Sequence
atgc intronic sequence ATGC exonic sequence...attgaaactttcatttgttatacatccgcagctaatattttcactttctgttgggtatgtggaagtaattgattttttttatttttgttgctctgtgaagTGTGGCCAAGGAAGTACAGATGATGAACTAAGTCCTACATGTGTGTCGTCTTTGTTGGGAATCCGAATAGAAGAAGTGGCTGCAGGTCTATGGCACACGA
Basic information
species | Arabidopsis thaliana |
transcript | AT3G55580.1 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G55580.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA18G03870.1 (Glycine max), 3'ss of exon 7
attgaaactttcatttgttatacatccgcagctaatattttcactttctgttgg-gtatgtggaag-taattgatt-ttttttatttttgttgctctgtg------aagTGTGGCCAAGGAAGTACAGATGATGAACTAAGTCCTACATGTGTGTCGTCTTTGTTGGGAATCCGAATAGAAGAAGTGGCTGCAGGTCTATGGCACACGA
|| | | || | | || | | |||| | || | ||||| | ||| | | | || ||| || | ||| ||| |||| |||||||| ||||||||||||||||||||||| || || | || || || || || ||||| || | |||||| | ||| |||||||| || ||||| ||
-------ctgttactttaca-atatttatatttc-tattcgctctctttgttgttgcatgctaatgcttgttaattattctaaattaatgtcatcttgtgttggaaaagTGTGGGCAAGGAAGTACAGATGATGAACTGAGCCCGAGTTGCGTATCTTCCTTATTGGGTATTCAAATAGAGGGAGTTGCTGCAGGACTGTGGCATACTG
upper sequence: AT3G55580.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA11G34470.1 (Glycine max), 3'ss of exon 7
attgaaactttcatttgttatacatccgcagctaatattttcactttctgttgggtatgtggaagtaattgattttttt----tatttttgttgctctgt------gaagTGTGGCCAAGGAAGTACAGATGATGAACTAAGTCCTACATGTGTGTCGTCTTTGTTGGGAATCCGAATAGAAGAAGTGGCTGCAGGTCTATGGCACACGA
|| ||| ||| | ||| | | || || || | | | || |||||| | |||| ||| ||| |||||||| ||||||||||||||||||||| |||| || | || || || || || ||||| || |||||||| | ||| |||||||| || ||||| ||
---------ttactttacaatatttatctttctattcactctctttgttgctgcatgc-taatgcttgttaatttttatactatattaatgtcatcttgttttggaaaagTGTGGGCAAGGAAGTACAGATGATGAATTAAGCCCGAATTGCGTATCTTCCTTATTGGGTATTCGAATAGAGGGAGTTGCTGCAGGACTGTGGCATACTG
upper sequence: AT3G55580.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: Vv13s0019g02280.t01 (Vitis vinifera), 3'ss of exon 7
attgaaactttcatttgttatac-atccgcagctaatattttcactt-tctgttgggtatgtggaagtaattgattttttttatttt--tgttgctctgtgaagTGTGGCCAAGGAAGTACAGATGATGAACTAAGTCCTACATGTGTGTCGTCTTTGTTGGGAATCCGAATAGAAGAAGTGGCTGCAGGTCTATGGCACACGA
|| | | |||| || || | || | | |||| | | | | ||| | || ||| | ||||| | | ||| | || ||||||| ||||||||||| |||||||| |||||||| || ||||| || || || ||||||| | ||||| ||| |||||||| || ||||||||
----tcctttccttctgttttattattcttagtttggttgttcatgtgtaaggttatcatgataaggtttaaagtttgtcttattgtgatattgttttggttagTGTGGGCAAGGAAGTACTGATGATGAGCTAAGTCCAACTTGTGTATCTTCCTTACTGGGAATTCAGATAGAGAGAGTTGCTGCAGGCCTGTGGCACACTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttctgttgggtatgtggaagtaattgattttttttatttttgttgctctgtgaagTGTGGCCAAGGAAGTACAGATGATGAACTAAGTCCTACATGTGTGTCGTCTTTGTTGGGAATCCGAATAGAAGAAGTGGCTGCAGGTCTATGGCACACGA
aattgat putative branch site (score: 4)
ttttttttatttttgt CT-rich tract
aagtaattgatttttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
attgaaactttcatttgttatacatccgcagctaatattttcactttctgttgggtatgtggaagtaattgattttttttatttttgttgctctgtgaagTGTGGCCAAGGAAGTACAGATGATGAACTAAGTCCTACATGTGTGTCGTCTTTGTTGGGAATCCGAATAGAAGAAGTGGCTGCAGGTCTATGGCACACGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
-ttgaaac
- - - - - - - - - - tacatcc
- - - - - - - - - - - - - - - - - - - - - -ctttctg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gaagtaa