Sequence
atgc intronic sequence ATGC exonic sequenceAGAGAAAGCTATCTATCATACATTGAACATGCTTAGTCTTGATGTGACGAAGAAGTGCCTCGTGGCCGAGGGCTGGAGTCCTGTCTTTGCATCAAGAGAAgtgagttgttcattttgttgcactgtcaattgcaatattgaataacacattccttgactgtgagtttattgtttttttatcgtttacttagtataatggggttttgttgtgcag
Basic information
species | Arabidopsis thaliana |
transcript | AT4G39080.1 |
intron # | 9 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G39080.1 (Arabidopsis thaliana), 5'ss of exon 9
lower sequence: LOC_Os10g10500.1 (Oryza sativa), 5'ss of exon 9
AGAGAAAGCTATCTATCATACATTGAACATGCTTAGTCTTGATGTGACGAAGAAGTGCCTCGTGGCCGAGGGCTGGAGTCCTGTCTTTGCATCAAGAGAAgtgagttg-------ttcattttgttgcactgtcaattgcaatattgaataacacattccttgactgtgagtttattgtttttttatcgtttacttagtataatggggttttgttgtgcag
||| |||||||| || || ||||| |||||| | |||||||||||||| ||||| ||| | || || ||||| |||||||| || |||||| |||| | || | | |||| | |||||| | || | | | | ||||||| || | | | | || | | || || ||| ||| | | |
AGAAAAAGCTATTTACCACACATTAAACATGTTGAGTCTTGATGTGACAAAGAAATGCTTGGTTGCTGAGGGATGGAGTCCGGTGTTTGCAACAAGTCAGgtaaccagatgcactctcatccttctgcactttt--ttcttttgtctattgacacattt-ttagttttctatctgttttctggttttcattttctttatttcag-----------------
upper sequence: AT4G39080.1 (Arabidopsis thaliana), 5'ss of exon 9
lower sequence: GLYMA11G12120.1 (Glycine max), 5'ss of exon 9
AGAGAAAGCTATCTATCATACATTGAACATGCTTAGTCTTGATGTGACGAAGAAGTGCCTCGTGGCCGAGGGCTGGAGTCCTGTCTTTGCATCAAGAGAAgtgagttgttcattttgttgcactgtcaattgcaatattgaataacacattccttgact---gtgagtttattgtttttttatcgtttacttagtataatggg--gttttgttgtgcag------
|||||| |||| ||||||| |||||||||| || ||||||||||| || || || || ||||| ||||| ||||||||||| |||||| | | | || | || || | || | || | || ||| | || || | | || || | | ||| | | || | || | |||||| || || | |
GGAGAAATCTATTCATCATACCCTGAACATGCTGAGCCTTGATGTGACAAAAAAATGTCTTGTGGCTGAGGGGTGGAGTCCTGTTTTTGCAACTAAGCAGgt-atttattgttattctgatcctttattttataatg--agttttcattttgcctaaccagagttaataccttgggagggttttgtaaaattgatttaatggaacgtgttacctcgaattttcag
upper sequence: AT4G39080.1 (Arabidopsis thaliana), 5'ss of exon 9
lower sequence: GLYMA12G04330.1 (Glycine max), 5'ss of exon 9
AGAGAAAGCTATCTATCATACATTGAACATGCTTAGTCTTGATGTGACGAAGAAGTGCCTCGTGGCCGAGGGCTGGAGTCCTGTCTTTGCATCAAGAGAAgtgagttgttcattttgttgcactgtcaattgcaatattgaataacacattccttgactgtgagtttattgtttttttatcgtttacttagtataatggggttttgttgtgcag
|||||| |||| ||||||| |||||||||| || |||||||| || || || || || ||||| ||||| ||||||||||| |||||| | | | || | || || | |||| || | | || ||| |||| |||| | | || | ||||| || |||| | || | ||| | |||
GGAGAAATCTATTCATCATACCCTGAACATGCTGAGCCTTGATGTAACAAAAAAATGTCTTGTGGCTGAGGGGTGGAGTCCTGTTTTTGCAACTAAGCAGgt-atttattgttattgtgatcct-ttatttataat---gaatttt-catttc--gccttta--tttataattgatttaatgga-acatgttatctcgaattttcag-------Mapped EST sequences
Showing partial alignments of ESTs and genomic sequences. See full alignments
ATGC EST sequence
ATGC genomic sequence (exon)
ATGC genomic sequence (truncated intron)
EST:
gi|164091185|gb|EL992416.1|EL992416EST: GTGCCTCGTGGCCGAGGGCTGGAGTCCTGTCTTTGCATCAAGAGAA ATTCAAGATGCATTACAGCGTGCCGCCGTTGACTCCAATTCTCAAGTTGG
genomic: GTGCCTCGTGGCCGAGGGCTGGAGTCCTGTCTTTGCATCAAGAGAAgtgagttgtt ... tgttgtgcagATTCAAGATGCATTACAGCGTGCCGCCGTTGACTCCAATTCTCAAGTTGG
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
AGAGAAAGCTATCTATCATACATTGAACATGCTTAGTCTTGATGTGACGAAGAAGTGCCTCGTGGCCGAGGGCTGGAGTCCTGTCTTTGCATCAAGAGAAgtgagttgttcattttgttgcactgtcaattgcaatattgaataacacattccttgactgtgagtttattgtttttttatcgtttacttagtataatggggttttgttgtgcag
- - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA