Sequence
atgc intronic sequence ATGC exonic sequencegtatgtataatttgccactacacaacaagttcgaatccatttttactttgcttgatcaattctcatgattagctacttttactctgtttccagCTTGTGTTTTCATCATCAGCAACTGTGTATGGCTCTCCAAAAGAAGTTCCTTGTACAGAGGAGTTTCCAATTTCTGCTTTGAACCCATATGGACGAACAA
Basic information
species | Arabidopsis thaliana |
transcript | AT4G10960.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G10960.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA01G43540.2 (Glycine max), 3'ss of exon 3
-------gtatgtataatttgccactacacaacaagttcgaatccatttttactttgcttgatcaattctcatgattagctacttt-tactctgtttccagCTTGTGTTTTCATCATCAGCAACTGTGTATGGCTCTCCAAAAGAAGTTCCTTGTACAGAGGAGTTTCCAATTTCTGCTTTGAACCCATATGGACGAACAA
| || | | || | | | | ||| | | || || | | ||||| || || | || || ||||| ||||||||||| ||||||||||| ||||| | ||||| || ||||| || ||||| ||||| || | || || ||||||||||||||||||| |
aacaccttgaagtgtcttgtgaggttg-attataccttctacagctttgacgctccattcagctcacctcactgattttgtatttaattgaatgatttcagCTCGTGTTTTCATCTTCAGCAACTGTATATGGTTGGCCAAAGGAGGTTCCATGCACAGAAGAGTTCCCTCTGTCAGCAATGAACCCATATGGACGAACTA
upper sequence: AT4G10960.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA11G01940.3 (Glycine max), 3'ss of exon 3
-------gtatgtataatttgccactacacaacaagttcgaatccatttttactttgcttgatcaattctcatgattagctactt-ttactctgtttccagCTTGTGTTTTCATCATCAGCAACTGTGTATGGCTCTCCAAAAGAAGTTCCTTGTACAGAGGAGTTTCCAATTTCTGCTTTGAACCCATATGGACGAACAA
| || | | | | | | | ||| | | || | || | | ||||| || || || || || ||||| ||||| || || ||||||||||| ||||| | ||||| |||||||| || ||||| ||||| || | || || ||||||||||||||||||| |
aacaccttgaagtgtcttgcggggttg-attataccttctagcgctttgctgctccattctgctcgtctcactgattttgtatttatttgaatgatttcagCTCGTGTTCTCTTCTTCAGCAACTGTATATGGTTGGCCAAAGGAAGTTCCATGCACAGAAGAGTTCCCTCTGTCAGCAATGAACCCATATGGACGAACTA
upper sequence: AT4G10960.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA05G36850.1 (Glycine max), 3'ss of exon 3
----------gtatgtataatttgccactacacaacaagttcgaatccatttttactttgcttgatcaattctcatgattagctactt-ttactctgtttccagCTTGTGTTTTCATCATCAGCAACTGTGTATGGCTCTCCAAAAGAAGTTCCTTGTACAGAGGAGTTTCCAATTTCTGCTTTGAACCCATATGGACGAACAA
||| |||| | ||| || || | | | | | |||| | || | ||||| || || || || || ||||||||||| ||||| ||||||||||| ||||||| ||||| || || || ||||| || ||||| || | || || ||||||||||||||||| |
ttttgaagtgtcttgtggaattggt---tacgcattaattatattttcttgatgctgcaatctgattatttaac-tgattttatatttctttgaatgatttcagCTTGTGTTCTCATCTTCAGCAACTGTATATGGCTGGCCAAAGGAGGTCCCATGTACCGAAGAGTTCCCTTTGTCAGCAACAAACCCATATGGACGAACCA
upper sequence: AT4G10960.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv02s0025g01560.t01 (Vitis vinifera), 3'ss of exon 3
gtatgtataatttgccactac-acaacaagttcgaatccatttttactttgc----ttgatcaattctcatgattagctacttt-tactctgt-ttccagCTTGTGTTTTCATCATCAGCAACTGTGTATGGCTCTCCAAAAGAAGTTCCTTGTACAGAGGAGTTTCCAATTTCTGCTTTGAACCCATATGGACGAACAA
| ||| |||| ||| || | || | | || | ||| || || | | || | | || || | ||| || |||||||| |||||||||||||| ||||| ||||| | ||||| || ||||| |||||||| ||||| ||| | | ||| || |||||||||||||| |
tcctttattttttgtttttaccacgtttcttgtgatattactgtttatgtgcaactctgttctaatgtctccactgacttctaaattctcaacatttcagCTTGTTTTTTCATCATCAGCTACTGTTTATGGTTGGCCAAAGGAGGTTCCATGTACAGAAGAGTTCCCACTATGTGCAACAAATCCATATGGACGAACTA
upper sequence: AT4G10960.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv02s0025g01580.t01 (Vitis vinifera), 3'ss of exon 3
gtatgtataatttgccacta-cacaacaagttcgaatccatttttactttgc----ttgatcaattctcatgattagctactt-ttactctgt-ttccagCTTGTGTTTTCATCATCAGCAACTGTGTATGGCTCTCCAAAAGAAGTTCCTTGTACAGAGGAGTTTCCAATTTCTGCTTTGAACCCATATGGACGAACAA
||| || || || || | || | | || | ||| || |||| | || | | | | || || ||| | || |||||||| |||||||||||||| ||||| ||||| | ||||| || ||||| |||||||| ||||| || | | |||| || |||||||||||||| |
agatgcatgccttttttttagcatgtttcttgtgatgttactgtttatatgcaactctgttcaaatgtcttcactgatttctaatttctcaatatttcagCTTGTTTTTTCATCATCAGCTACTGTTTATGGTTGGCCAAAGGAGGTTCCATGTACAGAAGAGTTCCCGCTATGTGCTGCAAATCCATATGGACGAACCA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atttttactttgcttgatcaattctcatgattagctacttttactctgtttccagCTTGTGTTTTCATCATCAGCAACTGTGTATGGCTCTCCAAAAGAAGTTCCTTGTACAGAGGAGTTTCCAATTTCTGCTTTGAACCCATATGGACGAACAA
gcttgat putative branch site (score: 5)
cttttactctgtttcc putative PPT
tactttta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgtataatttgccactacacaacaagttcgaatccatttttactttgcttgatcaattctcatgattagctacttttactctgtttccagCTTGTGTTTTCATCATCAGCAACTGTGTATGGCTCTCCAAAAGAAGTTCCTTGTACAGAGGAGTTTCCAATTTCTGCTTTGAACCCATATGGACGAACAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG