Sequence
atgc intronic sequence ATGC exonic sequencegtaatgttactgataactctaaactgggtgattttgtagatcttcaaacttttttaattcgttgtactctgcattgtgtggtttggctcatatcaatgttatatctaccgttgcagGATGTCCATCATGGCAACGGAACCCAAGAGATATTCGAACAAAACAAATCT
Basic information
species | Arabidopsis thaliana |
transcript | AT3G18520.1 |
intron # | 10 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G18520.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: LOC_Os07g06980.2 (Oryza sativa), 3'ss of exon 9
------------gtaatgttactgataactctaaactgggtgattttgtagatctt-caaacttttttaattcgttgtactctgcattgtgtggtttggctcat---atcaatgttat--atctaccgttgcagGATGTCCATCATGGCAACGGAACCCAAGAGATATTCGAACAAAACAAATCT
|| || | | | || || ||| ||| | | || || || | || || ||| |||| || | | | ||||||||||||||| |||||||| ||||| || |||||||| || |||| |||
gtaatgctagttacaagtttgcatttgaacttataccattgcattctgttggcatcatggacccccccaaaaaaagatagtgcctcaaatggatgttaatccatctcatcagtggtgctcaattgttgttgcagGATGTCCACCATGGCAATGGAACACAGGAGATATTTGATGGGGACAATTCT
upper sequence: AT3G18520.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GLYMA05G07990.1 (Glycine max), 3'ss of exon 11
gtaatgttactgataactcta-aactgggtgattttgta-gatcttc--aaacttttttaattcgttgtactctgcattgtgtggtttggctcatatcaatgttatatctaccgttgcagGATGTCCATCATGGCAACGGAACCCAAGAGATATTCGAACAAAACAAATCT
|||| || || | | || || ||| |||| ||| ||| || | | |||| | | ||| ||| | || | | | | || || || |||||||| |||||||| || || || ||||| ||||| |||||||||||||||
gtaacgtcgctactcataatatgccttactgaaattgtgtgattttcctgaaggccggggctacattgttat-taaattatgttttatgagttgattgagcttcatgatta---ttacagGATGTTCATCATGGAAATGGGACACAAGAAATATTTGAACAAAACAAATCT
upper sequence: AT3G18520.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: EFJ31239 (Selaginella moellendorffii), 3'ss of exon 8
gtaatgttactgataactctaaactgggtgattttgtagatcttcaaacttttttaattcgttgtactctgcattgtgtggtttggctcatatcaatgttatatctaccgttgcagGATGTCCATCATGGCAACGGAACCCAAGAGATATTCGAACAAAACAAATCT
| |||| || | | | ||| || | | | ||| | | ||||||||||| |||||||| || ||||| |||||||| ||||| || | |||
--------------------------------------------------------gtgcgttcctgtcaccgctaccttctttatgccaaacc--tcttacaacgcgacttgcagGATGTTCATCATGGTAATGGAACGCAAGAGATTTTCGAGCACGATCCATCC
upper sequence: AT3G18520.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: EFJ34365 (Selaginella moellendorffii), 3'ss of exon 8
gtaatgttactgataactctaaactgggtgattttgtagatcttcaaacttttttaattcgttgtactctgcattgtgtggtttggctcatatcaatgttatatctaccgttgcagGATGTCCATCATGGCAACGGAACCCAAGAGATATTCGAACAAAACAAATCT
| |||| || | | | ||| ||| | | | ||| | | ||||||||||| |||||||| || ||||| |||||||| ||||| || | |||
--------------------------------------------------------gtgcgttcctgtcaccgctaccttctttatgtcaaacc--tcttacaacgcgacttgcagGATGTTCATCATGGTAATGGAACGCAAGAGATTTTCGAGCACGATCCATCC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttgtactctgcattgtgtggtttggctcatatcaatgttatatctaccgttgcagGATGTCCATCATGGCAACGGAACCCAAGAGATATTCGAACAAAACAAATCT
atatcaatgttatat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaatgttactgataactctaaactgggtgattttgtagatcttcaaacttttttaattcgttgtactctgcattgtgtggtttggctcatatcaatgttatatctaccgttgcagGATGTCCATCATGGCAACGGAACCCAAGAGATATTCGAACAAAACAAATCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA