Sequence
atgc intronic sequence ATGC exonic sequencegtaagcgtaatatgaatctcttaattaccctccagaaagctaattgtgtcccttgttataaaaaaagtcagctttggtatgtcatcaaagaaatcagctttgatcacattctttttcttggtgcagCTACCCAGGAACTGGATGCATTTGCACTTCTTGCGGGCTATAGGAATTGCTATGTCTATGAGGGCAGGTGTTGCTGCTGATGCTGCAGCCGCTTTGCTTT
Basic information
species | Arabidopsis thaliana |
transcript | AT1G22770.1 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G22770.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GRMZM5G844173_T01 (Zea mays), 3'ss of exon 9
gtaagcgtaatatgaatctcttaattaccctcca-gaaagctaattgtgtcccttgttata-aaaaaagtcagctttggtatgt-catcaaagaaatcagctttgatcacattctttttcttggtgcagCTACCCAGGAACTGGATGCATTTGCACTTCTTGCGGGCTATAGGAATTGCTATGTCTATGAGGGCAGGTGTTGCTGCTGATGCTGCAGCCGCTTTGCTTT
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----gtatgacatacttcaca-gattattttgagtgcaaaattatcaagttgcctacgatacaaaattgtccggccacatttgtgtgtgtaaattttcattaactgtgatacttttattttatttgtagCTTCCAAAGAATTGGATGCATCTGCATTTCTTGCGTGCCATTGGAACTGCAATGTCAATGAGAGCTGGTATTGCTGCTGATACAGCTGCTGCTCTGCTTT
upper sequence: AT1G22770.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA09G07240.1 (Glycine max), 3'ss of exon 9
gtaagcgtaatatgaatctcttaattaccctccagaaagctaattgtgtcccttgttataaaaaaagtcagctttggtatgtcatcaaagaaatcagctttgatcacattctttttc----ttggtgcagCTACCCAGGAACTGGATGCATTTGCACTTCTTGCGGGCTATAGGAATTGCTATGTCTATGAGGGCAGGTGTTGCTGCTGATGCTGCAGCCGCTTTGCTTT
| | | ||| | | | | ||| | | | | | | | | | |||| ||| | || |||| | | || | ||||| || || || ||||||||||| || |||||||| |||||||| | ||| ||||| ||||| | ||||| ||||||||||||||||| || |||||||
-----------------------------atgtgtgcatttggatgttttcatctgcagaaacattatgaaagcttgaacccaactgactgattcagttttt-ttaccttctctctaaatgttaatacagCTTCCTAGAAATTGGATGCATTTTCATTTCTTGCGTGCTATAGGGACTGCAATGTCCATGAGATCTGGTGTAGCTGCTGATGCTGCAGCTGCATTGCTTT
upper sequence: AT1G22770.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA20G30980.1 (Glycine max), 3'ss of exon 3
gtaagcgtaatatgaatctcttaattaccctccagaaagctaattgtgtcccttgttataaaaaaagtcagct--ttggtatgtcatcaaagaaatcagctttgatcacattctttttcttggtgcagCTACCCAGGAACTGGATGCATTTGCACTTCTTGCGGGCTATAGGAATTGCTATGTCTATGAGGGCAGGTGTTGCTGCTGATGCTGCAGCCGCTTTGCTTT
||| || | | ||| | | | | || | | ||| || || || | ||| ||| | | | | | || ||||||| || || || ||||||||||||||||||||||| || ||||| | ||| ||||| ||||| || ||| | || ||||||||||| || ||| | ||||
-------------caattatgtatgtgtattgcagtgggattactaaactttgtgaaagatttaaaaccaactgactgatgtgtt---------------tttcttttctgttatatgtttaatgcagCTTCCTAGAAATTGGATGCATTTGCACTTCTTGCGTGCAATAGGGACTGCAATGTCCATGAGAGCTGGTATAGCCGCTGATGCTGCCGCTGCTCTTCTTT
upper sequence: AT1G22770.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA10G36600.1 (Glycine max), 3'ss of exon 9
gtaagcgtaatatgaatctcttaattaccctccagaaagctaattgtgtcccttgttataaaaaaagtcagctttggtatgtcatcaaagaaatcagctttgatcacattctttttcttggtgcagCTACCCAGGAACTGGATGCATTTGCACTTCTTGCGGGCTATAGGAATTGCTATGTCTATGAGGGCAGGTGTTGCTGCTGATGCTGCAGCCGCTTTGCTTT
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----------------------gatttaaaaccatacaa-taactgactgatgtgtt-tgaaagatttaaaacc--atacaataactgactgatgtgtttttcttttttgttatatgttattgcagCTTCCTAGAAATTGGATGCATTTGCATTTCTTGCGTGCAATAGGGACTGCAATGTCCATGAGAGCTGGTATAGCCGCTGATGCTGCAGCTGCTCTTCTTT
upper sequence: AT1G22770.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: Vv18s0157g00020.t01 (Vitis vinifera), 3'ss of exon 10
gtaagcgtaatatgaatctcttaattaccctccagaaagctaattgtgtcccttgttataaaaaaagtcagctttggtatgtcatcaaagaaatcagctttgatcacattctttttcttggtgcagCTACCCAGGAACTGGATGCATTTGCACTTCTTGCGGGCTATAGGAATTGCTATGTCTATGAGGGCAGGTGTTGCTGCTGATGCTGCAGCCGCTTTGCTTT
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---------------------gaatgaaattgtggatttagaacagatttagacattgttcaactaatgaa-ttcagt-tgtcatcaatgc--tcatatctaaat-tgcttttcttattgatatagCTCCCAAGGAACTGGATGCATTTGCATTTCTTGCGTGCAATTGGTACTGCAATGTCCATGAGAGCAGGGATTGCTGCAGATGCTGCTGCAGCATTACTTT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctttggtatgtcatcaaagaaatcagctttgatcacattctttttcttggtgcagCTACCCAGGAACTGGATGCATTTGCACTTCTTGCGGGCTATAGGAATTGCTATGTCTATGAGGGCAGGTGTTGCTGCTGATGCTGCAGCCGCTTTGCTTT
ctttgat putative branch site (score: 5)
tcacattctttttctt CT-rich tract
attcttttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagcgtaatatgaatctcttaattaccctccagaaagctaattgtgtcccttgttataaaaaaagtcagctttggtatgtcatcaaagaaatcagctttgatcacattctttttcttggtgcagCTACCCAGGAACTGGATGCATTTGCACTTCTTGCGGGCTATAGGAATTGCTATGTCTATGAGGGCAGGTGTTGCTGCTGATGCTGCAGCCGCTTTGCTTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG