Sequence
atgc intronic sequence ATGC exonic sequencegtaagtatatcgccgacaatgatcatcgaggaatgcatattcacctatccttaccgtgtttttgtttgtcgtcatgggctcactactgcagGTAATGAAGATAAACCCGGAGAAGAAACAAATCGATTCTTTTGTGGCTTCTGACTTTGACCTCACAGGCTATGATCCTCACAAGAAGATAGAAATGAAAA
Basic information
species | Arabidopsis thaliana |
transcript | AT2G16370.1 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT2G16370.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA11G12280.1 (Glycine max), 3'ss of exon 9
------gtaagtatatcgccgacaatgatcatcgaggaatgcatattcacctatccttaccgtgtttttgtttgtcgtcatgggctcactac---tgcagGTAATGAAGATAAACCCGGAGAAGAAACAAATCGATTCTTTTGTGGCTTCTGACTTTGACCTCACAGGCTATGATCCTCACAAGAAGATAGAAATGAAAA
|||| | | | || | | | || ||| || |||| | | | ||| || || | || | | | || | ||||||||||||| |||||||| | || |||||||||||||||||||| || | |||| ||| |||| ||||||| |||||||||||||||| |
gtatgtgtaaatgttttaaggattttatttgctttaacgtagatgcccacagatatataccat-tatgcgttcgtataaattgcctaaatttctatttagATTTTGAAGATAAACCCAAAGAAGAAAGATATAGATTCTTTTGTGGCTTCTGATTTCAAGCTCATAGGATATGTTCCTCACCAGAAGATAGAAATGAAGA
upper sequence: AT2G16370.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA12G04480.1 (Glycine max), 3'ss of exon 10
-----------------------------gtaagtatatcgccgacaatgatcatcgaggaatgcatattcacctatccttaccgtgtttttgtttgtcgtcatgggctcactactgcagGTAATGAAGATAAACCCGGAGAAGAAACAAATCGATTCTTTTGTGGCTTCTGACTTTGACCTCACAGGCTATGATCCTCACAAGAAGATAGAAATGAAAA
| || | | | | | || | | | |||| || || || | | ||||| | | | || ||| | ||| | ||||||||||||| |||||||| | || |||||||||||||| |||| || | |||| ||| |||||||||||| |||||||||||||||| |
gtatgtgtaaatgtttaaggatttcgtttgctttaatgtagatgctcacaaatatttaccattatgcattcgtataaa-ttgccttttccttgttgattacc-taaactt-ctatt-cagATTTTGAAGATAAACCCAAAGAAGAAAGATATAGATTCTTTTGTGGCAGCTGATTTCAAGCTCATAGGATATGATCCTCACCAGAAGATAGAAATGAAGA
upper sequence: AT2G16370.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA06G01280.3 (Glycine max), 3'ss of exon 10
gtaagtatatcgccgacaatgatcatcgaggaatgcatattcacctatccttaccgtgtttttgtttgtcgtcatgggctcactactgcagGTAATGAAGATAAACCCGGAGAAGAAACAAATCGATTCTTTTGTGGCTTCTGACTTTGACCTCACAGGCTATGATCCTCACAAGAAGATAGAAATGAAAA
||| || || | | | | | | | | || || | |||| |||||| | | | | | ||||| |||||||||| || |||||||| | || ||||||||||||||| |||| || | |||| |||||||||||||||| ||||||| || |||||
gtatgtgtaatgtt--tagcacttctttaagtttatcttttgactctt--ttac-------ttgtttaccccctaatgtacttcattgcagACTTTGAAGATAAATCCAAAGAAGAAAGATATAGATTCTTTTGTGGCTGCTGATTTCAAGCTCATAGGCTATGATCCTCACCAGAAGATTGATATGAAGC
upper sequence: AT2G16370.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA04G01240.1 (Glycine max), 3'ss of exon 10
gtaagtatatcgccgacaatgatcatcgaggaatgcatattc-acctatccttaccgtgtttttgtttgtcg---tcatgggctcactactgcagGTAATGAAGATAAACCCGGAGAAGAAACAAATCGATTCTTTTGTGGCTTCTGACTTTGACCTCACAGGCTATGATCCTCACAAGAAGATAGAAATGAAAA
||| | | || | | || || | ||| | |||| |||| | | | || | ||||| || ||||||| || | |||||| | || ||||||||||||||| |||| || | |||| |||||||||||||||| ||||||| || |||||
----------------gtatgtgtaatgtttaacacttcttttactttatcttttggctcttttacttgttgaccccctaatctacttcttgcagACTTTGGAGATAAATCCAAAAAAGAAAGATATAGATTCTTTTGTGGCTGCTGATTTCAAGCTCATAGGCTATGATCCTCACCAGAAGATTGATATGAAGC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atattcacctatccttaccgtgtttttgtttgtcgtcatgggctcactactgcagGTAATGAAGATAAACCCGGAGAAGAAACAAATCGATTCTTTTGTGGCTTCTGACTTTGACCTCACAGGCTATGATCCTCACAAGAAGATAGAAATGAAAA
tttttgttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagtatatcgccgacaatgatcatcgaggaatgcatattcacctatccttaccgtgtttttgtttgtcgtcatgggctcactactgcagGTAATGAAGATAAACCCGGAGAAGAAACAAATCGATTCTTTTGTGGCTTCTGACTTTGACCTCACAGGCTATGATCCTCACAAGAAGATAGAAATGAAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG