Sequence
atgc intronic sequence ATGC exonic sequencegtaagtgctttttaagatccattataagatgaatctttatgagtttaacttatgggctaaccttgcagGAAGAGAGGCAAAGAGCTTTGGTGCAGTTACAGTGGAAGGTGATGAGTGACAATCCACCTGAGGAGCAAGAAGTAAACTCAAACAAG
Basic information
species | Arabidopsis thaliana |
transcript | AT1G22275.1 |
intron # | 12 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G22275.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: GLYMA13G01840.1 (Glycine max), 3'ss of exon 12
----gtaagtgctttttaagatccatta------taagatgaatct--ttatgagtttaacttatgggctaaccttgcagGAAGAGAGGCAAAGAGCTTTGGTGCAGTTACAGTGGAAGGTGATGAGTGACAATCCACCTGAGGAGCAAGAAGTAAACTCAAACAAG
| || | | || ||| ||| | || | | | |||| | || | | | || | ||||||||||| |||||||| |||||| ||||||| |||||||| |||||||||||||| || ||||| |||||||| || ||||| ||
gtatggaataccctgatatgataaattgatttcttgtcataatttttattattatatttattctttggaatatattgcagGAAGACAGGCAAAGGGCTTTGTTGCAGTTGCAGTGGAAAGTGATGAGTGACAAGCCCAAAGAGGACCAAGAAGTGAATTCAAAACAG
upper sequence: AT1G22275.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: GLYMA20G35130.1 (Glycine max), 3'ss of exon 3
----gtaagtgctttttaagatccatta------taagatgaatct--ttatgagtttaacttatgggctaaccttgcagGAAGAGAGGCAAAGAGCTTTGGTGCAGTTACAGTGGAAGGTGATGAGTGACAATCCACCTGAGGAGCAAGAAGTAAACTCAAACAAG
| || ||| || ||| |||| | || | | | |||| | || | | | || | ||||||||||| |||||||| |||||| ||||||| |||| ||| |||||||||||||| || ||||| |||||||| || ||||| ||
gtatggaataccttgatatgataaattaatttattgtcataatttttattattatatttattctttggaatatattgcagGAAGACAGGCAAAGGGCTTTGTTGCAGTTGCAGTTGAAAGTGATGAGTGACAAGCCCAAAGAGGACCAAGAAGTGAATTCAAAACAG
upper sequence: AT1G22275.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: GLYMA13G07980.1 (Glycine max), 3'ss of exon 6
----gtaagtgctttttaagatccatta------taagatgaatct--ttatgagtttaacttatgggctaaccttgcagGAAGAGAGGCAAAGAGCTTTGGTGCAGTTACAGTGGAAGGTGATGAGTGACAATCCACCTGAGGAGCAAGAAGTAAACTCAAACAAG
| || ||| || ||| |||| | || | | | |||| | || | | | || | ||||||||||| |||||||| |||||| |||| || |||||||| |||||||||||||| || ||||| |||||||| || ||||| |
gtatggaataccttgatatgataaattaatttcttgtcataatttttattattatatttattctttggaatatattgcagGAAGACAGGCAAAGGGCTTTGTTGCAATTGCAGTGGAAAGTGATGAGTGACAAGCCCAAAGAGGACCAAGAAGTGAATTCAAAACAT
upper sequence: AT1G22275.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: GLYMA14G34810.1 (Glycine max), 3'ss of exon 12
-------gtaagtgctttttaagatccatt--ataagatgaatctt--tatgagtttaacttatgggctaaccttgcagGAAGAGAGGCAAAGAGCTTTGGTGCAGTTACAGTGGAAGGTGATGAGTGACAATCCACCTGAGGAGCAAGAAGTAAACTCAAACAAG
|| || | | || ||| | || | | || ||| | || | || | || | ||||||||||| |||||| | |||||| ||||||| |||||||| |||||||||||||| || ||||| |||||||| || ||||| ||
gtatggaatacctgatacaacaaatttatttcttctcataatttttcttattatatttatttttcggaatatattgcagGAAGACAGGCAACGGGCTTTGTTGCAGTTGCAGTGGAAAGTGATGAGTGACAAGCCCAAAGAGGACCAAGAAGTGAATTCAAAACAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aagatccattataagatgaatctttatgagtttaacttatgggctaaccttgcagGAAGAGAGGCAAAGAGCTTTGGTGCAGTTACAGTGGAAGGTGATGAGTGACAATCCACCTGAGGAGCAAGAAGTAAACTCAAACAAG
ggctaac putative branch site (score: 2)
attataagatgaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagtgctttttaagatccattataagatgaatctttatgagtttaacttatgggctaaccttgcagGAAGAGAGGCAAAGAGCTTTGGTGCAGTTACAGTGGAAGGTGATGAGTGACAATCCACCTGAGGAGCAAGAAGTAAACTCAAACAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT