Sequence
atgc intronic sequence ATGC exonic sequencegtaggcgggttgttgcttttcttttcttttgcagtttgattttccttgcagcctttaaggactccaaataaatgatgcagATCAAAATAGGAATGGATGTTGCAGCTTCAGAGTTCTTCACTAAAGATGGGAAATATGATTTGAATTTTAAGAAACAACCAAATGATGGAGCTCACGTTC
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv17s0000g04540.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: LOC_Os09g20820.1 (Oryza sativa), 3'ss of exon 3
----gtaggcgggttgttgcttttcttttcttttg---------cagtttgattttccttgcagcctttaaggactccaaataaa---tgatgcagATCAAAATAGGAATGGATGTTGCAGCTTCAGAGTTCTTCACTAAAGATGGGAAATATGATTTGAATTTTAAGAAACAACCAAATGATGGAGCTCACGTTC
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gtctgcagtcatcttgttttatttcccaccttttcaatgtggaccaccttttttttttttgtaacttataat-actgtgaacccatcctactgcagATTAAAATTGGAATGGATGTTGCAGCATCAGAGTTTCTTACAAAGGATGGAAGCTATGACTTAAACTTTAAGAATCAGCCTAATGATGGAGCTCATGTTC
upper sequence: Vv17s0000g04540.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GRMZM2G034848_T01 (Zea mays), 3'ss of exon 3
gtaggcgggttgttgcttttct--tttcttttgca----gtttgattttccttgcagcc---tttaaggactccaaataaat---gatgcagATCAAAATAGGAATGGATGTTGCAGCTTCAGAGTTCTTCACTAAAGATGGGAAATATGATTTGAATTTTAAGAAACAACCAAATGATGGAGCTCACGTTC
| | | | | | || |||| || || |||||||| | || ||| | ||| |||| |||||||||||||| |||||||||||||| || ||||||||| | || || |||||||| |||||| | || |||||||| || || |||||||||| || ||||
----gtgtgatatcatctaactagtttcattggccacttgtttgattgttctcttgattttattttgaattttaaaacaaatcctaatgcagATCAAAATTGGAATGGATGTTGCGGCATCAGAGTTCCTTACAAAGGATGGGAACTATGATCTAAACTTTAAGAATCAGCCTAATGATGGAGTCCATGTTC
upper sequence: Vv17s0000g04540.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GRMZM2G009030_T01 (Zea mays), 3'ss of exon 3
-------gtaggcgggttgttgcttttcttttcttttgcagtttgattttccttgcagcctttaaggactccaaataaat---gatgcagATCAAAATAGGAATGGATGTTGCAGCTTCAGAGTTCTTCACTAAAGATGGGAAATATGATTTGAATTTTAAGAAACAACCAAATGATGGAGCTCACGTTC
| | | | || ||| | || | | || |||||| | | | |||| |||||||||||||| || ||||||||||| || || |||||| | || || |||||||| |||||| | || |||||||| || || ||||||||||| || |||
gtgtgatatcatctaactagtttcattggccacttgtttgattgctctcttgttttttactttaaatgttaaacacaaatcctaatgcagATCAAAATTGGTATGGATGTTGCGGCATCTGAGTTCCTTACAAAGGATGGGAACTATGATCTAAACTTTAAGAATCAGCCTAATGATGGAGCCCATATTC
upper sequence: Vv17s0000g04540.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA06G23080.1 (Glycine max), 3'ss of exon 3
gtaggcgggttgttgcttttcttttcttttgcagtttgatt--ttccttgcagcctttaaggactccaaataaatgatgcagATCAAAATAGGAATGGATGTTGCAGCTTCAGAGTTCTTCACTAAAGATGGGAAATATGATTTGAATTTTAAGAAACAACCAAATGATGGAGCTCACGTTC
|| || | ||| || | || | || | ||||| | | |||| | | | | ||| |||| |||||| |||||||| ||||||||||||||||||||||| | |||||| |||||||| ||||||||||| || |||||||||||||||||||||||||| ||||
gtgggtgatgctttgattat-ttctgttacataatttgaatattcacttgtgctgatctggaaataaaaaacaatggcgcagATTAAAATAGGCATGGATGTTGCAGCTTCAGAGTTTTACACTAAGGATGGGAAGTATGATTTGAACTTCAAGAAACAACCAAATGATGGAGCTCATGTTC
upper sequence: Vv17s0000g04540.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA15G25390.1 (Glycine max), 3'ss of exon 4
gtaggcgggttgttgcttttcttttcttttgcagtttgatt--ttccttgcagcctttaaggactccaaataaatgatgcagATCAAAATAGGAATGGATGTTGCAGCTTCAGAGTTCTTCACTAAAGATGGGAAATATGATTTGAATTTTAAGAAACAACCAAATGATGGAGCTCACGTTC
| | ||| || | || | || | ||||| | | |||| | | | | ||| ||||| ||||||| |||||||| ||||||||||||||||||||||| | |||||| |||||||| ||||||||||| || |||||||| ||||||||||||||||| ||||
----gtgaagctttgattat-ttctgttgcatactttgaatattcacttgtgctgatctggaaataaaaaaaaatggtgcagATTAAAATAGGTATGGATGTTGCAGCTTCAGAGTTTTACACTAAGGATGGGAAGTATGATTTGAACTTCAAGAAACAGCCAAATGATGGAGCTCATGTTC
upper sequence: Vv17s0000g04540.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA18G22780.1 (Glycine max), 3'ss of exon 4
gtaggcgggttgttgcttttcttttcttttgcagtttgat--tttccttgcagcctttaaggactccaaataaatgatgcagATCAAAATAGGAATGGATGTTGCAGCTTCAGAGTTCTTCACTAAAGATGGGAAATATGATTTGAATTTTAAGAAACAACCAAATGATGGAGCTCACGTTC
|| || | ||| || | || | || | ||||| || |||| | | | | ||| |||| ||||||| |||||||| ||||||||||||||||||||||| | |||||| |||||||| ||||||||||| || |||||||| ||||||||||||||||| ||||
gtgggtgaagctttgattat-ttctgttgcataatttgaaaattcacttgtgctgatctggaaataaaaaacaatggtgcagATTAAAATAGGTATGGATGTTGCAGCTTCAGAGTTTTACACTAAGGATGGGAAGTATGATTTGAACTTCAAGAAACAGCCAAATGATGGAGCTCATGTTC
upper sequence: Vv17s0000g04540.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA04G24920.1 (Glycine max), 3'ss of exon 2
gtaggcgggttgttgcttttcttttcttttgcagtttgatt--ttccttgcagcctttaaggactccaaataaatgatgcagATCAAAATAGGAATGGATGTTGCAGCTTCAGAGTTCTTCACTAAAGATGGGAAATATGATTTGAATTTTAAGAAACAACCAAATGATGGAGCTCACGTTC
|| || | | ||| || | || | || | ||||| | | |||| | | | | ||| |||| ||||||| ||||| || ||||||||||||||||||||||| | |||||| |||||||| ||||||||||| || | |||||| ||||||||||||||||| ||||
gtgggtgaagttttgattat-ttctgttgcataatttgaatattcacttgtgctgatctggaaataaaaaacaatggtgcagATTAAAATTGGTATGGATGTTGCAGCTTCAGAGTTTTACACTAAGGATGGGAAGTATGATTTGAACTTCATGAAACAGCCAAATGATGGAGCTCATGTTC
upper sequence: Vv17s0000g04540.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: AT1G74030.1 (Arabidopsis thaliana), 3'ss of exon 3
--------------------------------------gtaggcgggttgttgcttttcttttcttttgcagttt-----gattttccttgcagcctttaaggactc------caaataaatgatgcagATCAAAATAGGAATGGATGTTGCAGCTTCAGAGTTCTTCACTAAAGATGGGAAATATGATTTGAATTTTAAGAAACAACCAAATGATGGAGCTCACGTTC
| | | ||| | | ||| | | || || || | || ||| | |||| | |||| | |||||||||||||||||||||||||||| || ||||| || |||| |||||||| | ||| |||||||| || |||||||| ||||| |||||||||||||| |
gtaatcaagttctctttctttttaatgctaatacttgctaaagttgcatgtcatctgtgtttccctaaacaacttctggcagcttcggtgtcaatcttacaccactcacataatatataatttttgcagATCAAAATAGGAATGGATGTTGCTGCATCAGAATTTTTCATGAAAGATGGTAGATACGATTTGAACTTCAAGAAACAGCCAAACGATGGAGCTCACGTAC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cttttgcagtttgattttccttgcagcctttaaggactccaaataaatgatgcagATCAAAATAGGAATGGATGTTGCAGCTTCAGAGTTCTTCACTAAAGATGGGAAATATGATTTGAATTTTAAGAAACAACCAAATGATGGAGCTCACGTTC
gtttgat putative branch site (score: 5)
aaataaatgat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaggcgggttgttgcttttcttttcttttgcagtttgattttccttgcagcctttaaggactccaaataaatgatgcagATCAAAATAGGAATGGATGTTGCAGCTTCAGAGTTCTTCACTAAAGATGGGAAATATGATTTGAATTTTAAGAAACAACCAAATGATGGAGCTCACGTTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA