Sequence
atgc intronic sequence ATGC exonic sequence...ttgtttaattatatgtttactgttttgcttatgtttgactctgggattagaaaattattgtattggtagtgattcttaaaattggttcctaatttagtagGTTGTAAATGGACTGCTTGAAAGAGAAGACTGGAAGACTGCCATAAAATTGCCGATCGGAATGGTCCCTGCAG
Basic information
species | Arabidopsis thaliana |
transcript | AT4G21540.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G21540.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA08G06300.1 (Glycine max), 3'ss of exon 3
--------------------------------------------------------ttgtttaattatatgtttactgtt--ttgcttatgtttgactctgggattagaaaattattgtattggtagtgattcttaaa---attggttcctaa----tttagtagGTTGTAAATGGACTGCTTGAAAGAGAAGACTGGAAGACTGCCATAAAATTGCCGATCGGAATGGTCCCTGCAG
|||| | | ||| ||| | ||| || | | || | | | | | ||| | || || | | ||| ||| | | | || | |||||||||||||||||||||||||| | || | |||||| | ||||| || || |||| | ||| | || |||||||
gttagttcattgacattattgttgttggttgcagttcgtaccaagtaccattgtgattgtggtaatggctgtcaactaatgattgttttgatgtttcttttgtac-acatcattgtc-taatgtttctctttcataatcttactagcgccacacatttttagtagGTTGTAAATGGACTGCTTCAGAGGCAGGACTGGGACACTGCAATTAAGATGCCCCTTGGAGTAGTTCCTGCAG
upper sequence: AT4G21540.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA13G31980.1 (Glycine max), 3'ss of exon 3
-ttgtttaattatatgtttactgttttgcttatgtttgactctgggattagaaaattattgtattggtagtgattcttaaaattggttcctaatttagtagGTTGTAAATGGACTGCTTGAAAGAGAAGACTGGAAGACTGCCATAAAATTGCCGATCGGAATGGTCCCTGCAG
| | ||| | |||||| || || ||| | | || | | | | | | | ||| | || | || |||||||||||||||||||||| ||| ||||||| || ||| | || || ||||| |||| | || | || |||||||
gtaacctgtgtattctagaatacttttgcac-tggttcacttttgatttcttgtttattaattgtttttcttaatctgacaaacattgccctttttagtagGTTGTAAATGGACTTCTTCAAAGAGAGGATTGGGATACGGCAATAAAGATGCCCCTTGGGGTAGTTCCTGCAG
upper sequence: AT4G21540.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv00s0181g00250.t01 (Vitis vinifera), 3'ss of exon 3
ttgtttaattatatgtttactgttttgc-ttatgtttgactctgggattagaaa--attattgtattggtagtgattcttaaaattggttcctaatttagtagGTTGTAAATGGACTGCTTGAAAGAGAAGACTGGAAGACTGCCATAAAATTGCCGATCGGAATGGTCCCTGCAG
| |||| || || | || |||| | | || | |||| ||| || | | |||||| |||| ||| | |||||||||| ||||||||||||||||||||||| || ||| | |||| ||||| |||| || || | | |||||||
---tcctcttatctgcctaaatctgtgtgttattactcaaccttgagttaggtgtgatttctgatccctttctctttcttataattttttcacattttagtagGTAGTAAATGGACTGCTTGAAAGAGATGATTGGGATTCTGCAATAAAGATGCCTATTGGGGTTATTCCTGCAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.attagaaaattattgtattggtagtgattcttaaaattggttcctaatttagtagGTTGTAAATGGACTGCTTGAAAGAGAAGACTGGAAGACTGCCATAAAATTGCCGATCGGAATGGTCCCTGCAG
tcctaat putative branch site (score: 2)
aaaattattgtatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttgtttaattatatgtttactgttttgcttatgtttgactctgggattagaaaattattgtattggtagtgattcttaaaattggttcctaatttagtagGTTGTAAATGGACTGCTTGAAAGAGAAGACTGGAAGACTGCCATAAAATTGCCGATCGGAATGGTCCCTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG