Sequence
atgc intronic sequence ATGC exonic sequencegtaaattttctgtatgtattttcctactaaaattcttttgtgatccctttgtatgtgttctaatgggtgtctcacacttagGTTGCTACCATTCTTCTCTGTTGTGCATTTTTCTATGACATCTTTTGGGTATTCATATCACCACTAATCTTCAAGCAAAGTGTAATGATTGCG
Basic information
species | Arabidopsis thaliana |
transcript | AT1G05820.1 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G05820.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA08G47600.2 (Glycine max), 3'ss of exon 8
--------gtaaattttctgtatgtattttcctactaaaattcttttgtgatcc-ctttgt-atgtgt-------------tctaatgg--------gtgtctcacact-tagGTTGCTACCATTCTTCTCTGTTGTGCATTTTTCTATGACATCTTTTGGGTATTCATATCACCACTAATCTTCAAGCAAAGTGTAATGATTGCG
| ||| | | | | || || | | ||| || | | | | |||||| |||| | |||||| | ||| | | |||||||| || | || || |||||||| ||| |||||||||| ||||||||||||||||| ||| | || ||| | | ||||| ||||||||
gtacccaaatggattctttatgtctacaatcaaataatcatttttctcttactcactttgttatgtatctattaaaacagctctaataatttctcatgcatctgatataatagGTTGCAACTGTACTCCTTTGTTGTGCCTTTGTCTATGACATTTTTTGGGTATTCATATCTCCAGTGATTTTCCACGAGAGTGTTATGATTGCC
upper sequence: AT1G05820.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA18G53880.1 (Glycine max), 3'ss of exon 8
-----------------------------------------gtaaattttctgtatgtatt-ttcctactaaaattcttttgtgatccctttgtatgtgttctaatgggtgtctcacacttagGTTGCTACCATTCTTCTCTGTTGTGCATTTTTCTATGACATCTTTTGGGTATTCATATCACCACTAATCTTCAAGCAAAGTGTAATGATTGCG
||| |||| || || | || ||| || | || | | |||| ||| | | | | | ||||||| || | || || |||||||| ||| |||||||||| ||||||||||||||||| ||| | || ||| | | ||||| ||||||||
gtacccaaatggattctttatttctacaatcaaataatcaattaatcattcttctcttaccctttttgttatgtatctattaaaacagctctactaat-ttctcatgcatctgatataat-agGTTGCAACTGTACTCCTTTGTTGTGCTTTTGTCTATGACATTTTTTGGGTATTCATATCTCCAGTGATTTTCCATGAGAGTGTTATGATTGCA
upper sequence: AT1G05820.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA10G44490.1 (Glycine max), 3'ss of exon 9
---------------------gtaaattttctgtatgtattttcctactaaaattcttttgtgatccctttgtatgtgttctaa--------tgggtgtctcaca-cttagGTTGCTACCATTCTTCTCTGTTGTGCATTTTTCTATGACATCTTTTGGGTATTCATATCACCACTAATCTTCAAGCAAAGTGTAATGATTGCG
|| || || || ||||| | |||| | | || ||| || | | | | | | | ||| | | | |||||||| || | || || |||||||||||| | || ||||||||||||||||||||||| || | || ||| || | ||||| |||||| |
gtacctgaatgaattccttgtgtttatattatgctgttatttccttactcatttcgttccaatatctgttggaacatttctcacaatttgcttatgcatctgatatcatagGTTGCAACTGTACTCCTATGTTGTGCATTTGTATACGACATCTTTTGGGTATTCATATCTCCTGTGATATTCCAGAAGAGTGTTATGATTACA
upper sequence: AT1G05820.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA20G39260.1 (Glycine max), 3'ss of exon 8
---------------------gtaaattttctgtatgtattttcctactaaaattcttttgtgatccctttgtatgtgttctaa--------tgggtgtctcaca-cttagGTTGCTACCATTCTTCTCTGTTGTGCATTTTTCTATGACATCTTTTGGGTATTCATATCACCACTAATCTTCAAGCAAAGTGTAATGATTGCG
|| || || | ||||| | ||| | | | ||| || | | | | | | | ||| | | | |||||||| || | || || |||||||||||| | || ||||||||||||||||||||||| ||| | || ||| || | ||||| |||||| |
gtacctgaatgagttccttgtgtttatattgtactgctatttccacactcatttagctccaatatctgttggaacatttctcacaatttgcttatgcatctgatatcatagGTTGCAACTGTACTCCTTTGTTGTGCATTTGTATACGACATCTTTTGGGTATTCATATCTCCAGTGATATTCCAGAAGAGTGTTATGATTACA
upper sequence: AT1G05820.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: Vv05s0062g01250.t01 (Vitis vinifera), 3'ss of exon 9
-----------gtaaattttctgt-atgtattttcctactaaaattcttttgtgatccctttgtatgtgttct--------aatgggtgtctcacacttagGTTGCTACCATTCTTCTCTGTTGTGCATTTTTCTATGACATCTTTTGGGTATTCATATCACCACTAATCTTCAAGCAAAGTGTAATGATTGCG
||| | | ||| || | | | ||||||| | | | | || ||| | | | | ||| ||| |||||||| | | ||||| |||||||||||| | ||||||||||| ||||| |||||||||||| |||| ||||| | ||||| ||||| ||
atatttataagaagaatgagaaatcacttatcttaatgttttgaatcttttgataactcatgctacacactcttgcctgacatttgttatctt-cacacagGTTGCTTCTGTACTTCTTTGTTGTGCATTTGTTTATGACATCTTCTGGGTCTTCATATCACCAGTAATATTCAAAGACAGTGTTATGATAGCA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctaaaattcttttgtgatccctttgtatgtgttctaatgggtgtctcacacttagGTTGCTACCATTCTTCTCTGTTGTGCATTTTTCTATGACATCTTTTGGGTATTCATATCACCACTAATCTTCAAGCAAAGTGTAATGATTGCG
attctttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaattttctgtatgtattttcctactaaaattcttttgtgatccctttgtatgtgttctaatgggtgtctcacacttagGTTGCTACCATTCTTCTCTGTTGTGCATTTTTCTATGACATCTTTTGGGTATTCATATCACCACTAATCTTCAAGCAAAGTGTAATGATTGCG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG