Sequence
atgc intronic sequence ATGC exonic sequencegtaaattatttgctaaatatctataaactgtagtcaacgtccaggttttgaatgattttgtaaactgtattcttgccacagGGGCACAGTTCGTTATGCTAGTGTGCATGCTCATCTTGGTCGAACAGGTAGCAGGAGAGATGACTTGGAATCTCTTGCTTACACTCTTGTCTTTCTTCTT
Basic information
species | Glycine max |
transcript | GLYMA06G09190.1 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA06G09190.1 (Glycine max), 3'ss of exon 8
lower sequence: LOC_Os01g54100.2 (Oryza sativa), 3'ss of exon 7
-----------gtaaattatttgctaaatatctataaactgtagtcaacgtccaggttttgaatgattttgtaa----actgtattcttgccac------agGGGCACAGTTCGTTATGCTAGTGTGCATGCTCATCTTGGTCGAACAGGTAGCAGGAGAGATGACTTGGAATCTCTTGCTTACACTCTTGTCTTTCTTCTT
||| || | | | ||| | | | | | ||| | ||| || | | | |||| | | | |||| | ||||| |||||||| ||||||||||| ||||| ||||| || ||| |||||| | || ||||| || |||||||| |||||||| || || ||||||||
gaaatagagccctaatttctgtcttgaatgccaactcattct--tcatgttgtaggcttatagcaaatcagtaactctgccttgcttttgctgctatttcagGGGGACAGTTCGCTATGCTAGTGTTCATGCACATCTAGGGAGAATCGGTAGCCGAAGGGATGATTTAGAATCTCTAGCTTACACACTAGTTTTTCTTCTA
upper sequence: GLYMA06G09190.1 (Glycine max), 3'ss of exon 8
lower sequence: LOC_Os01g10150.2 (Oryza sativa), 3'ss of exon 8
------gtaaattatttgcta-aatatctataaact-gtagtcaacgtccaggttttgaatgattttgtaaactgtattcttgccacagGGGCACAGTTCGTTATGCTAGTGTGCATGCTCATCTTGGTCGAACAGGTAGCAGGAGAGATGACTTGGAATCTCTTGCTTACACTCTTGTCTTTCTTCTT
|| | ||| || || |||| | | | | || | | | | | | ||| | || ||||||| || ||||||||||||||||||||||| || | || |||| || |||||||||||||| | ||||| ||||| ||||| ||| | || |||||
gtttgaatagaaagtttattacgatgcctatcattttgcacattactttattgatgcgctcttcctgtttgtctgc-tactgtaaacagGGGTACTGTTCGTTATGCTAGTGTGCATGCCCACTTGGGAAGAACTGGATGCAGGAGAGATGACCTTGAATCCCTTGCATACACACTTATTTTCCTTCTC
upper sequence: GLYMA06G09190.1 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM2G095634_T01 (Zea mays), 3'ss of exon 1
------------------------------------------------------------------------------------------------------gtaaattatttgctaaatatctataaactg--tagtcaacgtccaggttttgaatgattttgtaaactgt----attcttgccacagGGGCACAGTTCGTTATGCTAGTGTGCATGCTCATCTTGGTCGAACAGGTAGCAGGAGAGATGACTTGGAATCTCTTGCTTACACTCTTGTCTTTCTTCTT
|| | |||| ||| | || | | | | || || | || | | || ||||| | || |||||| ||| |||| ||||||||||| ||||| |||||||| |||||||||||||||| ||||| || |||||||| || || || || |||||||||||
gtatgcatggtagtagccattctttaactggacatggaatcagtctcttagtctctgttgagatggtacactaaacatattgtcacagtagctagtaaagctgtggtgcttatgcttcttatagttgaatcaaatgaaggagatactagtctt-actgttatgatacactgttactgctgctgtttcagGGGAACATTTCGCTATGCTAGTGTTCATGCACATCTTGGGAGAACAGGTAGCAGGAGGGATGATTTAGAATCTCTAGCATATACACTAGTCTTTCTTCTA
upper sequence: GLYMA06G09190.1 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM2G116151_T03 (Zea mays), 3'ss of exon 8
---------gtaaattatttgctaaat---atctataaa--ctgtagtca-----acgtccaggttttgaatgatt-ttgtaaactgtattct--tgccacagGGGCACAGTTCGTTATGCTAGTGTGCATGCTCATCTTGGTCGAACAGGTAGCAGGAGAGATGACTTGGAATCTCTTGCTTACACTCTTGTCTTTCTTCTT
|||| || ||| | |||| || || || || || || | | || | | || | || | | | || |||| || || ||||| |||||||| |||||||||||| | || |||| || |||||||| |||||| | ||||||||||| ||||| ||||| ||||||||
gtttgcaatagaaatacttcactaggttttatcttccaaggctttattctcccctacttctatgcttacattttttgtcatacatcactgtttaatggaacagAGGAACTGTTCGGTATGCTAGCGTGCATGCTCATTTGGGGAGAACTGGAAGCAGGAGGGATGACCTTGAATCTCTTGCCTACACACTTGTATTTCTTCTG
upper sequence: GLYMA06G09190.1 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM2G158177_T01 (Zea mays), 3'ss of exon 1
-------gtaaattatttgctaaatatctataaactgtagtcaacgtccaggttttgaatgattttgtaaactgtattcttgcca----cagGGGCACAGTTCGTTATGCTAGTGTGCATGCTCATCTTGGTCGAACAGGTAGCAGGAGAGATGACTTGGAATCTCTTGCTTACACTCTTGTCTTTCTTCTT
| |||| | | || | | | || || | || |||| ||||| | |||||| || |||||| || ||||| |||||||||||||||||||| | || |||| || || ||||||||||| | ||||| ||||| ||||| ||| | ||||||||
gttcgtttgggaatattagtttgatgtgcttta-ctactcacattatttca--ttggaatacttttgacatttgtatttgcttcataaacagGGGAACTGTTCGCTATGCTAGTGTGCATGCTCACTTGGGAAGAACTGGGAGTAGGAGAGATGATCTTGAATCCCTTGCATACACGCTTATTTTTCTTCTA
upper sequence: GLYMA06G09190.1 (Glycine max), 3'ss of exon 8
lower sequence: AT2G25760.2 (Arabidopsis thaliana), 3'ss of exon 8
gtaaattattt--gctaaatat-----ctataa-----actgtagtcaacg--tccaggttttgaatgattttgtaaactgtattcttgcca----cagGGGCACAGTTCGTTATGCTAGTGTGCATGCTCATCTTGGTCGAACAGGTAGCAGGAGAGATGACTTGGAATCTCTTGCTTACACTCTTGTCTTTCTTCTT
|||| || || |||| || || | | | | | ||| | | || ||| | | || | | | || || ||| || ||||| |||||||||||||| |||||||||||||| |||| | || |||| |||||| ||||||||||||||||||||||||| || ||||||
gtaagttgattcagctaggcataaagcctgtgagattgattcttatcagggacttcaactttagggtacttattaacgtgttggctttttcattttcagAGGAACAGTACGTTATGCTAGTGTACATGCTCATCTTGGCAGAACTTGCAGTCGGAGGGATGACCTGGAATCTCTTGCTTACACTCTTGTTTTCCTTCTT
upper sequence: GLYMA06G09190.1 (Glycine max), 3'ss of exon 8
lower sequence: Vv09s0002g03680.t01 (Vitis vinifera), 3'ss of exon 8
--------------------------------------------------gtaaattatttgctaaatatctataaactgtagtcaacgtccaggttttgaatgattttgtaaactgtattcttgccacagGGGCACAGTTCGTTATGCTAGTGTGCATGCTCATCTTGGTCGAACAGGTAGCAGGAGAGATGACTTGGAATCTCTTGCTTACACTCTTGTCTTTCTTCTT
|| | ||| | | ||| | | | || ||| ||| || ||| | ||| || | |||| | ||||| || || || |||||||||||||| |||||| | || |||| || || ||||||||||| |||||||||||||||||||||||| | || || ||
gtacaatcattgacaatttcttgttttataaatatttatgtactttccttctaccctgtttctttattatatttgcatattaa--aacctcctacttctgactcatta---gaataatggtctt---atagGGGAACTGTGCGATATGCTAGTGTGCACGCTCATTTGGGGAGAACTGGCAGTAGGAGAGATGATTTGGAATCTCTTGCTTACACTCTTATTTTCCTCCTC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.actgtagtcaacgtccaggttttgaatgattttgtaaactgtattcttgccacagGGGCACAGTTCGTTATGCTAGTGTGCATGCTCATCTTGGTCGAACAGGTAGCAGGAGAGATGACTTGGAATCTCTTGCTTACACTCTTGTCTTTCTTCTT
ttcttgcc CT-rich tract
ttttgaatgatttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaattatttgctaaatatctataaactgtagtcaacgtccaggttttgaatgattttgtaaactgtattcttgccacagGGGCACAGTTCGTTATGCTAGTGTGCATGCTCATCTTGGTCGAACAGGTAGCAGGAGAGATGACTTGGAATCTCTTGCTTACACTCTTGTCTTTCTTCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG