Sequence
atgc intronic sequence ATGC exonic sequence...tttgcaatattgttgcatcatgtgcaatattatgtttcagttggcacttttggttatcgtcttttgtactgatataacctcccaattattccatgaacagGTTGGTGACAAACTTTATATATACTTGGAGTATGTATCTGGTGGCTCCATCTATAAACTTCTTCAAGAATATGGCCAACTTGGTGAACTAGCAATTCGTA
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv16s0050g00770.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: LOC_Os04g47240.2 (Oryza sativa), 3'ss of exon 5
tttgcaatattgttgcatcatgtgcaatattatgtttcagttggcacttt--tggttatcgtcttttgtactgatataacctcccaattattccatga-acagGTTGGTGACAAACTTTATATATACTTGGAGTATGTATCTGGTGGCTCCATCTATAAACTTCTTCAAGAATATGGCCAACTTGGTGAACTAGCAATTCGTA
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---gaagttgcatgatagcatctaggatttcattaatgagttatttatgtaccacttttgattttcttttttggcttcacttattatttgtgccccaatacagGTTGATGATAAGCTTTATATATACTTGGAGTATGTATCTGGTGGATCTATCCATAAACTTCTACAAGAGTATGGACAGCTTGGTGAACAAGCAATACGCA
upper sequence: Vv16s0050g00770.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: LOC_Os02g44642.1 (Oryza sativa), 3'ss of exon 5
tttgcaatattgttgcatcatgtgcaatattatgtttcagttggcacttttggttatcgtcttttgtactgatataacctccca--attattccat---gaacagGTTGGTGACAAACTTTATATATACTTGGAGTATGTATCTGGTGGCTCCATCTATAAACTTCTTCAAGAATATGGCCAACTTGGTGAACTAGCAATTCGTA
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----ccacatt-ctgcagaattttacgaacttcacttttgcttgcactcctgactcctctgtttactttaaaaataactatacactatccatttattcaaaacagGTTGATGATAAACTTTATATATACCTGGAGTATGTTTCTGGTGGATCCATCCATAAACTACTCCAGGAGTATGGGCAATTTGGTGAACCTGCTATCCGCA
upper sequence: Vv16s0050g00770.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G175504_T01 (Zea mays), 3'ss of exon 4
-----tttgcaatattgttgcatcatgtgcaatattatgtttcagttggcacttttggttatcgtcttttgtactgatataacctcccaattattccatgaacagGTTGGTGACAAACTTTATATATACTTGGAGTATGTATCTGGTGGCTCCATCTATAAACTTCTTCAAGAATATGGCCAACTTGGTGAACTAGCAATTCGTA
|| ||| | ||| ||| | || || || | || | ||| | || | || | || | | | || | || ||| | |||||| || |||||||| ||||| ||||| ||||| |||||||| ||||| |||||||||| ||||||||||| || |||||||||| |||||| || |
gagagttcacaacagc-ttgtcacatat-cattaatagggttatggatgcattattt-tcat--ttttaggcatgaacttatacattatgtttgcccaaaattagGTTGAAGATAAACTTTACATATATTTGGAATATGTTTCTGGTGGATCCATACATAAACTTCTACAAGAATATGGACAGCTTGGTGAACCAGCAATACGCA
upper sequence: Vv16s0050g00770.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA10G37730.1 (Glycine max), 3'ss of exon 6
----tttgcaatattgttgcatcatgtgcaatattatgtttcagttggcacttttggttatcgtcttttgtactgatataa-cctcccaattattccatgaacagGTTGGTGACAAACTTTATATATACTTGGAGTATGTATCTGGTGGCTCCATCTATAAACTTCTTCAAGAATATGGCCAACTTGGTGAACTAGCAATTCGTA
| || || | || | | || |||| | | || | || ||| | || || || ||| | | || ||| || ||||||||||| |||||| ||||| |||||| | || ||||||||||| |||||||| |||||||||||||||||||||| ||| |||||||||||| |||||||
tgtttctggtggtttatctgataacatagaagtgggaatttc--tcgacagtatttgtttttgtggttc---cttatagaggcttctgaatcgccccttgaacagGTTGATGACAAGCTTTACATATACCTTGAATATGTATCTGGAGGCTCCATACATAAACTTCTTCAAGAATATGGGCAATTTGGTGAACTAGTTATTCGTA
upper sequence: Vv16s0050g00770.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA16G30030.2 (Glycine max), 3'ss of exon 5
---tttgcaatattgttgcatcatgtgcaatattatgtttcagttggcacttttggttatcgtcttttgtactgatataacct-cccaattattccatgaacagGTTGGTGACAAACTTTATATATACTTGGAGTATGTATCTGGTGGCTCCATCTATAAACTTCTTCAAGAATATGGCCAACTTGGTGAACTAGCAATTCGTA
||| || | || | |||| |||||| | ||| || | || || | | | |||| ||| || || || ||| || || | ||||||| || ||||| ||||| ||||| |||||||||| |||| |||||||| ||||||||||||||||||||||| ||| ||||||||||||| |||||||
tggtttacatttttact-tgtcat-cattatattagatacttgtttacagtatttgtctt--ttcagtctactcatagaaactgccaaatcatcccttaaacagGTAGGCGACAAGCTTTACATATATCTGGAGTATGTTGCTGGAGGCTCCATATATAAACTTCTTCAAGAATATGGACAATTTGGTGAACTAGCTATTCGTA
upper sequence: Vv16s0050g00770.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA09G24970.1 (Glycine max), 3'ss of exon 5
-----tttgcaatattgttgcatcatgtgcaatattatgtttcagttggcacttttggttatcgtcttttgtactgatataacctcccaattattccatgaacagGTTGGTGACAAACTTTATATATACTTGGAGTATGTATCTGGTGGCTCCATCTATAAACTTCTTCAAGAATATGGCCAACTTGGTGAACTAGCAATTCGTA
||| | | | | |||| ||||||| ||| || | || | || | || || ||| | ||| || || | ||||||| || ||||| ||||| ||||| |||||||||| |||| |||||||| ||||||||||||||||||||||| ||| ||||||||||||| |||||||
tacattttttcttgtcatcac-tcat-cataatattagaaacttgtttacagtatttttcttcagtctacttataga---aactgctgaatcatcccttaaacagGTAGGCGACAAGCTTTACATATATCTGGAGTATGTTGCTGGAGGCTCCATATATAAACTTCTTCAAGAATATGGACAATTTGGTGAACTAGCTATTCGTA
upper sequence: Vv16s0050g00770.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA20G30100.1 (Glycine max), 3'ss of exon 5
----tttgcaatattgttgcatcatgtgcaa-tattatgtttcagttggcacttttggttatcgtcttttgtactgatataacctcccaattattccatgaacagGTTGGTGACAAACTTTATATATACTTGGAGTATGTATCTGGTGGCTCCATCTATAAACTTCTTCAAGAATATGGCCAACTTGGTGAACTAGCAATTCGTA
| || || | || | | || | | || || | || | || | || || || | | || ||| | || ||||||||| | | |||| ||||| |||||| | |||||||||||||| |||||||| |||||||||||| ||||||||| ||| |||||||||||| |||||||
tgtttctggtggtttatctgataacatagaagtgggaatttctcaacggtatttgttattgtggttccttatagagg-----cttctaaatcaccccttgaacagGTCGATAACAAGCTTTACATATACCTTGAGTATGTATCTGGAGGCTCCATACATAAACTTCTTCGAGAATATGGGCAATTTGGTGAACTAGTTATTCGTA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.acttttggttatcgtcttttgtactgatataacctcccaattattccatgaacagGTTGGTGACAAACTTTATATATACTTGGAGTATGTATCTGGTGGCTCCATCTATAAACTTCTTCAAGAATATGGCCAACTTGGTGAACTAGCAATTCGTA
ttattcc CT-rich tract
aattatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tttgcaatattgttgcatcatgtgcaatattatgtttcagttggcacttttggttatcgtcttttgtactgatataacctcccaattattccatgaacagGTTGGTGACAAACTTTATATATACTTGGAGTATGTATCTGGTGGCTCCATCTATAAACTTCTTCAAGAATATGGCCAACTTGGTGAACTAGCAATTCGTA
- - - - - tgttgca
- - - - - - - - - catgtgc
- - - - - - - - - - - - - - - - - - -cagttgg
- - - - - - - - - - - - - - - - - - - - - - - cttttgg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - acctccc