Sequence
atgc intronic sequence ATGC exonic sequence...aaatagtcagctgctaattgtgaattttatatagtatgtgaaaaagtattgaaaaaataatgaagatggtggttatatatatgttgggatgtgtgtgaagGTGGATTGGACACCAGAGCTACACAGGAGATTCGTGGAGGCAGTGGAACAGTTAGGAGTGGACAAAGCTGTTCCTTCTCGAATTCTGGAGCTTATGGGAG
Basic information
species | Arabidopsis thaliana |
transcript | AT2G20570.2 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT2G20570.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA12G33430.1 (Glycine max), 3'ss of exon 1
aaatagtcagctgctaattgtgaattttata-tagtatgtgaaaaagtattgaaaaaataatgaagatggtggttatatatatgttgggatgtgtgtgaagGTGGATTGGACACCAGAGCTACACAGGAGATTCGTGGAGGCAGTGGAACAGTTAGGAGTGGACAAAGCTGTTCCTTCTCGAATTCTGGAGCTTATGGGAG
| | | |||| | ||| | | | || | | | | || |||||| | || || | | | | | | |||||||||||||||||||| ||||| |||||||| |||||||| | |||||||| ||| | |||||||| || ||||| ||||| | ||| ||||| ||||||||
-gggggagggggggatgcagtgagtgttagaactggctttgttgtattgtagtaataataatcgatttgttgtgtgcttgtttttcttgggttgtgtgaagGTGGATTGGACCCCAGAATTACACAGGCGATTCGTGCAAGCAGTGGAGCAGCTTGGAGTGGATAAGGCTGTGCCTTCAAGGATTTTGGAGATTATGGGAA
upper sequence: AT2G20570.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA13G37010.1 (Glycine max), 3'ss of exon 2
aaatagtcagc-tgctaattgtgaattt---tatatagtatgtgaaaaagtattgaaaaaataatgaagatggtggttatatatatgttgggatgtgtgtgaagGTGGATTGGACACCAGAGCTACACAGGAGATTCGTGGAGGCAGTGGAACAGTTAGGAGTGGACAAAGCTGTTCCTTCTCGAATTCTGGAGCTTATGGGAG
||| || | |||| || | | | | |||||| |||| | | | | | ||| | | | | | ||||| | |||| |||||||||||||| ||||| | |||||| |||||||| | |||||||| ||| | |||||||| || ||||| |||||| | ||| ||||| ||||||||
--gcagtgagtgttagaattttggaactggctttgatgtatgtattgtagtaataatgggtttgttgtgtgtgtgtgtttgtttttcttgggttatgtg--aagGTGGATTGGACCCCAGAATTGCACAGGCGATTCGTGCAAGCAGTGGAGCAGCTTGGAGTGGATAAGGCTGTGCCTTCTAGGATTTTGGAGATTATGGGAA
upper sequence: AT2G20570.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA12G13430.1 (Glycine max), 3'ss of exon 1
aaatagtcagctgctaattg-tgaatttta--tatagt-atgtgaaaaagtattgaaaaaataatgaagatggtggttatatatatgttgggatgtgtgtgaagGTGGATTGGACACCAGAGCTACACAGGAGATTCGTGGAGGCAGTGGAACAGTTAGGAGTGGACAAAGCTGTTCCTTCTCGAATTCTGGAGCTTATGGGAG
| |||| | ||| | || | | |||||| ||| | | |||||| | | | | | | | | | | | |||| |||||||| ||||||||||||| ||||| | |||||| |||||||| | || ||||||||| |||||||||| || || || ||||| | ||| ||||| ||||||||
-ttttgtcaaataaaaataacttgatctgaagtatagtcatggggtatagtattttatg--tga-gtacgtatttatgcttctttttctgggttgtgtgtgtagGTGGATTGGACCCCAGAATTGCACAGGCGATTCGTGCAAGCTGTGGAACAGCTAGGAGTGGATAAGGCGGTGCCTTCAAGGATTTTGGAGATTATGGGAA
upper sequence: AT2G20570.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA06G44330.1 (Glycine max), 3'ss of exon 1
aaatagtcagctg--ctaattgtgaatt-ttatatagtatgtgaaa-aagtattgaaaaaataatgaagatggtggttatatatatgttgggatgtgtgtgaagGTGGATTGGACACCAGAGCTACACAGGAGATTCGTGGAGGCAGTGGAACAGTTAGGAGTGGACAAAGCTGTTCCTTCTCGAATTCTGGAGCTTATGGGAG
| | || |||| || |||| |||| | | | | |||||| | | | | ||| | || | | | | || | |||||| ||||||||||||| ||||| | ||||| |||||||| | || ||||||||| |||||||||| || || || ||||| | ||| ||||| ||||||||
---tttttttttggtctaactgaaaattcttatttgagacctaactcgagtattaatatgtgagtatttatgttttttcttttcttatctgggt-tgtgtgtagGTGGATTGGACCCCAGAATTGCACAGACGATTCGTGCAAGCTGTGGAACAGCTAGGAGTGGATAAGGCGGTGCCTTCAAGGATTTTGGAGATTATGGGAA
upper sequence: AT2G20570.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv12s0028g03100.t01 (Vitis vinifera), 3'ss of exon 1
aaatagtcagctgcta--attgtgaattttatatagtatgtgaaaaagtattgaaaaaataatgaagatggtggttatatatatgttgggatgtgtgtgaagGTGGATTGGACACCAGAGCTACACAGGAGATTCGTGGAGGCAGTGGAACAGTTAGGAGTGGACAAAGCTGTTCCTTCTCGAATTCTGGAGCTTATGGGAG
|| | | | | | || | | | | | || |||| | | ||| || || || || |||||| ||||||||||||| |||||||| || ||||| || ||| |||||||||| ||| |||| ||||| ||||| || ||||| | ||| | ||| ||||||||
--atgatgaatgggagggagagagagtctctgaacttttctgttgtgttatttatttctatgtcctgattttgaaggagagaattttttgaactgtgtgtagGTGGATTGGACCCCAGAGCTGCATAGGAGGTTTGTGCAGGCAGTGGAGCAGCTAGGTGTGGATAAAGCAGTGCCTTCAAGGATTTTAGAGATTATGGGAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtattgaaaaaataatgaagatggtggttatatatatgttgggatgtgtgtgaagGTGGATTGGACACCAGAGCTACACAGGAGATTCGTGGAGGCAGTGGAACAGTTAGGAGTGGACAAAGCTGTTCCTTCTCGAATTCTGGAGCTTATGGGAG
aaaaaataatgaagat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
aaatagtcagctgctaattgtgaattttatatagtatgtgaaaaagtattgaaaaaataatgaagatggtggttatatatatgttgggatgtgtgtgaagGTGGATTGGACACCAGAGCTACACAGGAGATTCGTGGAGGCAGTGGAACAGTTAGGAGTGGACAAAGCTGTTCCTTCTCGAATTCTGGAGCTTATGGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT
- - - - - ctgctaa
- - - - - - - - - - - - - - - - - - - -gaaaaag
- - - - - - - - - - - - - - - - - - - - - - - - - - -aaaataa