Sequence
atgc intronic sequence ATGC exonic sequencegtaatttgtctttgtattgtctattggtcatcttgcttcagttcttgtcatttgattttgtattcatctttttttcttcaaatctacagAGTTTCGGTGGCTTTTGTGCACTTACATATCTGAGTTTTGCACCCGAAGGACTCAAACAAGTGCTAATAACTGGAGGAATTCCACCAATTGGTAAAGCAT
Basic information
species | Arabidopsis thaliana |
transcript | AT3G61540.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G61540.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA09G39020.1 (Glycine max), 3'ss of exon 3
------------gtaatttgtctttgtattgtctattggtcatcttgcttcagttcttgtcatttgattttgtattcatctttttttcttcaaatct-acagAGTTTCGGTGGCTTTTGTGCACTTACATATCTGAGTTTTGCACCCGAAGGACTCAAACAAGTGCTAATAACTGGAGGAATTCCACCAATTGGTAAAGCAT
|| || ||||||| | | || | || | | | ||| || | ||| || || || || || | | | |||| | ||||| ||||||||| | |||||| ||||||||||||| ||||||| || ||||| || ||||||||||||||||| || ||||| | | ||
taggagctttggttagaatgcctttgtacc-tttgaaaccaatatagccttggaattccatgcttgcttac-tcttcttccgttcttttttaattgtgatagAGCTATGGTGGATTTTGTGCAGTCACATATTTGAGTTTTGCACCACAAGGACTGAAGCAAGTCCTTATAACTGGAGGAATTCCTCCGATTGGCAGTGGAT
upper sequence: AT3G61540.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA18G47320.1 (Glycine max), 3'ss of exon 3
gtaatttgtctttgtattgtctattggtcatcttgcttcagttcttgtcatttgatt--ttgtattcatctttttttcttcaaatct----------acagAGTTTCGGTGGCTTTTGTGCACTTACATATCTGAGTTTTGCACCCGAAGGACTCAAACAAGTGCTAATAACTGGAGGAATTCCACCAATTGGTAAAGCAT
|| || ||||||| | | || | || | | | ||| || | ||||| || |||| ||| | | | |||| | ||||| ||||||||| | || ||| ||||||| ||||| ||||| | || ||||| || ||||||||||||||||| || ||||| | ||
-tagaatgcctttgtaacctttgaaaccaatatagccttggaattccatgcttgcttactcttattctgtttctttttttctatttttttttttgtggtagAGCTATGGTGGATTTTGTGCAGTCACGTATTTGAGTTTCGCACCAAAAGGATTGAAGCAAGTCCTTATAACTGGAGGAATTCCTCCGATTGGAGGTGGAT
upper sequence: AT3G61540.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv15s0046g02160.t01 (Vitis vinifera), 3'ss of exon 3
gtaatttgt-ctttgta--ttgtctattggtcatcttgcttcagttcttg--tcatttgatt--ttgtattcatc------tttttttcttcaaatctacagAGTTTCGGTGGCTTTTGTGCACTTACATATCTGAGTTTTGCACCCGAAGGACTCAAACAAGTGCTAATAACTGGAGGAATTCCACCAATTGGTAAAGCAT
|||| | || || ||| | | | ||| | || | | | | || ||| | | ||| | | || || | || | | | ||||| || ||||| |||||||| |||| ||| ||||||||||||| ||||| | |||||||| || ||||||| |||||||| |||||||| | | |
--aattcccgcattataatttgcttgtggtgcattgcattaaagctttggaattatatgactcataaaatttaccaaaagcttgttcttttttattttgcagAGCTTTGGTGGTTTTTGTGCGGTTACCTATTTGAGTTTTGCACCAAAAGGATTGAAACAAGTCCTTCTAACTGGGGGAATTCCTCCAATTGGAAGTGGCT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gcttcagttcttgtcatttgattttgtattcatctttttttcttcaaatctacagAGTTTCGGTGGCTTTTGTGCACTTACATATCTGAGTTTTGCACCCGAAGGACTCAAACAAGTGCTAATAACTGGAGGAATTCCACCAATTGGTAAAGCAT
atttgat putative branch site (score: 5)
ttcatctttttttctt putative PPT
attttgtattcatctt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaatttgtctttgtattgtctattggtcatcttgcttcagttcttgtcatttgattttgtattcatctttttttcttcaaatctacagAGTTTCGGTGGCTTTTGTGCACTTACATATCTGAGTTTTGCACCCGAAGGACTCAAACAAGTGCTAATAACTGGAGGAATTCCACCAATTGGTAAAGCAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA