Sequence
atgc intronic sequence ATGC exonic sequencegtaaattatttgcttaatatctataaactgtagtaaacgtccaggttttgaatgattttgtaaactatatacttgccacagGGGCACAGTTCGTTATGCTAGCGTGCATGCTCATCTTGGTAGAACAGGTAGTAGGAGAGATGACTTAGAATCTCTTGCTTACACTCTTGTCTTTCTTCTT
Basic information
species | Glycine max |
transcript | GLYMA04G09070.2 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA04G09070.1 (Glycine max), 3'ss of exon 8
lower sequence: LOC_Os01g54100.2 (Oryza sativa), 3'ss of exon 7
-----------gtaaattatttgcttaatatctataaact------gtagtaaacgtccaggttttgaatgattttg--taaactatatacttgccacagGGGCACAGTTCGTTATGCTAGCGTGCATGCTCATCTTGGTAGAACAGGTAGTAGGAGAGATGACTTAGAATCTCTTGCTTACACTCTTGTCTTTCTTCTT
||| || | | | ||| | | | | || ||| | | || | | | | | || | | | | |||||| |||||||| |||||||| || ||||| ||||| || |||| ||||| | || ||||| ||||||||||| |||||||| || || ||||||||
gaaatagagccctaatttctgtcttgaatgccaactcattcttcatgttgtaggcttatagcaaatcagtaactctgccttgcttttgctgctatttcagGGGGACAGTTCGCTATGCTAGTGTTCATGCACATCTAGGGAGAATCGGTAGCCGAAGGGATGATTTAGAATCTCTAGCTTACACACTAGTTTTTCTTCTA
upper sequence: GLYMA04G09070.1 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM2G095634_T01 (Zea mays), 3'ss of exon 1
------------------------------------------------------------------------------------------------------gtaaattatttgcttaatatctataaactg--tagtaaacgtccaggttttgaatgattttgtaaactat--atact--tgccacagGGGCACAGTTCGTTATGCTAGCGTGCATGCTCATCTTGGTAGAACAGGTAGTAGGAGAGATGACTTAGAATCTCTTGCTTACACTCTTGTCTTTCTTCTT
|| | ||||| ||| | || | | | | || || | || | | || ||| | | || || |||||| ||| |||| |||||||| || ||||| |||||||| ||||||||||| ||||| ||||| ||||||||||| || || || || |||||||||||
gtatgcatggtagtagccattctttaactggacatggaatcagtctcttagtctctgttgagatggtacactaaacatattgtcacagtagctagtaaagctgtggtgcttatgcttcttatagttgaatcaaatgaaggagatactagtctt-actgttatgatacactgttactgctgctgtttcagGGGAACATTTCGCTATGCTAGTGTTCATGCACATCTTGGGAGAACAGGTAGCAGGAGGGATGATTTAGAATCTCTAGCATATACACTAGTCTTTCTTCTA
upper sequence: GLYMA04G09070.1 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM2G116151_T03 (Zea mays), 3'ss of exon 8
-------------gtaaattatttg-cttaatatctataaactgtagtaa-----acgtccaggttttgaatgatt-ttgtaaactatatact--tgccacagGGGCACAGTTCGTTATGCTAGCGTGCATGCTCATCTTGGTAGAACAGGTAGTAGGAGAGATGACTTAGAATCTCTTGCTTACACTCTTGTCTTTCTTCTT
|| | | | | || || | | || || | || || | | || | | || | || | | | || |||| || || ||||| ||||||||||||||||||||| | || ||||| || || ||||| |||||| | ||||||||||| ||||| ||||| ||||||||
gtttgcaatagaaatacttcactaggttttatcttccaaggctttattctcccctacttctatgcttacattttttgtcatacatcactgtttaatggaacagAGGAACTGTTCGGTATGCTAGCGTGCATGCTCATTTGGGGAGAACTGGAAGCAGGAGGGATGACCTTGAATCTCTTGCCTACACACTTGTATTTCTTCTG
upper sequence: GLYMA04G09070.1 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM2G158177_T01 (Zea mays), 3'ss of exon 1
-------gtaaattatttgcttaatatctataaactgtagtaaacgtccaggttttgaatgattttgtaaactatatacttgcca----cagGGGCACAGTTCGTTATGCTAGCGTGCATGCTCATCTTGGTAGAACAGGTAGTAGGAGAGATGACTTAGAATCTCTTGCTTACACTCTTGTCTTTCTTCTT
| |||| | || || | | | | | | || || |||| ||||| | | ||| || |||||| || ||||| |||||||| ||||||||||| | || ||||| || |||||||||||||| | ||||| ||||| ||||| ||| | ||||||||
gttcgtttgggaatattagtttgatgtgctttactactcacattatttca---ttggaatacttttgacatttgtatttgcttcataaacagGGGAACTGTTCGCTATGCTAGTGTGCATGCTCACTTGGGAAGAACTGGGAGTAGGAGAGATGATCTTGAATCCCTTGCATACACGCTTATTTTTCTTCTA
upper sequence: GLYMA04G09070.1 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM2G045259_T02 (Zea mays), 3'ss of exon 8
-gtaaattatttgc-ttaatatc-tataaactgtagtaaacgtccaggttttgaatgattttgtaaactatatacttgcca----cagGGGCACAGTTCGTTATGCTAGCGTGCATGCTCATCTTGGTAGAACAGGTAGTAGGAGAGATGACTTAGAATCTCTTGCTTACACTCTTGTCTTTCTTCTT
| || ||| ||| ||| | |||| |||||| ||||| | | | | || |||||| || ||||| ||||||||||||||||| || | || ||||| || |||||||||||||| | ||||| || || ||||||||| | ||||||||
gttcggttgggaatattagtatgatatgctttaccactcacgttatttcattgaatacttttgacatttgtgtttgcttcataaacagGGGAACTGTTCGCTATGCTAGCGTGCATGCCCACTTGGGAAGAACTGGGAGTAGGAGAGATGATCTTGAATCCCTCGCATACACTCTTATTTTTCTTCTC
upper sequence: GLYMA04G09070.1 (Glycine max), 3'ss of exon 8
lower sequence: AT2G25760.2 (Arabidopsis thaliana), 3'ss of exon 8
gtaaattattt-------gcttaatatctataa-actg-----tagtaaacgtccaggttttgaatgattttgtaaactatatacttgcca-----cagGGGCACAGTTCGTTATGCTAGCGTGCATGCTCATCTTGGTAGAACAGGTAGTAGGAGAGATGACTTAGAATCTCTTGCTTACACTCTTGTCTTTCTTCTT
|||| || || || ||| || | | | || || | ||| | || ||| | | ||| ||| || ||||| ||||||||||| || |||||||||||||| ||||| | ||| |||| |||||| | ||||||||||||||||||||||| || ||||||
gtaagttgattcagctaggcataaagcctgtgagattgattcttatcagggacttcaactttagggtacttattaacgtgttggctttttcattttcagAGGAACAGTACGTTATGCTAGTGTACATGCTCATCTTGGCAGAACTTGCAGTCGGAGGGATGACCTGGAATCTCTTGCTTACACTCTTGTTTTCCTTCTT
upper sequence: GLYMA04G09070.1 (Glycine max), 3'ss of exon 8
lower sequence: Vv09s0002g03680.t01 (Vitis vinifera), 3'ss of exon 8
--------------------------------------------------gtaaattatttgcttaatatctataaactgtagtaaacgtccaggttttgaatgattttgtaaactatatacttgccacagGGGCACAGTTCGTTATGCTAGCGTGCATGCTCATCTTGGTAGAACAGGTAGTAGGAGAGATGACTTAGAATCTCTTGCTTACACTCTTGTCTTTCTTCTT
|| | ||| ||| ||| | | | || |||| ||| || ||| | ||| || || ||| | ||||| || || || |||||||| ||||| |||||| | || ||||| || |||||||||||||| || ||||||||||||||||||||| | || || ||
gtacaatcattgacaatttcttgttttataaatatttatgtactttccttctaccctgtttctttattatatttgcatatta--aaacctcctacttctgactcatta---gaataatggtctt---atagGGGAACTGTGCGATATGCTAGTGTGCACGCTCATTTGGGGAGAACTGGCAGTAGGAGAGATGATTTGGAATCTCTTGCTTACACTCTTATTTTCCTCCTC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.actgtagtaaacgtccaggttttgaatgattttgtaaactatatacttgccacagGGGCACAGTTCGTTATGCTAGCGTGCATGCTCATCTTGGTAGAACAGGTAGTAGGAGAGATGACTTAGAATCTCTTGCTTACACTCTTGTCTTTCTTCTT
aatgattttgtaaact 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaattatttgcttaatatctataaactgtagtaaacgtccaggttttgaatgattttgtaaactatatacttgccacagGGGCACAGTTCGTTATGCTAGCGTGCATGCTCATCTTGGTAGAACAGGTAGTAGGAGAGATGACTTAGAATCTCTTGCTTACACTCTTGTCTTTCTTCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG