Sequence
atgc intronic sequence ATGC exonic sequence...tcaaaatatttttctggtcttgatgaatgttgttgctgttagtctttgtattgcccaatttggaattttgttagctaatgttctttggagttttccacagGATATGGAACCATGAGGAGGCTACACTGCTTAACAGTTTTGATAATCATGATTTTCCCGACAAAGGAATTTCTAAGCTCTGCCTTGTAAATGAGCTTGAT
Basic information
species | Glycine max |
transcript | GLYMA18G44210.1 |
intron # | 17 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA18G44210.1 (Glycine max), 3'ss of exon 17
lower sequence: AT5G01770.1 (Arabidopsis thaliana), 3'ss of exon 17
tcaaaatatttttctggtcttgatgaatgttgttgctgttagtctttgt----attgcccaatttggaattttgttagctaatgttctttggagttttccacagGATATGGAACCATGAGGAGGCTACACTGCTTAACAGTTTTGATAATCATGATTTTCCCGACAAAGGAATTTCTAAGCTCTGCCTTGTAAATGAGCTTGAT
||| | | || | | | | | |||| |||||| ||||| ||| |||| || || || |||| | ||||| | ||||| || || || ||||| | ||||| ||| | |||||||| |||||||||||||| || ||||||||||| ||||| ||||||
----aatcctccattcactcaaatacctcatctaaaaactgctttttgacttaattgcctctgttggacacttggactctaagtttagctgtctttcctgtcagGGTGTGGAATTACGAGGAAGCAACTCTTCTTAATGGCTTTGACAATAACGATTTTCCTGACAAAGGAATTTCAAATCTCTGCCTTGTCAATGAACTTGAT
upper sequence: GLYMA18G44210.1 (Glycine max), 3'ss of exon 17
lower sequence: AT3G08850.1 (Arabidopsis thaliana), 3'ss of exon 17
------tcaaaatatttttctggtcttgatgaatgttgttgctgttagtctttgtattgcccaatttggaattttgttagctaatgttctttggagttttccacagGATATGGAACCATGAGGAGGCTACACTGCTTAACAGTTTTGATAATCATGATTTTCCCGACAAAGGAATTTCTAAGCTCTGCCTTGTAAATGAGCTTGAT
| ||| | | | |||||| | ||| ||||| ||| | | | || | || || | |||| ||| | || | |||||| ||||||| || || || || || | ||||| |||||||||||||| |||||||||||||| ||||||||||| | ||||| |||||
ttccctttgaaacttatcttaaactttgatgttctctcttgggacc--tctttttatcgagaagcctt-aactgcactaagtatttcacttta---tttctcttagAGTGTGGAACTATGAGGAAGCAACTCTTCTCAATGGCTTTGACAATCATGATTTTCCTGACAAAGGAATTTCAAAGCTCTGCCTCATCAATGAACTTGAC
upper sequence: GLYMA18G44210.1 (Glycine max), 3'ss of exon 17
lower sequence: Vv08s0058g00890.t01 (Vitis vinifera), 3'ss of exon 17
---tcaaaatatttttctggtcttgatgaatgttgttgctgttagtctttgtattgcccaatttggaattttgttagctaatg-ttctttggagttttccacagGATATGGAACCATGAGGAGGCTACACTGCTTAACAGTTTTGATAATCATGATTTTCCCGACAAAGGAATTTCTAAGCTCTGCCTTGTAAATGAGCTTGAT
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ttatataagcctaaattaggtgtt--tgaatggctcacttatcatcatttcatttatcttttctgtttgcttatgcattaattcttcatttttgtttttc--agGATTTGGAATTATGATGAAGCTACCCTTCTCAACAGCTTTGACAATCATAATTTTCCTGATAAAGGAATTTCTAAACTCTGCCTTGTGAACGAGCTTGAT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttgtattgcccaatttggaattttgttagctaatgttctttggagttttccacagGATATGGAACCATGAGGAGGCTACACTGCTTAACAGTTTTGATAATCATGATTTTCCCGACAAAGGAATTTCTAAGCTCTGCCTTGTAAATGAGCTTGAT
agctaat putative branch site (score: 3)
ttttccac putative PPT
aattttgtta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tcaaaatatttttctggtcttgatgaatgttgttgctgttagtctttgtattgcccaatttggaattttgttagctaatgttctttggagttttccacagGATATGGAACCATGAGGAGGCTACACTGCTTAACAGTTTTGATAATCATGATTTTCCCGACAAAGGAATTTCTAAGCTCTGCCTTGTAAATGAGCTTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT
- - - - - tttctgg
- - - - - - - - - cttgatg
- - - - - - - - - - - - - - - tgttgct
- - - - - - - - - - - - - - - - - - - - -gtctttg
- - - - - - - - - - - - - - - - - - - - - - - - - -tgcccaa