Sequence
atgc intronic sequence ATGC exonic sequence...gtttgatatattcttcagttgcgagctcacaatttctaggtaggactgcataaattctgtagaatttagagatctgatcttcatactcttcatattgcagGTATTCAGGGGAAGTTAAGAGATTACCAATTAGCTGGTTTAAACTGGCTCATTCGGCTGTATGAGAACGGCATAAATGGGATTCTTGCAGATGAAATG
Basic information
species | Arabidopsis thaliana |
transcript | AT5G18620.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G18620.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA07G38050.2 (Glycine max), 3'ss of exon 4
---gtttgatatattcttcagttg-cgagctcacaatttctaggtaggactgcataaattctgtagaatttagagatctgatcttcatactcttcatattgcagGTATTCAGGGGAAGTTAAGAGATTACCAATTAGCTGGTTTAAACTGGCTCATTCGGCTGTATGAGAACGGCATAAATGGGATTCTTGCAGATGAAATG
||| | | || | ||| | | || |||| ||| | ||| | | | | || | | ||| | | | || | ||||||| || |||||| | || ||||||||| | ||||| ||||||||||||| || |||||||||| ||||||||||| ||||| ||||||||||||
tttttttactttggggtttatttgtctaacttgtggattctttgtattcgtatctaatgtttttgtcacttgaa--tgtgacatggct--tgtttgttcaacagGTATCCAAGGGAAGATGAGGGATTACCAACTTGCTGGGCTAAACTGGCTCATACGATTGTATGAGAATGGCATAAATGGTATTCTGGCAGATGAAATG
upper sequence: AT5G18620.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA17G02640.1 (Glycine max), 3'ss of exon 4
---gtttgatatattcttcagttg-cgagctcacaatttctaggtaggactgcataaattctgtagaatttagagatctgatcttcatactcttcatattgcagGTATTCAGGGGAAGTTAAGAGATTACCAATTAGCTGGTTTAAACTGGCTCATTCGGCTGTATGAGAACGGCATAAATGGGATTCTTGCAGATGAAATG
||| | | | | ||| | | || |||| ||| | ||| | | | | || | | ||| || | | ||| | |||| || || |||||| | || ||||||||| | ||||| ||||||||||||| || |||||||||| ||||||||||| ||||| ||||||||||||
tttttttactttggggattatttgtctaacttgtggattctttgtattcgtatctaatgtttttgtcacttgaa--tttgacattgct--tgttcgttcaacagGCATCCAAGGGAAGATGAGGGATTACCAACTTGCTGGGCTAAACTGGCTCATACGATTGTATGAGAATGGCATAAATGGTATTCTGGCAGATGAAATG
upper sequence: AT5G18620.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA13G28720.1 (Glycine max), 3'ss of exon 4
gtttgatatattcttcagttgcgagctcacaatttctaggtaggactgcataaattctgtagaatttagagat-ctgatc-ttcatactcttcatattgcagGTATTCAGGGGAAGTTAAGAGATTACCAATTAGCTGGTTTAAACTGGCTCATTCGGCTGTATGAGAACGGCATAAATGGGATTCTTGCAGATGAAATG
|| | | | || | || || || || || || | | | | || || || || | | | || ||||||| || ||||| | || ||||||||| | ||||| ||||||||||||| || |||||||||| || |||||||| ||||| || |||||||||
--gtgttgtccaacaaatatgtcaatccattcatttataatatttttgaattttttgttcacgtgtcatgaatgctcattgttagttttttattctttacagGTATCCAAGGGAAAATGAGGGATTACCAACTGGCTGGACTAAACTGGCTCATACGATTGTATGAGAATGGAATAAATGGAATTCTGGCTGATGAAATG
upper sequence: AT5G18620.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA15G10370.1 (Glycine max), 3'ss of exon 4
gtttgatatattcttcagttgcgagctcacaatttctaggtaggactgcataaattctgtagaatttagagatctgatc-ttcatactcttcatattgcagGTATTCAGGGGAAGTTAAGAGATTACCAATTAGCTGGTTTAAACTGGCTCATTCGGCTGTATGAGAACGGCATAAATGGGATTCTTGCAGATGAAATG
| | | | | | | | | || ||| || | || | | | | | || || || | | | | ||| ||||||| || ||||| | || |||||||| | ||||| ||||||||||||| || |||||||||| || |||||||| ||||| || |||||||||
-tgtattgtctaacaaatacgtggatctattcatttatagtatttttgatttttttttcttgtgtcttgaatgctcattgcttgttttttattcattacagGTATCCAAGGGAAAATGAGGGATTACCAGCTGGCTGGACTAAACTGGCTCATACGATTGTATGAGAATGGAATAAATGGAATTCTGGCTGATGAAATG
upper sequence: AT5G18620.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv05s0020g01780.t01 (Vitis vinifera), 3'ss of exon 4
gtttgatatattcttcagttgcga-gc-tcacaatttctaggtaggactgcataaattctgtagaatttagagatctgatcttcatactcttcatattgcagGTATTCAGGGGAAGTTAAGAGATTACCAATTAGCTGGTTTAAACTGGCTCATTCGGCTGTATGAGAACGGCATAAATGGGATTCTTGCAGATGAAATG
|| ||| | | || || || | ||| ||| || ||| || | ||| | | | | || || | ||||||||||||| ||| | |||||||||||| | ||||| ||||||||||||| |||||||||||||| ||||| ||||| || || ||||||||||||
-ttagatcttgctgttgtttaagatgcattacagtttttaaa-aggtggttattgttgttgtgccctcccccccccccccccccgcccttttttttcctcagGTATTCAGGGAAAGATGAGAGATTACCAACTTGCTGGCCTAAACTGGCTCATACGGCTGTATGAGAATGGCATCAATGGAATCCTCGCAGATGAAATG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctgcataaattctgtagaatttagagatctgatcttcatactcttcatattgcagGTATTCAGGGGAAGTTAAGAGATTACCAATTAGCTGGTTTAAACTGGCTCATTCGGCTGTATGAGAACGGCATAAATGGGATTCTTGCAGATGAAATG
atctgat putative branch site (score: 4)
tcttcatactcttc CT-rich tract
tagaattta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtttgatatattcttcagttgcgagctcacaatttctaggtaggactgcataaattctgtagaatttagagatctgatcttcatactcttcatattgcagGTATTCAGGGGAAGTTAAGAGATTACCAATTAGCTGGTTTAAACTGGCTCATTCGGCTGTATGAGAACGGCATAAATGGGATTCTTGCAGATGAAATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG