatgctgaatagcttcccttttttattttagctcattcttgcttttacctccatcaagttttttcccttagcaccatacatgtgtttgttagGAACATGCAAAAGGTGGAAAATGTATTGTTTTCACTCAAACAAAACGCGATGCTGATCGATTGGCATATGCTATGGCAAGAAACTTCAGATGTGAGGCTC---------------------------------------------------
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--------------------------------------------------------------------------------------------gtgagcactcttctgaatgtatgatgtgtt-ttatagtttgcaccgttaacgactcttttctct--acac----------ttccacaggagcatgctaatggtggaaaatgtattgtgtttactcaaactaaacgagagGCAGATAGATTAGCATATGCTATGGGCAGGAGCTATGCATGTCAGGCGCTTCATGGGGATATTTCACAGAATCAGAGAGAAAGGACACTATCAGGATTTC
upper sequence: Vv12s0142g00670.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: LOC_Os12g41715.1 (Oryza sativa), 3'ss of exon 4
gtatgaacccaggacttcattttgtttctttctcctaatttttactgtttccagagctttaggttttctgtatgttaaagtttttgcaaatgctgaatagcttcccttttttattttagctcattcttgcttttacctccatcaagttttttcccttagcaccatacatgtgtttgttagGAACATGCAAAAGGTGGAAAATGTATTGTTTTCACTCAAACAAAACGCGATGCTGATCGATTGGCATATGCTATGGCAAGAAACTTCAGATGTGAGGCTC
|| |||| ||||| || | || | || | | | ||| || || |||||| || || | ||| ||| | | ||| ||| |||| |||||||||||||| ||||| ||||| || || ||||||||| | ||||||||||||||| | || | |||| | | ||| || |||| |
-------------------------------------------------------------------gtgaatgt---agtttactgtcattttttatgtttgaccatatcgaccttaa---atactaatttttact---ataaaatgctttaaatta--attgttcattcattt--cagGAGCATGCAAAAGGTGGTAAATGCATTGTATTTACACAAACAAAAAGAGATGCTGATCGATTGTCCTACACCATGGGTCGGAGTTTCCAGTGCCAGGCCC
upper sequence: Vv12s0142g00670.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G565140_T01 (Zea mays), 3'ss of exon 4
gtatgaacccaggacttcattttgtttctttctcctaatttttactgtttccagagctttaggttttctgtatgttaaagtttttgcaaatgctgaatagcttcccttttttattttagctcattcttgcttttacctccatcaagttttttcccttagcaccatacatgtgtttgttagGAACATGCAAAAGGTGGAAAATGTATTGTTTTCACTCAAACAAAACGCGATGCTGATCGATTGGCATATGCTATGGCAAGAAACTTCAGATGTGAGGCTC
| | ||| | || || | |||| | |||| || || | | || | |||||| | ||| | |||||||||||||||||||| || || |||||||| || ||||||||| | ||||| ||| ||||| || | |||| ||| ||| ||||||||| |
-----------------------------------------------------------------------------------gtcggggtttattatatttgtcccattaaaatttaatt---tctttgttctaatttgctggagca-----cgttagcaatttgtttgtttcgtgtagGAACATGCAAAAGGTGGCAAGTGCATTGTTTTTACACAAACAAAAAGGGATGCAGATAGATTGTCACACAATATGAGTCGAAGTTTCCAATGTGAGGCGC
upper sequence: Vv12s0142g00670.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA02G45030.1 (Glycine max), 3'ss of exon 4
gtatgaacccaggacttcattttgtttctttctcctaatttttactgtttccagagctttaggttttctgtatgttaaagtttttgcaaatgctgaatagcttcccttttttattttagctcattcttgcttttacctccatcaagttttttcccttagcaccatacatgtgtttgttagGAACATGCAAAAGGTGGAAAATGTATTGTTTTCACTCAAACAAAACGCGATGCTGATCGATTGGCATATGCTATGGCAAGAAACTTCAGATGTGAGGCTC
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--------------------------------------------------------------------------ctaaaaagatagtagaccct----atttttaattagaaaaactagttaaggaa-gctttttgttaaaggattttttgtctctcctaaagatatgt-cgtttgttagGAACATGCAAAAGGAGGAAAGTGTATTGTTTTCACTCAAACAAAACGTGATGCTGATCGATTATCGTATGCCATGGCAAGAAGTGTTAAATGTGAGGCTT
upper sequence: Vv12s0142g00670.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA14G03760.1 (Glycine max), 3'ss of exon 4
gtatgaacccaggacttcattttgtttctttctcctaatttttactgtttccagagctttaggttttctgtatgttaaagtttttgcaaatgctgaatagcttcccttttttattttagctcattcttg---cttttacctccatcaagttttttcccttagcaccatacatgtgtttgttagGAACATGCAAAAGGTGGAAAATGTATTGTTTTCACTCAAACAAAACGCGATGCTGATCGATTGGCATATGCTATGGCAAGAAACTTCAGATGTGAGGCTC
| | | || | || || || |||| | || || | ||| | || || |||| || | || ||| |||||||||||||||||||||| ||||| || ||||||||||||||||||||||| |||||||||||||| ||||| | |||||||||| | | ||||||||||
-------------------------------------------------------------------------------ggactaaaagatagtaaacc-ctatttttatttagaaaaactagttaaggaaacttcttgctggatttttttttgtctcctaaagatatatcc---tttgttagGAACATGCAAAAGGAGGAAAGTGCATTGTTTTCACTCAAACAAAACGTGATGCTGATCGATTATCATATACCATGGCAAGAAGTGTTAAATGTGAGGCTT
upper sequence: Vv12s0142g00670.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA08G41510.1 (Glycine max), 3'ss of exon 5
gtatgaacccaggact--tcattttgtttctttctcctaatttttactgtttccagagctttaggttttctgta-tgttaaagtttttgcaaatgct---gaatagcttcccttttttattttagct-cattcttg-cttttacctccat---caagttttt--tcccttagc--accatacatgtgtttgttagGAACATGCAAAAGGTGGAAAATGTATTGTTTTCACTCAAACAAAACGCGATGCTGATCGATTGGCATATGCTATGGCAAGAAACTTCAGATGTGAGGCTC
|||||| ||| || |||| | | | | | | | || | | | ||| ||| || | | || | | | ||| | | | ||| || | ||| || | | || | | | || | ||||| || | || | | |||| | | || || |||| ||||||||||| || || ||||| |||||||||||||||||||| ||||| |||||||||||||| |||||| ||||||| || | | ||||| ||||||
gtatgacttcagatacaatctttttctctttatttttttgcatcagctatagtttgtgttttttgttatcattgctatttatttataagcagttattttagtatatttttcttttactaaaatgattgcaatttagtctgtctggtccatatacaggcttctaatgcctttcctaatggtatatac-tttggtagGAACATGCGAATGGAGGAAAGTGTATTGTTTTCACTCAAACGAAACGTGATGCTGATCGATTATCATATGTCATGGCAAAAAGCCTTAGATGCGAGGCTT
upper sequence: Vv12s0142g00670.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA18G14670.1 (Glycine max), 3'ss of exon 4
gtatgaacccagga-------cttcattttgtttctttctcctaatt---tttactgtttccagagctttaggttttctgtatgttaaagtttttgcaaatgctgaatagcttcccttttttattttagctcattcttgcttttacctccatcaagtttt-ttcccttagc--accatacatgtgtttgttagGAACATGCAAAAGGTGGAAAATGTATTGTTTTCACTCAAACAAAACGCGATGCTGATCGATTGGCATATGCTATGGCAAGAAACTTCAGATGTGAGGCTC
||||||| | | ||| ||| ||| ||| | | ||| |||| | | | || ||| | ||| ||| | || | || || || | | ||| | | | ||| || | | | || | || |||| | | || || | |||| ||||||||||| || || ||||| |||||||||||||||||||| ||||| ||||||||||| || |||||| ||||||| || | | |||||||||||
gtatgaattcggatacaatcttttctctttatttttttgcatcagctatatttgtggttttcttatcattgctatttatttataa-gaagctattttagttgttgttgtttttactaaaatgattgcaatttagtctgcctggtctgtggacaggcttctattgcctttcctaatggtatatat-tttggtagGAACATGCGAATGGAGGAAAGTGTATTGTTTTCACTCAAACGAAACGTGATGCTGATCGGTTATCATATGTCATGGCAAAAAGCCTTAGATGTGAGGCCT
upper sequence: Vv12s0142g00670.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: AT3G22330.1 (Arabidopsis thaliana), 3'ss of exon 4
gtatgaacccaggacttcattttgtttctttctcctaatttttactgtttccagagctttaggttttctgtatgttaaagtttttgcaaatgctgaatagcttcccttttttattttagctcattcttgcttttacctccatcaagttttttcccttagcaccatacatgtgtttgttagGAACATGCAAAAGGTGGAAAATGTATTGTTTTCACTCAAACAAAACGCGATGCTGATCGATTGGCATATGCTATGGCAAGAAACTTCAGATGTGAGGCTC
|| | || | || ||| || || ||| | || | | | ||||| || | || |||| || || | | | |||| || | || || | | |||| | | || || | | |||| ||||| ||||| |||||||| |||||||| || ||||||||||| ||||||||||| | ||||||| |||| |||| ||||| |||||| |||
-----------------------gtatgctttcctta--ctttgctattaaacgagtatgagttaaattttgtgtta----ttcagtaa---ctgagtaagttatttgtgtattttttcggagttgtcagttgtatatggaaagagtt---------aataatatcaattttccttgcagGAGCATGCCAAAGGAGGAAAATGCATTGTTTTTACACAAACAAAACGAGATGCTGATCGCCTTTCATATGCATTGGCTAGAAGCTTCAAATGTGAAGCTT
upper sequence: Vv12s0142g00670.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: AT3G22310.1 (Arabidopsis thaliana), 3'ss of exon 4
gtatgaacccaggacttcattttgtttctttctcctaatttttactgtttccagagctttaggttttctgtatgttaaagtttttgcaaatgctgaatagcttcccttttttattttagctcattcttgcttttacctcca-tcaagttttttcccttagcaccatacatgtgtttgttagGAACATGCAAAAGGTGGAAAATGTATTGTTTTCACTCAAACAAAACGCGATGCTGATCGATTGGCATATGCTATGGCAAGAAACTTCAGATGTGAGGCTC
|| ||||||| || || | |||| | || | || || | | || |||| || | |||| |||| || | |||| || || | | | || ||||||||| ||||| |||||||| ||||| || || ||||||||||| ||||| ||||| | |||| || |||||| || || | |||||| |||
----------------------------------------------------------gtatgttttctttacttt---gctttt----aagccaatta---tctgtatcttgttttgattc---ttcatttttgtttccagtcgtgatttta----taacatcttc----tcctttacagGAACATGGCAAAGGAGGAAAATGCATTGTCTTTACCCAAACAAAACGTGATGCAGATCGCCTTGCATTTGGATTGGCAAAAAGCTATAAATGTGAAGCTT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cttgcttttacctccatcaagttttttcccttagcaccatacatgtgtttgttagGAACATGCAAAAGGTGGAAAATGTATTGTTTTCACTCAAACAAAACGCGATGCTGATCGATTGGCATATGCTATGGCAAGAAACTTCAGATGTGAGGCTC
aagtttttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgaacccaggacttcattttgtttctttctcctaatttttactgtttccagagctttaggttttctgtatgttaaagtttttgcaaatgctgaatagcttcccttttttattttagctcattcttgcttttacctccatcaagttttttcccttagcaccatacatgtgtttgttagGAACATGCAAAAGGTGGAAAATGTATTGTTTTCACTCAAACAAAACGCGATGCTGATCGATTGGCATATGCTATGGCAAGAAACTTCAGATGTGAGGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG