Sequence
atgc intronic sequence ATGC exonic sequencegtaaaaagcacacaaaagcgtttccacatttttttatcaaatgctaaaatcaaaatttgaaggaaggtcaaaagtgctatttctcattaaaatcaaattctcattttcatcagGGGAACGAAGACTAGAAGCTGGTGCAATGGTCCTCGCTGATAAAGGTATCGTGTGCATTGACGAGTTTGATAAGATGAATGATCAGGACCGAGTTGCTAT
Basic information
species | Arabidopsis thaliana |
transcript | AT5G46280.1 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G46280.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: LOC_Os05g39850.1 (Oryza sativa), 3'ss of exon 7
gtaaaaagcacacaaaagcgtttccacatttttttatcaaatgctaaaatcaaaatttgaaggaaggtcaaaagtgctatttctcattaaaatcaaattctcattttcatcagGGGAACGAAGACTAGAAGCTGGTGCAATGGTCCTCGCTGATAAAGGTATCGTGTGCATTGACGAGTTTGATAAGATGAATGATCAGGACCGAGTTGCTAT
| | || ||| ||| | | || | |||| || | | | || | | ||| || |||| || || |||||||| ||||| || |||||| ||| | || |||||||| |||||||||||||||||||||||||||||||| |||||
------------------------------------------gtaattattgaaacttgtttcatacatatttgt-ttgattcttataggtctgagcgatttcttgtggttagGTGAGAGAAGGCTGGAGGCTGGTGCCATGGTTCTTGCTGATCGTGGTGTTGTCTGCATTGATGAGTTTGATAAGATGAATGATCAGGACCGAGTGGCTAT
upper sequence: AT5G46280.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GRMZM2G162445_T01 (Zea mays), 3'ss of exon 7
gtaaaaagcacacaaaagcgtttccacatttttttatcaaatgctaaaatcaaaatttgaaggaaggtcaaaagtgctat-ttctcattaaaatcaaattctcattttc--atcagGGGAACGAAGACTAGAAGCTGGTGCAATGGTCCTCGCTGATAAAGGTATCGTGTGCATTGACGAGTTTGATAAGATGAATGATCAGGACCGAGTTGCTAT
| || | | || || | | | | | || ||| | ||| | ||| || || | |||| ||||||||| |||| || ||||||||||| ||||| || |||||| ||| |||| |||||||| ||||||||||| ||||||||||| ||||||||||||||
-----------------------------------gtaaattacacaactcta--ctcagtgcatgtgcattggtgtcgtattcctgtaaaagtctcatgacaaatttctgttcagGGGAAAGAAGGCTTGAAGCTGGTGCCATGGTTCTTGCTGATCGTGGTGTCGTCTGCATTGATGAGTTTGATAAAATGAATGATCAAGACCGAGTTGCTAT
upper sequence: AT5G46280.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GRMZM2G100639_T01 (Zea mays), 3'ss of exon 7
gtaaaaagcacacaaaagcgtttccacatttttttatcaaatgctaaaatcaaaatttgaaggaaggtcaaaagtgctatttctcattaaaatcaaattctca--ttttcatcagGGGAACGAAGACTAGAAGCTGGTGCAATGGTCCTCGCTGATAAAGGTATCGTGTGCATTGACGAGTTTGATAAGATGAATGATCAGGACCGAGTTGCTAT
| || | | || || | || | | | | | |||| || | ||| | || | |||| |||||||| ||||| || ||||||||||| ||||| || |||||| ||| | || |||||||| ||||||||||| ||||||||||| || |||||||||||
-----------------------------------gtaaattacacaactcta--cttagtgca---ttggtattcatattcct-gtaaaagcctcatggcgagtttttgttcagGGGAGCGAAGGCTTGAAGCTGGTGCCATGGTTCTTGCTGATCGTGGTGTTGTCTGCATTGATGAGTTTGATAAAATGAATGATCAAGATCGAGTTGCTAT
upper sequence: AT5G46280.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA08G08920.1 (Glycine max), 3'ss of exon 7
gtaaaaagcacacaaaagcgtttccacatttttttatcaaatgctaaaatcaaaatttgaaggaaggtcaaaagtgctatttctcattaaaatcaaattctcattttcatcagGGGAACGAAGACTAGAAGCTGGTGCAATGGTCCTCGCTGATAAAGGTATCGTGTGCATTGACGAGTTTGATAAGATGAATGATCAGGACCGAGTTGCTAT
||| || | | | | | || | | ||| | || || | || |||| | | | | || || | ||||| | |||| || | | ||||||| |||| || |||||||| |||||||| || ||||| | |||| | || |||||||| || ||||| |||||||||||||| || || ||||||||
--gtaaatcattcgtcatgggctatatatatatatat-atata-tatatgcataattctatta----ttacatctgtcatctaagga-aaaattgtaatctctttcttct-agGGGAAAGAAGGCTTGAAGCTGGGGCAATGGTGCTTGCTGACAGAGGTGTTGTCTGCATTGATGAATTTGACAAGATGAATGATCAAGATCGTGTTGCTAT
upper sequence: AT5G46280.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA05G25980.1 (Glycine max), 3'ss of exon 7
gtaaaaagcacacaaaagcgtttccacatttttttatcaaatgctaaaatcaaaatttgaaggaaggtcaaaagtgctatttctcattaaaatcaaattctcattttcatc-----agGGGAACGAAGACTAGAAGCTGGTGCAATGGTCCTCGCTGATAAAGGTATCGTGTGCATTGACGAGTTTGATAAGATGAATGATCAGGACCGAGTTGCTAT
| |||| | | | || | | || | | || | |||| || ||| | | |||| | ||| ||| |||| || |||||||| |||||||| || ||||| | |||| | || |||||||| || ||||| |||||||||||||| || || ||||||||
-------------------------------gtaaatcattcgtcttgggctatatatatgcataattctattattacatctgtcatctaagcaaaaattgtaatttctttcttctagGAGAAAGAAGGCTTGAAGCTGGGGCAATGGTTCTTGCTGACAGAGGTGTTGTCTGCATTGATGAATTTGACAAGATGAATGATCAAGATCGTGTTGCTAT
upper sequence: AT5G46280.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: Vv10s0003g03080.t01 (Vitis vinifera), 3'ss of exon 7
gtaaaaagcacacaaaagcgtttccacatttttttatcaaatgctaaaatcaaa-atttgaaggaaggtcaaaagtgctatttctcattaaaatcaaattctcattttcatcagGGGAACGAAGACTAGAAGCTGGTGCAATGGTCCTCGCTGATAAAGGTATCGTGTGCATTGACGAGTTTGATAAGATGAATGATCAGGACCGAGTTGCTAT
| |||||| | | ||| || | | | | | | | ||| | || || || | || |||||||| ||| |||| |||||||||||||| ||||| || |||||| |||| | || || ||||| |||||||| |||||||||||||| || || ||||||||
----------------------------gtaatttatct--caccaggcccaagcatgttagcgttatttggcaat--tgcttcagactagtattctctttcc-ttgtcatcagGAGAAAGAAGGCTAGAAGCTGGTGCCATGGTTCTTGCTGATCGAGGTGTTGTTTGTATTGATGAGTTTGACAAGATGAATGATCAAGATCGTGTTGCTAT
upper sequence: AT5G46280.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: PP1S9_156V6.1 (Physcomitrella patens), 3'ss of exon 7
------------------------------------------------------------gtaaaaagcacacaaaagcgtttccacatttttttatcaaatgctaaaatcaaaatttgaaggaaggtcaaaagtgctatttctcattaaaatc---aaattctcattttcat---cagGGGAACGAAGACTAGAAGCTGGTGCAATGGTCCTCGCTGATAAAGGTATCGTGTGCATTGACGAGTTTGATAAGATGAATGATCAGGACCGAGTTGCTAT
|| || | || | || || | | | | | | | |||||| | | || || || || ||| | || || | || | | |||| || | || ||||| || || || ||||| | || || || || ||||||||||||||||||||||| |||| ||||| ||||||||| ||||
gtaagatatgtactccattctccttagttgtagccctaaggaagtgatttcatactgacgatacttggcggatgggagattatcgtaccattctcacaacctatcagacttcaaatttctatacaagttggtcttg-tagatcacatgactattctgaatgtggtatctctacaaacagGAGAGAGGAGGCTAGAGGCAGGGGCGATGGTTTTAGCCGACCGCGGCATAGTGTGCATTGACGAGTTTGATAAAATGAGTGATCTTGACCGAGTTTCTAT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gaaggaaggtcaaaagtgctatttctcattaaaatcaaattctcattttcatcagGGGAACGAAGACTAGAAGCTGGTGCAATGGTCCTCGCTGATAAAGGTATCGTGTGCATTGACGAGTTTGATAAGATGAATGATCAGGACCGAGTTGCTAT
ttctcattttcatc CT-rich tract
tatttctcattaaaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaaaagcacacaaaagcgtttccacatttttttatcaaatgctaaaatcaaaatttgaaggaaggtcaaaagtgctatttctcattaaaatcaaattctcattttcatcagGGGAACGAAGACTAGAAGCTGGTGCAATGGTCCTCGCTGATAAAGGTATCGTGTGCATTGACGAGTTTGATAAGATGAATGATCAGGACCGAGTTGCTAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG