Sequence
atgc intronic sequence ATGC exonic sequence...cttgcagcaaattgtaagtctttttgtttggtgatttggttttgaagcttgtggaattcaaatctgatcaattggtgttttttccttctgtgttgcttagTTAATAGGTTCTCTACAGAAGAAATATTCAATTGGGTCCTTTGAGTTGTTGAGTAAAACAGCGCCGATTCAAGCTTTTTCGCTTCTTGTTGTCGGTCCTT
Basic information
species | Arabidopsis thaliana |
transcript | AT5G42420.2 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G42420.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA01G45700.1 (Glycine max), 3'ss of exon 3
--cttgcagcaaattgtaagtctttttgtttggtgatttggttttgaagcttgtggaattcaaatctgatcaattggtgttttttccttctgtgttgct-tagTTAATAGGTTCTCTACAGAAGAAATATTCAATTGGGTCCTTTGAGTTGTTGAGTAAAACAGCGCCGATTCAAGCTTTTTCGCTTCTTGTTGTCGGTCCTT
| | | || || | | | | | || | ||| || ||| | |||||| ||| | ||| | || || ||||| || ||| ||| |||||||||||| || ||||||||||||||||| || ||||| ||| |||||||||| || || |||||||| ||| |||||| || | ||||| |
tttctactactaaa-gtcaattgtggtatatgct-attattttgtgatgtttgtgggatttat-tcttttttataactgatttttattttcaacttgtaacagTCAATAGGTTCTCTTCAAAAGAAATATTCAATTGGATCTTTTGAATTGCTGAGTAAAACTGCTCCCATTCAAGCGCTTTTTCTTCTTATTCTTGGTCCAT
upper sequence: AT5G42420.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA11G00210.2 (Glycine max), 3'ss of exon 3
-cttgcagcaaat--tgtaagtctttttgtttggtgatttggttttgaagcttgtggaattcaaatctgatcaattggtgttttttccttctgtgttgcttagTTAATAGGTTCTCTACAGAAGAAATATTCAATTGGGTCCTTTGAGTTGTTGAGTAAAACAGCGCCGATTCAAGCTTTTTCGCTTCTTGTTGTCGGTCCTT
||| | | | | || | | | | | || | ||| || ||| | ||| || ||| ||| | || |||||||| ||| | ||| |||||||||||| || ||||||||||||||||| || ||||| ||| |||||||||| || || || ||||| ||| |||||| || | ||||| |
acttactactactaaagtcaattgtggtatatgct-attattttgtgatgtttgggggatttct-tcttttttataactgttttttt-ttcaacttgtaacagTCAATAGGTTCTCTTCAAAAGAAATATTCAATTGGATCTTTTGAATTGCTGAGTAAAACTGCTCCCATCCAAGCGCTTTTTCTTCTTATTCTTGGTCCAT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.agcttgtggaattcaaatctgatcaattggtgttttttccttctgtgttgcttagTTAATAGGTTCTCTACAGAAGAAATATTCAATTGGGTCCTTTGAGTTGTTGAGTAAAACAGCGCCGATTCAAGCTTTTTCGCTTCTTGTTGTCGGTCCTT
atctgat putative branch site (score: 4)
ttttttccttctgtgt putative PPT
aattcaaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
cttgcagcaaattgtaagtctttttgtttggtgatttggttttgaagcttgtggaattcaaatctgatcaattggtgttttttccttctgtgttgcttagTTAATAGGTTCTCTACAGAAGAAATATTCAATTGGGTCCTTTGAGTTGTTGAGTAAAACAGCGCCGATTCAAGCTTTTTCGCTTCTTGTTGTCGGTCCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - cagcaaa
- - - - - - - - - - - - tgtttgg
- - - - - - - - - - - - - - - - - - -ggttttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -tcaaatc