Sequence
atgc intronic sequence ATGC exonic sequencegtaagtgctttacttattatatgtaaatatttttagattcccaagcttttgtcgaatctaaccatggatgtctttctccagATACCCAAATCCGTCATCTTTTACATATGAAAAACGTCTCTTTTGTCCTTTTGAGTATGCGCTGCAGCCTCCCCGTTGGTATAAAAATGACTCTATTGCT
Basic information
species | Arabidopsis thaliana |
transcript | AT4G11800.1 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G11800.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: LOC_Os07g01540.1 (Oryza sativa), 3'ss of exon 8
------------gtaagtg---ctttacttattatatgtaaatatttttagattcccaagcttttgtcgaatctaaccatggatgtctt-----tctccagATACCCAAATCCGTCATCTTTTACATATGAAAAACGTCTCTTTTGTCCTTTTGAGTATGCGCTGCAGCCTCCCCGTTGGTATAAAAATGACTCTATTGCT
||| ||| ||| ||| ||| | | | | ||| || || ||| | |||| | | || | | |||||||||||| || || || ||||||||||| | || ||||| |||||| ||||||||| ||||| ||||| | |||||||| | ||| ||| |||
gttctccgtgaagtatgtggaacttagtccattttatttgtgcaatat-ggatattgtagtttctgtttcctttaactttctgtaattttggaatatacagATACCCAAACCCATCGTCATTTACATATGAGATGCGCTTCTTTAGTCCTTATGAGTATGCCCTGCAACCTCCACCTTGGTATAGAGCTGAACATATAGCT
upper sequence: AT4G11800.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA14G08860.1 (Glycine max), 3'ss of exon 7
--------------gtaagtgctttacttatta-----tatgtaaatatttttagattcccaagcttttgtcgaatctaaccatggatgtctttctccagATACCCAAATCCGTCATCTTTTACATATGAAAAACGTCTCTTTTGTCCTTTTGAGTATGCGCTGCAGCCTCCCCGTTGGTATAAAAATGACTCTATTGCT
| | || || | | | | || || | | ||||| |||| | | || | ||| | | ||| || |||||||| ||| | || |||||||||| ||||| ||| ||||||||||||||| || || ||||| | |||||||||| || || |||
cctttgcagtgccatttaatgtttcaagtttcaactctcttgcaatgttctgtagatgtatttttttttccttcaatgacttattgttgttctgttgcagGTATCCAAATCCATCAGCATTCACATATGAAAGGCGTCTTTTTGTTCCTTTTGAGTATGCTCTTCAACCTCCTCCTTGGTATAAAGCAGAGCAGATAGCT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atatttttagattcccaagcttttgtcgaatctaaccatggatgtctttctccagATACCCAAATCCGTCATCTTTTACATATGAAAAACGTCTCTTTTGTCCTTTTGAGTATGCGCTGCAGCCTCCCCGTTGGTATAAAAATGACTCTATTGCT
atctaac putative branch site (score: 2)
tgtctttctcc putative PPT
tttagatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagtgctttacttattatatgtaaatatttttagattcccaagcttttgtcgaatctaaccatggatgtctttctccagATACCCAAATCCGTCATCTTTTACATATGAAAAACGTCTCTTTTGTCCTTTTGAGTATGCGCTGCAGCCTCCCCGTTGGTATAAAAATGACTCTATTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG