Sequence
atgc intronic sequence ATGC exonic sequencegtttttattcttaaacccgtcttatagaattctgaaaccgaacaaatttctagtccttttgactttgttatcttggttttcaccttctttatctagTCTATAAGAAACGATGATTTGGAGGAAATCCGAGAGTTAGGCCATGGAACATATGGATCTGTTTACCATGGAAAATGGAAAGGCTCAGATGTTGCAATAA
Basic information
species | Arabidopsis thaliana |
transcript | AT5G57610.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G57610.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA13G01190.2 (Glycine max), 3'ss of exon 5
-----------gtttttattcttaaacccgtcttatagaattctgaaaccgaacaaatttctag---tccttttgactttgttatcttggttttcac------ct--tctttatctagTCTATAAGAAACGATGATTTGGAGGAAATCCGAGAGTTAGGCCATGGAACATATGGATCTGTTTACCATGGAAAATGGAAAGGCTCAGATGTTGCAATAA
| || | | | || | | ||| | ||||| | ||||||| | ||| || ||| | || || || | || |||| | || |||||||||||||| ||||| ||| | || |||||| |||||| ||||||| ||||| ||||||||||| || || ||||| || |
gttttctttccatcttactcatccattatgttctcatcatttcatgttttaaggtcttttctggctttccttttcccacatgcgtctaggatttgatggtaggctgatcatttttcagACTATTAACAATGATGATTTGGAGGAGATCCGTGAGCTTGGTTCTGGAACCTATGGAGCTGTTTATCATGGGAAATGGAAAGGTTCTGACGTTGCCATTA
upper sequence: AT5G57610.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv11s0052g01480.t01 (Vitis vinifera), 3'ss of exon 2
-----------------------------------------------------gtttttattcttaaacccgtcttatagaattctgaaaccgaacaaatttctagtccttttgactttgttatcttggtt----ttcaccttctttatctagTCTATAAGAAACGATGATTTGGAGGAAATCCGAGAGTTAGGCCATGGAACATATGGATCTGTTTACCATGGAAAATGGAAAGGCTCAGATGTTGCAATAA
||||| | | | || | | | | | | | | ||| | || | | | | || |||||| | ||| | |||| ||| |||||| ||||||| || || || ||||| ||| || |||||| |||||||||||||||||||||| || || ||||| |||||||
gttctcgaccaatatacaccattatttttgtaaaacatctctttggaaatcacacctttatctcttcattatctcttctccatcttagtgtctttttactatttcatgcattttatttcctctgcctaactcgaatttgtgttctttctttagACAATAAAAAATGATGATCTGGAGGAGATTCGGGAATTAGGTTCTGGTACGTATGGAGCTGTTTACCATGGAAAATGGAAGGGGTCTGATGTAGCAATAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.acaaatttctagtccttttgactttgttatcttggttttcaccttctttatctagTCTATAAGAAACGATGATTTGGAGGAAATCCGAGAGTTAGGCCATGGAACATATGGATCTGTTTACCATGGAAAATGGAAAGGCTCAGATGTTGCAATAA
ttttgac putative branch site (score: 3)
ttttcaccttctttat putative PPT
tttgttat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtttttattcttaaacccgtcttatagaattctgaaaccgaacaaatttctagtccttttgactttgttatcttggttttcaccttctttatctagTCTATAAGAAACGATGATTTGGAGGAAATCCGAGAGTTAGGCCATGGAACATATGGATCTGTTTACCATGGAAAATGGAAAGGCTCAGATGTTGCAATAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG