Sequence
atgc intronic sequence ATGC exonic sequencegtactggtttttcatgatggctcttattgtcttcttaaaatagcttttactctagatacttgtgtatttttatgatgtcttgaaagattatttgttggggtttcatcttggccagGGAACTGTTGTGGAAGGCACTATACAGCAATTGTTTGAAGGACACCATATGAACTATATTGAATGCATAAATGTGGATTATAAATCAACAAGGAAAGAAT
Basic information
species | Glycine max |
transcript | GLYMA10G23680.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA10G23680.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os12g30540.1 (Oryza sativa), 3'ss of exon 6
gtactggtttttcatgatggctcttattgtcttcttaaaatagcttttactctagatacttgtgtatttttatgatgtcttgaaagattatttgttggggtttcatcttggccagGGAACTGTTGTGGAAGGCACTATACAGCAATTGTTTGAAGGACACCATATGAACTATATTGAATGCATAAATGTGGATTATAAATCAACAAGGAAAGAAT
| | ||| | | | || |||| | |||||| | |||| || || || | | | ||||| ||||||||||||||| || || | ||||| |||||||| ||||| || |||||||| || ||||| ||||| ||||||||||| | || |||||||
---------------------------------------gtgaatattataacaaacattt---tattat----atgtct---acgatttgttattaactttgcgt-tgacccagGAAACTGTTGTGGAAGGAACAATTGAACAATTATTTGAAGGCCACCACATAAACTATATCGAGTGCATTAATGTTGATTATAAATCTAACAGAAAAGAAT
upper sequence: GLYMA10G23680.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os01g56490.1 (Oryza sativa), 3'ss of exon 6
gtactggtttttcatgatggctcttattgtcttcttaaaatagcttttactctagatacttgtgtatttttatgatgtcttgaaagattatttgttggggtttcatcttggccagGGAACTGTTGTGGAAGGCACTATACAGCAATTGTTTGAAGGACACCATATGAACTATATTGAATGCATAAATGTGGATTATAAATCAACAAGGAAAGAAT
| |||| | | | || ||| | || || || | | | | || ||||||||| ||||||||| || || || || | |||||||| || |||||||| |||||||| ||||| ||||| || || ||||| |||||||||||||
-------------------------------------gttggacatttatttttgttatatgtaagataataaatagtgtttcatcaatgtacaacta---ctctctcgattcagGGAACTACTGTGGAAGGGACAATTCAACAGCTATTTGAAGGTCATCATATGAATTATATTGAGTGCATTAATGTTGACTACAAATCTACAAGGAAAGAAT
upper sequence: GLYMA10G23680.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G014805_T01 (Zea mays), 3'ss of exon 6
gtactggtttttcatgatggctcttattgtcttcttaaaatagcttttactctagatacttgtgtatttttatgatgtcttgaaagattatttgttggggtttcatcttggccagGGAACTGTTGTGGAAGGCACTATACAGCAATTGTTTGAAGGACACCATATGAACTATATTGAATGCATAAATGTGGATTATAAATCAACAAGGAAAGAAT
| | | | || | | || ||| | || | | | | | ||| || |||| | | |||||||||||||||||||| || || | ||||| || ||||| ||||| || || || ||||| ||||| || ||||| |||||||| | || |||||||
---------------------------------------------gtgaatat-gacaataatgaattatcattacacc--aatttactttttattaacttttctttctacacagGGAACTGTTGTGGAAGGAACAATTGAACAATTATTCGAAGGCCACCACATTAATTACATTGAGTGCATTAACGTGGACTATAAATCTAACAGAAAAGAAT
upper sequence: GLYMA10G23680.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv13s0073g00610.t01 (Vitis vinifera), 3'ss of exon 6
gtactggtttttcatgatggctcttattgtcttcttaaaatagcttttactctagatacttgtgtatttttatgatgtcttgaaagattatttgttggggtttcatcttggccagGGAACTGTTGTGGAAGGCACTATACAGCAATTGTTTGAAGGACACCATATGAACTATATTGAATGCATAAATGTGGATTATAAATCAACAAGGAAAGAAT
| ||| |||| | | | | || | | ||| | | ||| || || | ||| || ||||| ||| | | ||||||||||||||||| || ||||||||||| || |||||||| |||||||||||||||||||||||||| |||||||| |||||||||||||| || ||||
-------------gtataggcgcttaacattgccacttgttggacttcagtgcttataa----gcaagtttgggaaatcattaaat-ttgattgtta---tttttaatggctcagGGAACTGTTGTGGAGGGTACTATACAGCAGTTATTTGAAGGGCACCATATGAACTATATTGAATGCATTAATGTGGACTATAAATCAACAAGAAAGGAAT
upper sequence: GLYMA10G23680.1 (Glycine max), 3'ss of exon 2
lower sequence: PP1S123_138V6.1 (Physcomitrella patens), 3'ss of exon 6
gtactggtttttca-tgatggctcttattgtcttcttaaaatagcttttactctagatacttgtgtatttttatgatgtcttgaaagattatttgttggggtttcatcttggccagGGAACTGTTGTGGAAGGCACTATACAGCAATTGTTTGAAGGACACCATATGAACTATATTGAATGCATAAATGTGGATTATAAATCAACAAGGAAAGAAT
||| | | || || | ||| |||||||| | ||| | || || ||| || ||| | || | || | || || | ||| | |||||||||| ||| || ||||| || |||||| |||| ||||| || || |||||||| || || ||||| ||||| ||||||||||||||| ||||||| |
gtatggataaatctctgttagct----atgtcttctcg-----gttttcaa---gagtagctgggtacatt-atgtttactggtgggaatcctt-ctgtgctttta-------cagGGAACTGCTGTCGAGGGCACAATCCAGCAACTGTTCGAAGGGCATCACATGAACTACATAGAGTGCATCAATGTTGATTATAAATCAACACGGAAAGAGT
upper sequence: GLYMA10G23680.1 (Glycine max), 3'ss of exon 2
lower sequence: EFJ14291 (Selaginella moellendorffii), 3'ss of exon 4
gtactggtttttcatgatggctcttattgtcttcttaaaatagcttttactctagatacttgtgtatttttatgatgtcttgaaagattatttgttggggtttcatcttggc-cagGGAACTGTTGTGGAAGGCACTATACAGCAATTGTTTGAAGGACACCATATGAACTATATTGAATGCATAAATGTGGATTATAAATCAACAAGGAAAGAAT
|| || | ||| | | | | ||| | ||| | |||| ||| ||||| || |||||||| | || ||||| || |||||||| |||||||||||||| |||||||| ||||| || || | || ||||
-------------------------------------------------------------gtttactgctattttcttcacgttaaatgttttctaacaccaagctccactacagAGTACTGCTGTTGAAGGTACCATACAGCAGCTTTTCGAAGGCCATCATATGAATTATATTGAATGCATCAATGTGGACTATAAGTCCACTCGAAAGGAAT
upper sequence: GLYMA10G23680.1 (Glycine max), 3'ss of exon 2
lower sequence: EFJ18164 (Selaginella moellendorffii), 3'ss of exon 4
gtactggtttttcatgatggctcttattgtcttcttaaaatagcttttactctagatacttgtgtatttttatgatgtcttgaaagattatttgttggggtttcatcttggc-cagGGAACTGTTGTGGAAGGCACTATACAGCAATTGTTTGAAGGACACCATATGAACTATATTGAATGCATAAATGTGGATTATAAATCAACAAGGAAAGAAT
|| || | ||| | | | | ||| | ||| | |||| ||| ||||| || |||||||| | || ||||| ||||||||||| |||||||||||||| |||||||| || || || || | || ||||
-------------------------------------------------------------gtttactgctattttcttcacgttaaatgttttctaacaccaagctccactacagAGTACTGCTGTTGAAGGTACCATACAGCAGCTTTTCGAAGGCCACCATATGAATTATATTGAATGCATCAATGTGGACTACAAGTCCACTCGAAAGGAAT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgtgtatttttatgatgtcttgaaagattatttgttggggtttcatcttggccagGGAACTGTTGTGGAAGGCACTATACAGCAATTGTTTGAAGGACACCATATGAACTATATTGAATGCATAAATGTGGATTATAAATCAACAAGGAAAGAAT
tttcatctt CT-rich tract
ttgaaagattattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtactggtttttcatgatggctcttattgtcttcttaaaatagcttttactctagatacttgtgtatttttatgatgtcttgaaagattatttgttggggtttcatcttggccagGGAACTGTTGTGGAAGGCACTATACAGCAATTGTTTGAAGGACACCATATGAACTATATTGAATGCATAAATGTGGATTATAAATCAACAAGGAAAGAAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA