Sequence
atgc intronic sequence ATGC exonic sequencegtgggtactgggtaggtgttttgttatgttgtggttttgttctctctttctttctcagtcactttctttctctctctctctgtgaatcttgttcaatatccaattacatgtggagggactagggagttaagttacttatgcacatctgaactgtgctctgattgggtggaattggattttgggaacagGTTGATGGGGAAAGTTGCATCTGATAAGTGCCACAAGTGGGTCTTTAAAGAGCCCACAGAATGTGAACCAAATATCTCCAACTACTGGCAGAGCTCCTTT
Basic information
species | Glycine max |
transcript | GLYMA13G34980.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA13G34980.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G302293_T01 (Zea mays), 3'ss of exon 3
gtgggtactgggtaggtgttttgttatgttgtggttttgttctctctttctttctcagtcactttctttctctctctctctgtgaatcttgttcaatatccaattacatgtggagggactagggagttaagttacttatgcacatctgaactgtgc-tctgattgggtggaattg--gattttgggaacagGTTGATGGGGAAAGTTGCATCTGATAAGTGCCACAAGTGGGTCTTTAAAGAGCCCACAGAATGTGAACCAAATATCTCCAACTACTGGCAGAGCTCCTTT
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-------------------------------------------------------------------------------------atttcgga-ggcatacaat-acatacat-gagtcatggacgataatgtgctaatagaca---gacccatgggtccgtttgatttggaccgtcgctcccgcatgcagGCTGATGGGAAAGGTGGCCTCTGATAAATGTCACAAATGGGTCTTCAAGGAACCTTCTGAATGCGAGCCCAACATCTCCAACTACTGGCAGAGCTCCTTC
upper sequence: GLYMA13G34980.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G132251_T01 (Zea mays), 3'ss of exon 3
gtgggtactgggtaggtgttttgttatgttgtggttttgttctctctttctttctcagtcactttctttctctctctctctgtgaatcttgttcaatatccaattacatgtggagggactagggagttaagttacttatgcacatctgaactgtgctctgattgggtggaattggattt--tgggaacagGTTGATGGGGAAAGTTGCATCTGATAAGTGCCACAAGTGGGTCTTTAAAGAGCCCACAGAATGTGAACCAAATATCTCCAACTACTGGCAGAGCTCCTTT
| ||| | || ||| |||||| | | | || | | | ||||| | | | | ||| || || || |||| ||||||| || || || |||||||| || ||||| |||||||| || || || | ||||| || || || ||||||||||||||||||||||| ||
-------------------------------------------------------------------------------------agcttttggggcatgcaaacgcatgtgaatcatgaatgatgt--gctcaagaccgtgggtctgattttgggttt---tggacccccttctccttcctgcatgcagGCTGATGGGAAAGGTGGCCTCTGATAAATGTCACAAATGGGTCTTCAAGGAACCTTCTGAATGCGAGCCCAACATCTCCAACTACTGGCAGAGCTCTTTC
upper sequence: GLYMA13G34980.1 (Glycine max), 3'ss of exon 3
lower sequence: AT5G53900.2 (Arabidopsis thaliana), 3'ss of exon 3
gtgggtactgggtaggtgttttgttatgttgtggttttgttctctctttctttctcagtcactttctttctctctctctctgtgaatcttgttcaatatccaattacatgtggagggactagggagttaagttacttatgcacatctgaactgtgctctgattgggtggaattggattttgggaacagGTTGATGGGGAAAGTTGCATCTGATAAGTGCCACAAGTGGGTCTTTAAAGAGCCCACAGAATGTGAACCAAATATCTCCAACTACTGGCAGAGCTCCTTT
|||||||||||||||||||| | | || || || || | || | || || | | |||| | || | |||| | | | | | | |||||| ||||| | | ||| || | ||| || || | ||| |||||||| |||||||| |||||||| || ||||||||||| || ||||| || | |||| |||||||||| | | || |||||||| || || |||
gtgggtactgggtaggtgttatat-ataa-gtaattatggacca----------aaagataattagattatataaacacaccctaatc--acttaacttatgattaaagatataattatttacaacacaagtta-ttatgatcttgtga---------tgttcatgtgatat---atct-----gcagATTGATGGGTAAAGTTGCTTCTGATAAATGTCACAAGTGGGTTTTCAAAGAACCATCTGAATCTGAACCAAATCTTGCTAATTACTGGCAAAGTTCTTTT
upper sequence: GLYMA13G34980.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv19s0014g02320.t01 (Vitis vinifera), 3'ss of exon 3
gtgggtactgggtaggtgttttgttatgttgtggttttgttctctctttctttctcagtcactttctttctctctctctctgtgaatcttgttcaatatccaattacatgtggagggactagggagttaagttacttatgcacatctgaactgtgctctgattgggtggaattggattttgggaacagGTTGATGGGGAAAGTTGCATCTGATAAGTGCCACAAGTGGGTCTTTAAAGAGCCCACAGAATGTGAACCAAATATCTCCAACTACTGGCAGAGCTCCTTT
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gtgggtactgggtaggtgtttttatttgatttcatctctctctccctctctttccctctctccctcattccctccctctctctctctcaacaatagggaggaagcagaaa-agtgaaaaaataaaaataaaaaacaaaaattcctctaca-tgggctttgataggatgaatt--gcttttatgagcagGTTGATGGGGAAGGTTGCATCTGATAAGTGTCATAAATGGGTTTTCAAAGAGCCTTCAGAGTGTGAACCAAATGTCTCCAACTACTGGCAGAGTTCTTTT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.acttatgcacatctgaactgtgctctgattgggtggaattggattttgggaacagGTTGATGGGGAAAGTTGCATCTGATAAGTGCCACAAGTGGGTCTTTAAAGAGCCCACAGAATGTGAACCAAATATCTCCAACTACTGGCAGAGCTCCTTT
ctctgat putative branch site (score: 4)
atttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgggtactgggtaggtgttttgttatgttgtggttttgttctctctttctttctcagtcactttctttctctctctctctgtgaatcttgttcaatatccaattacatgtggagggactagggagttaagttacttatgcacatctgaactgtgctctgattgggtggaattggattttgggaacagGTTGATGGGGAAAGTTGCATCTGATAAGTGCCACAAGTGGGTCTTTAAAGAGCCCACAGAATGTGAACCAAATATCTCCAACTACTGGCAGAGCTCCTTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT