Sequence
atgc intronic sequence ATGC exonic sequencegtgagtgtttatcttttcttctatcccgataaccatggcaccatagaatgtttatcatctattttcatttatgtgatgaatctcagTTAAGAAAGGTGACAAAGGTGTAGACTTGGTTGCATCACTTTGCAAGATATATGACGCCTCAGAAGATGAGTTGAGGATAGTAATTGACAAGGCAAATAA
Basic information
species | Arabidopsis thaliana |
transcript | AT3G12280.1 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G12280.2 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA04G36700.1 (Glycine max), 3'ss of exon 8
--gtgagtgtttatcttttcttctatcccgataaccatggcaccatagaatgt------ttatcatctattttcatttatgtgatgaatct------cagTTAAGAAAGGTGACAAAGGTGTAGACTTGGTTGCATCACTTTGCAAGATATATGACGCCTCAGAAGATGAGTTGAGGATAGTAATTGACAAGGCAAATAA
|| || || | | | | | || | | | | | | |||| ||| | | ||| | || | || || | ||||||||||| || |||||||||| ||| | |||||||||||||||| ||||| || | || |||||||||||||||| | || || || || |||||
aaaagactgatttgcctctatacaattctaacgtctaaataaataataaatgcaacagcttaaaggacaatatcactaatatcatcaaattttcattcagTTAAGAAAAGTAACAAAGGTGTGGACCTCCTTGCATCACTTTGCAACATATACAACACTTCTGAAGATGAGTTGAGGAAAACCATGGAGAAAGCCAATAA
upper sequence: AT3G12280.2 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA13G26170.1 (Glycine max), 3'ss of exon 6
--gtgagtgtttatcttttcttctatcccgataaccatggcaccatagaatgt------ttatcatctattttcatttatgtgatgaatct------cagTTAAGAAAGGTGACAAAGGTGTAGACTTGGTTGCATCACTTTGCAAGATATATGACGCCTCAGAAGATGAGTTGAGGATAGTAATTGACAAGGCAAATAA
|| || || | | | | | || || | | | | | | || ||| | | || | || | || || | ||||||||||| || |||||||||| ||| | |||||||||||||||| ||||| || | || |||||||||||||||| | || || || || |||||
aaaagactgatttgcctgtatacaattccaacgtctaaataaataataattgcaacaacttaaaggacaatagcactaatatcatcaaattttcattcagTTAAGAAAAGTAACAAAGGTGTGGACCTCCTTGCATCACTTTGCAACATATACAACACTTCTGAAGATGAGTTGAGGAAAACCATGGAGAAAGCCAATAA
upper sequence: AT3G12280.2 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA15G36890.1 (Glycine max), 3'ss of exon 7
------gtgagt-gtttatcttttcttcta-tcccgataaccatggcaccatagaatgtttatcatctattttcatttatgtgatgaatct------cagTTAAGAAAGGTGACAAAGGTGTAGACTTGGTTGCATCACTTTGCAAGATATATGACGCCTCAGAAGATGAGTTGAGGATAGTAATTGACAAGGCAAATAA
||| | || | | | || || | || | | || | | || | || || || | || | || || | ||||||||||| || |||||||||| ||| | |||||||||||||||| ||||| || | || |||||||||||||||| | || || || || |||||
aaaagactgatttgtctgtatacaattgtaatgcctaaataaatagtaattgtgacagcctaaaggacgttagcactaatattatcaaattttcattcagTTAAGAAAAGTAACAAAGGTGTGGACCTCCTTGCATCACTTTGCAACATATACAACACTTCTGAAGATGAGTTGAGGAAAACCATGGAGAAAGCCAATAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.accatggcaccatagaatgtttatcatctattttcatttatgtgatgaatctcagTTAAGAAAGGTGACAAAGGTGTAGACTTGGTTGCATCACTTTGCAAGATATATGACGCCTCAGAAGATGAGTTGAGGATAGTAATTGACAAGGCAAATAA
cgataac putative branch site (score: 3)
tttatcatctattttc 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgagtgtttatcttttcttctatcccgataaccatggcaccatagaatgtttatcatctattttcatttatgtgatgaatctcagTTAAGAAAGGTGACAAAGGTGTAGACTTGGTTGCATCACTTTGCAAGATATATGACGCCTCAGAAGATGAGTTGAGGATAGTAATTGACAAGGCAAATAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT