Sequence
atgc intronic sequence ATGC exonic sequence...tcattttatgttatattgattaagcaataacatctagattcgaaattttgatttctgcttacctgatatatcattatttgctcaacaatatgtatcgtagGTCCTAATGGAAGTGGCAAGAGTTCCCTTTTCCGAGTATTAGGAGGTCTATGGCCCCTGGTGTCTGGACATATTGTGAAGCCAGGAGTTGGTTCTGATCT
Basic information
species | Arabidopsis thaliana |
transcript | AT4G39850.3 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G39850.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA05G31270.1 (Glycine max), 3'ss of exon 6
tcattttatgttatattgattaagcaataacatctagattcgaaattttgatttctgcttacctgatatatcattatttgctcaacaata--tgtatcgtagGTCCTAATGGAAGTGGCAAGAGTTCCCTTTTCCGAGTATTAGGAGGTCTATGGCCCCTGGTGTCTGGACATATTGTGAAGCCAGGAGTTGGTTCTGATCT
|| | | | || || | || || || ||| | ||||||| | | | | || | | ||||| | | | |||||| ||||| ||||| ||||| || | ||||| || ||||||||||| |||||| |||| ||||||||||||||||| || |||||||| ||||||||
--atctgaaaggactatgtttcacttgtataattggatttttaaaataagatttctaatggttaattgttttgacatgtaattcacaattattttgctgaagGTCCAAATGGCAGTGGAAAGAGCTCGTTATTCCGGGTTTTAGGAGGTCTTTGGCCCTTGGTATCTGGACATATTGTGAAACCTGGAGTTGGATCTGATCT
upper sequence: AT4G39850.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA08G14480.1 (Glycine max), 3'ss of exon 5
tcattttatgttatattgattaagcaataacatctagattcgaaattttgatttctgcttacctgatatatcattatttgctcaacaata--tgtatcgtagGTCCTAATGGAAGTGGCAAGAGTTCCCTTTTCCGAGTATTAGGAGGTCTATGGCCCCTGGTGTCTGGACATATTGTGAAGCCAGGAGTTGGTTCTGATCT
|| | | || || || | || || | ||| ||| | ||||||| | | | | | | | ||||| | | | |||||| ||||| ||||| ||||| || | ||||| || ||||||||||| |||||| |||| ||||||||||||||||| || |||||||| ||||||||
-aatctgaaagtactatgtttcacttgtataat-tgaattttaaaataagatttctaatggttaattgttttgacacgtaattcacaattattttgctgaagGTCCAAATGGCAGTGGAAAGAGCTCGTTATTCCGGGTTTTAGGAGGTCTTTGGCCCTTGGTATCTGGACATATTGTGAAACCTGGAGTTGGATCTGATCT
upper sequence: AT4G39850.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA11G38160.1 (Glycine max), 3'ss of exon 8
------------------------------------------------------------------------------------------------tcattttatgttatattgattaagcaataacatctagattcgaaattttgatttctgcttacctgatatatcattatttgctcaacaatatgtatcgtagGTCCTAATGGAAGTGGCAAGAGTTCCCTTTTCCGAGTATTAGGAGGTCTATGGCCCCTGGTGTCTGGACATATTGTGAAGCCAGGAGTTGGTTCTGATCT
| ||| | | || ||| | | | | | || | | | || |||| | || ||| || | ||| | || | | | |||||| ||||| ||||| || || ||||||||||| || |||| ||||| ||||| || | ||||||||||||||||| || ||| |||| ||||||||
gtagctatctgagctcttttcagaattcagtggcctttctttctatttttatttattattcattgggcttgagtcagcattgaaagttgatgttatttattatctatttctttgttgtaagagtcattcttaaact--gatttgtgatggtttattgtttgacatgttattgatgcttct------tttgctgaagGTCCAAATGGCAGTGGAAAAAGCTCCCTTTTCCGGGTTCTAGGTGGTCTTTGGCCATTGATATCTGGACATATTGTGAAACCTGGAATTGGCTCTGATCT
upper sequence: AT4G39850.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA18G02110.1 (Glycine max), 3'ss of exon 9
-----------------------------------------------------------------------------------tcattttatgttatattgattaagcaataacatctagattcgaaattttgatttctgcttacctgatatatcattatttgctcaacaatatgtatcgtagGTCCTAATGGAAGTGGCAAGAGTTCCCTTTTCCGAGTATTAGGAGGTCTATGGCCCCTGGTGTCTGGACATATTGTGAAGCCAGGAGTTGGTTCTGATCT
| | ||| | || ||| | | | | | || | | | ||||| | || || ||| || | ||| || | || | |||||| ||||| ||||| || || ||||||||||| || |||| ||||| ||||| || | ||||||||||| ||||| || ||| |||| ||||||||
gtagctatctgaactctctttttagtggccgatttttatttatttttcagggggcttgagtcagcattgaaagttgatgttatttactttctatttctttgttgtaagagtcattgttaaact--gatttttgttggttgattgtttgacatgttattggcgcttc-----tttg-gctgaagGTCCAAATGGCAGTGGAAAAAGCTCCCTTTTCCGGGTTCTAGGTGGTCTTTGGCCATTGATATCTGGACATATAGTGAAACCTGGAATTGGCTCTGATCT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttttgatttctgcttacctgatatatcattatttgctcaacaatatgtatcgtagGTCCTAATGGAAGTGGCAAGAGTTCCCTTTTCCGAGTATTAGGAGGTCTATGGCCCCTGGTGTCTGGACATATTGTGAAGCCAGGAGTTGGTTCTGATCT
tgatatatcattattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tcattttatgttatattgattaagcaataacatctagattcgaaattttgatttctgcttacctgatatatcattatttgctcaacaatatgtatcgtagGTCCTAATGGAAGTGGCAAGAGTTCCCTTTTCCGAGTATTAGGAGGTCTATGGCCCCTGGTGTCTGGACATATTGTGAAGCCAGGAGTTGGTTCTGATCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC