Sequence
atgc intronic sequence ATGC exonic sequencegtgcgtttatagaatcattctcatcgctgatttatacaatcttatactactctacatgtgtctacatatgtaacaacattcatctgttttcactattttacagGTTGCAGAGATTGTCAAGGATCGTCCTTCGTGGTTCCGCGAATGTCGAGCTGTTGAAGTTATGAACGTGTTGCCAACTGCCAATGGTGGAACCGTTGAGC
Basic information
species | Arabidopsis thaliana |
transcript | AT1G52150.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G52150.3 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA08G21620.2 (Glycine max), 3'ss of exon 5
gtgcgtttatagaatcattctcatcgctgatttatacaatcttatactactctacatgtgtctacatatgtaacaacattcatctgttttcac---tattttacagGTTGCAGAGATTGTCAAGGATCGTCCTTCGTGGTTCCGCGAATGTCGAGCTGTTGAAGTTATGAACGTGTTGCCAACTGCCAATGGTGGAACCGTTGAGC
| |||| | || || | || | ||| | | | || || |||||| || | || ||| ||||||||||| || |||| ||||| |||| |||||| ||||| || ||||||||||| ||| | || ||| |||| || || |||||||||||| ||||||
----------------------gtaagtgatcga-actattatttatatttactgatggtttggcttgagtt-catcattcacatgatcaaacatactctttccagGTTGCAGAAATCCTCAAAGATCGGCCTTTGTGGTTTCGCGATTGCCGAGCTGTTGATGTTCTCAATGTGCTGCCCACAGCAAATGGTGGAACCATTGAGC
upper sequence: AT1G52150.3 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA07G01940.1 (Glycine max), 3'ss of exon 5
gtgcgtttatagaatcattctcatcgctgatttatacaatcttatactactctacatgtgtctacatatgtaacaacattcatctgttttcactattttacagGTTGCAGAGATTGTCAAGGATCGTCCTTCGTGGTTCCGCGAATGTCGAGCTGTTGAAGTTATGAACGTGTTGCCAACTGCCAATGGTGGAACCGTTGAGC
|| |||| || ||| | || | | | | || || || | ||| ||| | ||| | || ||| ||||||||||| || |||| |||| |||| |||||| ||||| || ||||||||||| ||| | || ||| |||| || || |||||||||||| ||||||
----------gtaagcattgagatttacaattatttatattactgattgttgggcttgagttta--tctgtcaca-cggtcaaacatactc-----tttccagGTTGCAGAAATCCTCAAAGATCAGCCTTTGTGGTTTCGCGATTGCCGAGCTGTTGATGTTCTCAATGTGCTGCCCACAGCAAATGGTGGAACCATTGAGC
upper sequence: AT1G52150.3 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv09s0002g03740.t01 (Vitis vinifera), 3'ss of exon 5
gtgcgtttatagaatcattctcatcgctgatttatacaatcttatactactctacatgtgtctacatatgtaacaacattcatctgttttcactattttacagGTTGCAGAGATTGTCAAGGATCGTCCTTCGTGGTTCCGCGAATGTCGAGCTGTTGAAGTTATGAACGTGTTGCCAACTGCCAATGGTGGAACCGTTGAGC
| || || || | || | || || || ||| || || | | || |||| | || |||||||||||||| |||||||||| || || ||||| ||||| || |||||||| || || |||| |||||||| ||||| ||||||||||| ||||||
---------------------gtaagttgggttttatctttttgtttcttcctttctgcagct---tattaaataa---ttaattggcttcattccatt-cagGTTGCAGAGATCCTCAAGGATCGGCCATCCTGGTTTCGCGATTGCCGAGCTGTGGATGTGCTGAATGTGTTGCCCACTGCAAATGGTGGAACTATTGAGC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.actctacatgtgtctacatatgtaacaacattcatctgttttcactattttacagGTTGCAGAGATTGTCAAGGATCGTCCTTCGTGGTTCCGCGAATGTCGAGCTGTTGAAGTTATGAACGTGTTGCCAACTGCCAATGGTGGAACCGTTGAGC
atgtaac putative branch site (score: 3)
ttttcact putative PPT
ttttcactatttta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgcgtttatagaatcattctcatcgctgatttatacaatcttatactactctacatgtgtctacatatgtaacaacattcatctgttttcactattttacagGTTGCAGAGATTGTCAAGGATCGTCCTTCGTGGTTCCGCGAATGTCGAGCTGTTGAAGTTATGAACGTGTTGCCAACTGCCAATGGTGGAACCGTTGAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA