Sequence
atgc intronic sequence ATGC exonic sequence...gatttaaaaccatacaataactgactgatgtgtttgaaagatttaaaaccatacaataactgactgatgtgtttttcttttttgttatatgttattgcagCTTCCTAGAAATTGGATGCATTTGCATTTCTTGCGTGCAATAGGGACTGCAATGTCCATGAGAGCTGGTATAGCCGCTGATGCTGCAGCTGCTCTTCTTT
Basic information
species | Glycine max |
transcript | GLYMA10G36600.2 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA10G36600.1 (Glycine max), 3'ss of exon 9
lower sequence: LOC_Os01g08700.8 (Oryza sativa), 3'ss of exon 10
--------------------------gatttaaaaccatacaataac-tgactgatgtgtttgaaagatttaaaaccatacaataactgactgatgtgtttt-----tcttttttgttatatgttat--tgcagCTTCCTAGAAATTGGATGCATTTGCATTTCTTGCGTGCAATAGGGACTGCAATGTCCATGAGAGCTGGTATAGCCGCTGATGCTGCAGCTGCTCTTCTTT
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gtatatcatacatctctctggctgttgtttcagtgctatcaatcaagatgacacat-catgcaatattatcataacagcacattatgtgttttgaatattttattgattgtcatagctttgttttatgttttagCTTCCAAAGAACTGGATGCATCTTCATTTCCTGCGTGCTATTGGAACTGCAATGTCAATGAGAGCTGGTATCGCTGCTGATACGTCTGCTGCTTTACTTT
upper sequence: GLYMA10G36600.1 (Glycine max), 3'ss of exon 9
lower sequence: GRMZM5G844173_T01 (Zea mays), 3'ss of exon 9
--------gatttaaaaccatacaataactg----actgatgtgtt-tgaaagatttaaaaccatacaataactgactgatgtgt---ttttcttt---tttgtta----tatgttatt-gcagCTTCCTAGAAATTGGATGCATTTGCATTTCTTGCGTGCAATAGGGACTGCAATGTCCATGAGAGCTGGTATAGCCGCTGATGCTGCAGCTGCTCTTCTTT
| || | | || | | || | | ||| | ||| |||| | | || ||||| ||||| || | || || ||| ||||| | ||||||| | |||||||||||| |||||||||||||||| || || ||||||||||| |||||||||||||| || |||||| | || |||||||| ||||
gtatgacatacttcacagattattttgagtgcaaaattatcaagttgcctacgatacaaaattgtccggccacatttgtgtgtgtaaattttcattaactgtgatacttttattttatttgtagCTTCCAAAGAATTGGATGCATCTGCATTTCTTGCGTGCCATTGGAACTGCAATGTCAATGAGAGCTGGTATTGCTGCTGATACAGCTGCTGCTCTGCTTT
upper sequence: GLYMA10G36600.1 (Glycine max), 3'ss of exon 9
lower sequence: GRMZM2G107101_T06 (Zea mays), 3'ss of exon 9
--------gatttaaaaccatacaataactgactgatgtgtttga--aagatttaaaaccatacaataac-tgactgatgtg--tttttcttttttgttatatgttatt----gcagCTTCCTAGAAATTGGATGCATTTGCATTTCTTGCGTGCAATAGGGACTGCAATGTCCATGAGAGCTGGTATAGCCGCTGATGCTGCAGCTGCTCTTCTTT
| || | | || | | | | | ||| | ||| |||| | || || | || | ||||| || ||| | ||||| | ||||||| | ||||||||||||| |||||||||||||||| || || ||||||||||| ||||||||||| || || |||||| | || |||||| | ||||
gtatgccatacttcacagattatccttgcaaaattgtcaagttgcctatgatacaaaattgtctaaccacatctttggttcaactttttgttaactgtggcactttattttttgtagCTTCCAAAAAATTGGATGCATCTGCATTTCTTGCGTGCGATTGGAACTGCAATGTCAATGAGAGCTGGCATTGCTGCTGATACAGCTGCTGCTTTGCTTT
upper sequence: GLYMA10G36600.1 (Glycine max), 3'ss of exon 9
lower sequence: AT1G22770.1 (Arabidopsis thaliana), 3'ss of exon 8
----------------------gatttaaaaccatacaa-taactgactgatgtgtt-tgaaagatttaaaacc--atacaataactgactgatgtgtttttcttttttgttatatgttattgcagCTTCCTAGAAATTGGATGCATTTGCATTTCTTGCGTGCAATAGGGACTGCAATGTCCATGAGAGCTGGTATAGCCGCTGATGCTGCAGCTGCTCTTCTTT
||| ||| | | ||| || | |||| | ||| | | | || | | | || | ||| | | | | | || ||||||| || || || |||||||||||||| |||||||| || ||||| | ||| ||||| ||||| || ||| | || |||||||||||||| ||| | ||||
gtaagcgtaatatgaatctcttaattaccctccagaaagctaattgtgtcccttgttataaaaaaagtcagctttggtatgtcatcaaagaaatcagctttgatcacattctttttcttggtgcagCTACCCAGGAACTGGATGCATTTGCACTTCTTGCGGGCTATAGGAATTGCTATGTCTATGAGGGCAGGTGTTGCTGCTGATGCTGCAGCCGCTTTGCTTT
upper sequence: GLYMA10G36600.1 (Glycine max), 3'ss of exon 9
lower sequence: Vv18s0157g00020.t01 (Vitis vinifera), 3'ss of exon 10
gatttaaaaccatacaataactgactgatgtgtttgaaagatttaaaaccatacaat--aactg--actgatgtgtttttcttttttgttata--tgttattgcagCTTCCTAGAAATTGGATGCATTTGCATTTCTTGCGTGCAATAGGGACTGCAATGTCCATGAGAGCTGGTATAGCCGCTGATGCTGCAGCTGCTCTTCTTT
|| | | | | | ||| | | | ||| | ||| | || | ||| | ||| ||| | | | || | |||| || || || ||||||||||||||||||||||||||||| || |||||||||||||||||||| || || || || |||||||| || || | ||||
------gaatgaaattgtggatttagaacagatttagacattgttcaactaatgaattcagttgtcatcaatgctcatatctaaattgcttttcttattgatatagCTCCCAAGGAACTGGATGCATTTGCATTTCTTGCGTGCAATTGGTACTGCAATGTCCATGAGAGCAGGGATTGCTGCAGATGCTGCTGCAGCATTACTTT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aaaccatacaataactgactgatgtgtttttcttttttgttatatgttattgcagCTTCCTAGAAATTGGATGCATTTGCATTTCTTGCGTGCAATAGGGACTGCAATGTCCATGAGAGCTGGTATAGCCGCTGATGCTGCAGCTGCTCTTCTTT
tgtttttcttttttgt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gatttaaaaccatacaataactgactgatgtgtttgaaagatttaaaaccatacaataactgactgatgtgtttttcttttttgttatatgttattgcagCTTCCTAGAAATTGGATGCATTTGCATTTCTTGCGTGCAATAGGGACTGCAATGTCCATGAGAGCTGGTATAGCCGCTGATGCTGCAGCTGCTCTTCTTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - -ccataca
- - - - - - - - - - - -actgatg