Sequence
atgc intronic sequence ATGC exonic sequencegtatgctgtttacgatataaattaagtttgacacgacagtgtgtgcaacttcttacatttttttcttcttatgtagCTTCTTGGCTGGTGTCTTGGCATGGAAAGACCCACAGGTCTTGGTTCCTGCTCTACAAGTTGCAGAGATTTTGATGGAAAAGCTTCCTGAAACATTCTCG
Basic information
species | Arabidopsis thaliana |
transcript | AT4G38600.1 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G38600.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA06G00600.2 (Glycine max), 3'ss of exon 7
gtatgctgtttacgatataaattaagtt----tgacacgacagtgtgtgca---acttcttacatt-tttttcttcttatgtagCTTCTTGGCTGGTGTCTTGGCATGGAAAGACCCACAGGTCTTGGTTCCTGCTCTACAAGTTGCAGAGATTTTGATGGAAAAGCTTCCTGAAACATTCTCG
| |||| | | |||| ||| | | | | | | || | | | | |||| | | | | || ||| ||||| |||||||| || ||||||||||| ||||| || ||||||||||| | ||| || |||| ||| | |||||||||||||||| || |||||
-----gtatttagaacttcaattgggttgctgttgctctatgttctctgtagaaaacttatgcattgtcactttgatgatatagTTTCTTAGCTGGTGTGTTAGCATGGAAAGATCCACATGTTTTGGTTCCTGCCTTGCAAATTTCAGAAATTCTTATGGAAAAGCTTCCTGGAATTTTCTCT
upper sequence: AT4G38600.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA04G00530.1 (Glycine max), 3'ss of exon 7
gtatgctgtttacgatataaattaagtt----tgacacgacagtgtgtgca-acttcttacatttttttcttcttatg---tagCTTCTTGGCTGGTGTCTTGGCATGGAAAGACCCACAGGTCTTGGTTCCTGCTCTACAAGTTGCAGAGATTTTGATGGAAAAGCTTCCTGAAACATTCTCG
| | || | | |||| ||| | | | | | | || | | | |||| || | | | ||| ||| ||||| |||||||| || ||||||||||| ||||| || ||||||||||| | ||| || | || ||| | |||||||||||||||| ||| |||||
-----gtatctagaacttcaattgggttgctgttgctctatgttctctgtagaatacttatgcattgtcactttgatgatatagTTTCTTAGCTGGTGTGTTAGCATGGAAAGATCCACATGTTTTGGTTCCTGCCTTGCAAATTTCGGAAATTCTTATGGAAAAGCTTCCTGGAACCTTCTCT
upper sequence: AT4G38600.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA12G03640.1 (Glycine max), 3'ss of exon 7
----------------gtatgctgtttacgatataaattaagtttgacacgacagtgtgtgcaacttcttacatttttttcttc-ttatgtagCTTCTTGGCTGGTGTCTTGGCATGGAAAGACCCACAGGTCTTGGTTCCTGCTCTACAAGTTGCAGAGATTTTGATGGAAAAGCTTCCTGAAACATTCTCG
| | || | | | | | ||| | | | | || || | |||| || || | || ||| ||||| ||||| ||||| ||||||||||| ||||| || ||| ||||||| | || |||| || ||| | |||||||||||||||| ||||||||
gtatgttgaaatttaattgagttgatattgcttgataccctcactgattttatgggtttagaaaatttatgcattgttgctttgatcatatagTTTCTTAGCTGGCGTCTTAGCATGGAAAGATCCACATGTTTTGCTTCCTGCCTTGAAAATTGCTGAAATTCTTATGGAAAAGCTTCCTGGGACATTCTCC
upper sequence: AT4G38600.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: Vv03s0038g02340.t01 (Vitis vinifera), 3'ss of exon 7
-----------------gtatgc-tgtttacgatataaatt---aagtttgacacgacagtgtgtgcaacttcttacatttttttctt-ctta--tgtagCTTCTTGGCTGGTGTCTTGGCATGGAAAGACCCACAGGTCTTGGTTCCTGCTCTACAAGTTGCAGAGATTTTGATGGAAAAGCTTCCTGAAACATTCTCG
||| | || | | ||| ||| | | || | | || || || | |||| || || || ||| | ||| ||||| |||||||| || ||||||||||| || || || ||||||||||| || ||| | || ||||| |||||||||| ||||||| || || ||
gtacttgcatttcaaatatatatatacatatattttttatttcaaaggtagttactagaatgc-tggaaatgcttatgcattgttattacttgattctagTTTCTTAGCTGGTGTTTTAGCATGGAAAGATCCTCAAGTGTTGGTTCCTGCCCTCCAAATAGCTGAGATCCTGATGGAAAAACTTCCTGGGACGTTTTCC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttaagtttgacacgacagtgtgtgcaacttcttacatttttttcttcttatgtagCTTCTTGGCTGGTGTCTTGGCATGGAAAGACCCACAGGTCTTGGTTCCTGCTCTACAAGTTGCAGAGATTTTGATGGAAAAGCTTCCTGAAACATTCTCG
ttcttac putative branch site (score: 2)
cttcttacattttttt CT-rich tract
atttttttcttcttat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgctgtttacgatataaattaagtttgacacgacagtgtgtgcaacttcttacatttttttcttcttatgtagCTTCTTGGCTGGTGTCTTGGCATGGAAAGACCCACAGGTCTTGGTTCCTGCTCTACAAGTTGCAGAGATTTTGATGGAAAAGCTTCCTGAAACATTCTCG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA