Sequence
atgc intronic sequence ATGC exonic sequencegtatgttatgtcccttgatgcttcgctgtttaaagtttaagtttcgttcaggtggaagttctttgcgtaatttatgtttcctctgtatgatcatgtttagGATGGTCAATGGTCTCCTTAAAACGGCTCAAGGGGTTCCTCCTGGTACAGCTACAACATTGATGCCACCACAGGAGGCAGCTATGAAACTTGAAGCCATG
Basic information
species | Arabidopsis thaliana |
transcript | AT3G60860.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G60860.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA03G02610.1 (Glycine max), 3'ss of exon 2
--gtatgttatgt-cccttgatgcttcgctgtttaaagtttaagtttcgttca--ggtggaagttctttgcgtaatttatgtttcctctgtatgatcatgtttagGATGGTCAATGGTCTCCTTAAAACGGCTCAAGGGGTTCCTCCTGGTACAGCTACAACATTGATGCCACCACAGGAGGCAGCTATGAAACTTGAAGCCATG
|| | | || || || ||||| || | | ||| | | | || | | | || | || || || | | | ||| || | ||||||||||||||| || |||||||| |||||||| || ||||||||| | | || ||| | ||||||| || || ||| | | |||||||| ||||||
gtgtttttcatacaccattcatgctagtgtggctgaggtt---atcttgatcgtcacttaatatactctttatagtt-atttctaattgttatattcct-cctagGATGGTCAATGGACTTCTTAAAACTGCTCAAGGTGTCCCTCCTGGTGTAACGACCACACTTTTGCCACCTCAAGAAGCAACACTAAAACTTGAGGCCATG
upper sequence: AT3G60860.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA18G45340.1 (Glycine max), 3'ss of exon 2
-gtatgttatgtccc-ttgatgcttcgctgtttaaagtttaagtttcgttca--ggtggaagttctttgcgtaatttatgtttcctctgtatgatcatgtttagGATGGTCAATGGTCTCCTTAAAACGGCTCAAGGGGTTCCTCCTGGTACAGCTACAACATTGATGCCACCACAGGAGGCAGCTATGAAACTTGAAGCCATG
|| | | || | || || || || | | | | || | | | | | | || | || ||||| | | | ||| || | ||||||||||||||| || |||||||| |||||||| || ||||||||| | || ||| | ||||||| || || ||| | | |||||||| ||||||
tgtttttcatacagcattcatagttgtgtggctgaggct---gtcttgattgtcacttaatatactctttatattttatatctaattgctatattcct-catagGATGGTCAATGGACTTCTTAAAACTGCTCAAGGTGTCCCTCCTGGTGTAATGACCACACTTTTGCCACCTCAAGAAGCAACATTAAAACTTGAGGCCATG
upper sequence: AT3G60860.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA01G34560.1 (Glycine max), 3'ss of exon 3
gtatgttatgtcccttgatgcttcgctgtttaaagtttaagtttcgttcaggtggaagttctttgcgtaatttatgtttcctctgtatgatcatgtttagGATGGTCAATGGTCTCCTTAAAACGGCTCAAGGGGTTCCTCCTGGTACAGCTACAACATTGATGCCACCACAGGAGGCAGCTATGAAACTTGAAGCCATG-
| | |||| || | | || | | | | || | || ||||| | | | ||| || | || |||||||||||| || |||||||| |||||||| || ||||||||| | || ||| | ||||||| || || ||| | | |||||||| ||||||
-------------------gtgtggctgaggctgtcttgattgtcactta-----atatactctttatattttatatctaattgttatattcct-cataagATGGTCAATGGACTTCTTAAAACTGCTCAAGGTGTCCCTCCTGGTGTAATGACCACACTTTTGCCACCTCAAGAAGCAACATTAAAACTTGAGGCCATGA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gttcaggtggaagttctttgcgtaatttatgtttcctctgtatgatcatgtttagGATGGTCAATGGTCTCCTTAAAACGGCTCAAGGGGTTCCTCCTGGTACAGCTACAACATTGATGCCACCACAGGAGGCAGCTATGAAACTTGAAGCCATG
taatttatgttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgttatgtcccttgatgcttcgctgtttaaagtttaagtttcgttcaggtggaagttctttgcgtaatttatgtttcctctgtatgatcatgtttagGATGGTCAATGGTCTCCTTAAAACGGCTCAAGGGGTTCCTCCTGGTACAGCTACAACATTGATGCCACCACAGGAGGCAGCTATGAAACTTGAAGCCATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC