Sequence
atgc intronic sequence ATGC exonic sequence...ctcttgtttaattatatgtttactgttttgcttatgtttgactctgggattagaaaattattgtattggtagtgattcttaaaattggttcctaatttagTAGGTTGTAAATGGACTGCTTGAAAGAGAAGACTGGAAGACTGCCATAAAATTGCCGATCGGAATGGTCCCTGCAG
Basic information
species | Arabidopsis thaliana |
transcript | AT4G21540.2 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G21540.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA08G06300.1 (Glycine max), 3'ss of exon 3
-----------------------------------------------------ctcttgtttaattatatgtttactgtt--ttgcttatgtttgactctgggattagaaaattattgtattggtagtgattcttaaa---attggttcctaa----tttagTAGGTTGTAAATGGACTGCTTGAAAGAGAAGACTGGAAGACTGCCATAAAATTGCCGATCGGAATGGTCCCTGCAG
|||| | | ||| ||| | ||| || | | || | | | | | ||| | || || | | ||| ||| | | | || | |||||||||||||||||||||||||| | || | |||||| | ||||| || || |||| | ||| | || |||||||
gttagttcattgacattattgttgttggttgcagttcgtaccaagtaccattgtgattgtggtaatggctgtcaactaatgattgttttgatgtttcttttgtac-acatcattgtc-taatgtttctctttcataatcttactagcgccacacatttttagtagGTTGTAAATGGACTGCTTCAGAGGCAGGACTGGGACACTGCAATTAAGATGCCCCTTGGAGTAGTTCCTGCAG
upper sequence: AT4G21540.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA13G31980.1 (Glycine max), 3'ss of exon 3
----ctcttgtttaattatatgtttactgttttgcttatgtttgactctgggattagaaaattattgtattggtagtgattcttaaaattggttcctaatttagTAGGTTGTAAATGGACTGCTTGAAAGAGAAGACTGGAAGACTGCCATAAAATTGCCGATCGGAATGGTCCCTGCAG
| ||| | | || || | | | | ||||| | | ||| || | || | || | || | || | || |||||||||||||||||||||| ||| ||||||| || ||| | || || ||||| |||| | || | || |||||||
gtaacctgtgtattctagaatacttttgcactggttcacttttgatttcttgtttattaattgtttttcttaat-------ctgacaaacattgccctttttagtagGTTGTAAATGGACTTCTTCAAAGAGAGGATTGGGATACGGCAATAAAGATGCCCCTTGGGGTAGTTCCTGCAG
upper sequence: AT4G21540.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv00s0181g00250.t01 (Vitis vinifera), 3'ss of exon 3
--ctcttgtttaattatatgtttactgttttgcttatgtttgactctgggattagaaaattattgtattggtagtgattcttaaaattggttcctaatttagTAGGTTGTAAATGGACTGCTTGAAAGAGAAGACTGGAAGACTGCCATAAAATTGCCGATCGGAATGGTCCCTGCAG
||||| | | || || | | | || || | |||| | || | ||| || | | |||||| |||| ||| | |||||||||| ||||||||||||||||||||||| || ||| | |||| ||||| |||| || || | | |||||||
tcctcttatctgcctaaatctgtgtgttattactcaaccttgagttaggtgt-----gatttctgatccctttctctttcttataattttttcacattttagtagGTAGTAAATGGACTGCTTGAAAGAGATGATTGGGATTCTGCAATAAAGATGCCTATTGGGGTTATTCCTGCAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gggattagaaaattattgtattggtagtgattcttaaaattggttcctaatttagTAGGTTGTAAATGGACTGCTTGAAAGAGAAGACTGGAAGACTGCCATAAAATTGCCGATCGGAATGGTCCCTGCAG
tcctaat putative branch site (score: 2)
ttcct CT-rich tract
tagaaaattattgtat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ctcttgtttaattatatgtttactgttttgcttatgtttgactctgggattagaaaattattgtattggtagtgattcttaaaattggttcctaatttagTAGGTTGTAAATGGACTGCTTGAAAGAGAAGACTGGAAGACTGCCATAAAATTGCCGATCGGAATGGTCCCTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- - - - - - - - - - - -tgttttg
- - - - - - - - - - - - - - - - - tgtttga
- - - - - - - - - - - - - - - - - - - - - - - - - -agaaaat