Sequence
atgc intronic sequence ATGC exonic sequence...caattatgtatgtgtattgcagtgggattactaaactttgtgaaagatttaaaaccaactgactgatgtgtttttcttttctgttatatgtttaatgcagCTTCCTAGAAATTGGATGCATTTGCACTTCTTGCGTGCAATAGGGACTGCAATGTCCATGAGAGCTGGTATAGCCGCTGATGCTGCCGCTGCTCTTCTTT
Basic information
species | Glycine max |
transcript | GLYMA20G30980.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA20G30980.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os01g08700.8 (Oryza sativa), 3'ss of exon 10
----------caattatgtatgtgt-attgcagtgggattactaaa-------ctttgtgaaagatt-taaaaccaactgactgatgtgtttt---tctttt-----ctgttata----tgtttaatgc---agCTTCCTAGAAATTGGATGCATTTGCACTTCTTGCGTGCAATAGGGACTGCAATGTCCATGAGAGCTGGTATAGCCGCTGATGCTGCCGCTGCTCTTCTTT
|| | | | ||| || ||||| || | | || | | || || ||| | | | || | | | ||||||||| | |||| ||| ||| ||||| ||| ||||||| | || ||||||||| | || ||| ||||||| || || ||||||||||| |||||||||||||| || |||||| | | |||||| | ||||
gtatatcatacatctctctggctgttgtttcagtgctatcaatcaagatgacacatcatgcaatattatcataacagcacatt-atgtgttttgaatattttattgattgtcatagctttgttttatgttttagCTTCCAAAGAACTGGATGCATCTTCATTTCCTGCGTGCTATTGGAACTGCAATGTCAATGAGAGCTGGTATCGCTGCTGATACGTCTGCTGCTTTACTTT
upper sequence: GLYMA20G30980.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM5G844173_T01 (Zea mays), 3'ss of exon 9
----------------caattatgt-atgtgtattgcagtgggattactaaactttgtgaaagatttaaaaccaactgactg-atgtgtttttcttttctgttatatgtttaa------tgcagCTTCCTAGAAATTGGATGCATTTGCACTTCTTGCGTGCAATAGGGACTGCAATGTCCATGAGAGCTGGTATAGCCGCTGATGCTGCCGCTGCTCTTCTTT
||||| | ||| | | || | | | || | || || || | |||| || |||| ||| |||| || ||||||| | |||||||||||| |||| ||||||||||| || || ||||||||||| |||||||||||||| || |||||| | || |||||||| ||||
gtatgacatacttcacagattattttgagtgcaaaattatcaagttgcctacgatacaaaattgtccggccacatttgtgtgtgtaaattttcattaactgtgatacttttattttatttgtagCTTCCAAAGAATTGGATGCATCTGCATTTCTTGCGTGCCATTGGAACTGCAATGTCAATGAGAGCTGGTATTGCTGCTGATACAGCTGCTGCTCTGCTTT
upper sequence: GLYMA20G30980.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G107101_T06 (Zea mays), 3'ss of exon 9
-----caattatgtatgtgt-attgcagtgggattactaaact--ttgtga---aagatt-taaaaccaactgactgatgtg--tttttcttttctgttata---tgtttaatgcagCTTCCTAGAAATTGGATGCATTTGCACTTCTTGCGTGCAATAGGGACTGCAATGTCCATGAGAGCTGGTATAGCCGCTGATGCTGCCGCTGCTCTTCTTT
| || | | | || | ||| || | | ||| || ||| | ||||| | || | ||||| || |||| | | ||| || ||||||| | ||||||||||||| |||| ||||||||||| || || ||||||||||| ||||||||||| || || |||||| | || |||||| | ||||
gtatgccatacttcacagattatccttgcaaaattgtcaagttgcctatgatacaaaattgtctaaccacatctttggttcaactttttgttaactgtggcactttattttttgtagCTTCCAAAAAATTGGATGCATCTGCATTTCTTGCGTGCGATTGGAACTGCAATGTCAATGAGAGCTGGCATTGCTGCTGATACAGCTGCTGCTTTGCTTT
upper sequence: GLYMA20G30980.1 (Glycine max), 3'ss of exon 3
lower sequence: AT1G22770.1 (Arabidopsis thaliana), 3'ss of exon 8
-------------caattatgtatgtgtattgcagtgggattactaaactttgtgaaagatttaaaaccaactgactgatgtgtt---------------tttcttttctgttatatgtttaatgcagCTTCCTAGAAATTGGATGCATTTGCACTTCTTGCGTGCAATAGGGACTGCAATGTCCATGAGAGCTGGTATAGCCGCTGATGCTGCCGCTGCTCTTCTTT
||| || | | ||| | | | | || | | ||| || || || | ||| ||| | | | | | || ||||||| || || || ||||||||||||||||||||||| || ||||| | ||| ||||| ||||| || ||| | || ||||||||||| || ||| | ||||
gtaagcgtaatatgaatctcttaattaccctccagaaagctaattgtgtcccttgttataaaaaaagtcagct--ttggtatgtcatcaaagaaatcagctttgatcacattctttttcttggtgcagCTACCCAGGAACTGGATGCATTTGCACTTCTTGCGGGCTATAGGAATTGCTATGTCTATGAGGGCAGGTGTTGCTGCTGATGCTGCAGCCGCTTTGCTTT
upper sequence: GLYMA20G30980.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv18s0157g00020.t01 (Vitis vinifera), 3'ss of exon 10
caattatgtatgtgtattgcagtgggattactaaactttgtgaaagatttaaaaccaactg--actgatgtgtttttcttttctgttatatgt-ttaatgcagCTTCCTAGAAATTGGATGCATTTGCACTTCTTGCGTGCAATAGGGACTGCAATGTCCATGAGAGCTGGTATAGCCGCTGATGCTGCCGCTGCTCTTCTTT
||| | | |||| ||| |||| || || |||| || | || || || | ||| | ||| || | | | || || |||| || || || |||||||||||||| |||||||||||||| || |||||||||||||||||||| || || || || |||||||| || || | ||||
gaatgaaat-tgtggatttagaacagatt--tagacattgttcaactaatgaattcagttgtcatcaatgctcatatctaaattgcttttcttattgatatagCTCCCAAGGAACTGGATGCATTTGCATTTCTTGCGTGCAATTGGTACTGCAATGTCCATGAGAGCAGGGATTGCTGCAGATGCTGCTGCAGCATTACTTT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gatttaaaaccaactgactgatgtgtttttcttttctgttatatgtttaatgcagCTTCCTAGAAATTGGATGCATTTGCACTTCTTGCGTGCAATAGGGACTGCAATGTCCATGAGAGCTGGTATAGCCGCTGATGCTGCCGCTGCTCTTCTTT
tgttatatgtttaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
caattatgtatgtgtattgcagtgggattactaaactttgtgaaagatttaaaaccaactgactgatgtgtttttcttttctgttatatgtttaatgcagCTTCCTAGAAATTGGATGCATTTGCACTTCTTGCGTGCAATAGGGACTGCAATGTCCATGAGAGCTGGTATAGCCGCTGATGCTGCCGCTGCTCTTCTTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - tgtatgt
- - - - - - - - -tgcagtg
- - - - - - - - - - - - - - - - - -ctttgtg
- - - - - - - - - - - - - - - - - - - - - - - - - - -accaact
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -actgatg