Sequence
atgc intronic sequence ATGC exonic sequencegtaggagatttcagcagtttttttcgttggattccggtttgagaacttaaatctcaaaagctttgtctttttttttgtgtagTTGTGTATCTTGATGCTGATACTATTGTGGTAAAGAACATTGAGGATCTGTTTAAGTGTTCTAAGTTTTGCGCAAACTTGAAGCATTCTGAGAGGCTAAA
Basic information
species | Arabidopsis thaliana |
transcript | AT5G18480.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G18480.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA20G37000.1 (Glycine max), 3'ss of exon 2
-------------------------------------------------------gtaggagatttcagcagtt---tttttcgttggattccggtttgagaacttaaatctcaaaagct-ttgtctttttt-------tttgtgtagTTGTGTATCTTGATGCTGATACTATTGTGGTAAAGAACATTGAGGATCTGTTTAAGTGTTCTAAGTTTTGCGCAAACTTGAAGCATTCTGAGAGGCTAAA
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gtatagtatttatgttttttgtgtcgggttatggaagttgtggaggatgctctaaactttccatttaggttattgcctttcaaatgggatgtagcttctcatgtttatgccctatgatttattggctgtcttgaatatgtatgtgcagTTGTTTATCTTGATGCTGATACTATTGTGGTTAAGAATATTGAAGAACTTTTCAAATGTGGAAAATTCTGTGCTAATTTAAAGCATTCTGAGAGGTTGAA
upper sequence: AT5G18480.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA10G30700.1 (Glycine max), 3'ss of exon 3
gtaggagatttcagcagtttttttcgttggattccggtttgagaacttaaatctcaaaagctttgtctttttttttgtgtagTTGTGTATCTTGATGCTGATACTATTGTGGTAAAGAACATTGAGGATCTGTTTAAGTGTTCTAAGTTTTGCGCAAACTTGAAGCATTCTGAGAGGCTAAA
|||| | ||| || | | | | |||| || |||||| ||| |||||||||||||||| ||||| ||||| ||||| || || || || ||| || || |
------------------------------------gtttatgcactatgatttattggctgtcttgaatgttttcctgcagTTGTTTATTTTGATGCTGATACTATAGTGGTTAAGAATATTGAAGAACTTTTCAAATGTGGAAAATTCT-------------------------------
upper sequence: AT5G18480.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv14s0036g00430.t01 (Vitis vinifera), 3'ss of exon 2
------------gtaggagatttcagcagtttttttcg----ttggattccggtttgagaacttaaatctcaaaagct--ttgtctttttttttgtgtagTTGTGTATCTTGATGCTGATACTATTGTGGTAAAGAACATTGAGGATCTGTTTAAGTGTTCTAAGTTTTGCGCAAACTTGAAGCATTCTGAGAGGCTAAA
| | | ||| | |||| | ||| | | | |||| | | | | | || | || || || || |||||| |||||||||||||| |||||||| || || | ||||||||||| ||||| || || || || || || |||||||||||||||||||| ||
tttttttatgttattaatcaatgtggcatgtcttttggcagattgattagtgtatctagaagaacagttttatttagtgattattgttattattttgcagTTGTATATCTTGATGCTGACACTATTGTTGTTAAAAGTATTGAGGATCTCTTTAAATGCGGGAAATTCTGTGCTAATTTGAAGCATTCTGAGAGGCTGAAMapped 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|19878999|gb|AU239830.1|AU239830EST: GGGTGTTTATACAAAGCTTAAGATCTTTAACATGACTGATTATAAGAAAG TTGTGTATCTTGATGCTGATACTATTGTGGTAAAGAACATTGAGGATCTGT
genomic: GGGTGTTTATACAAAGCTTAAGATCTTTAACATGACTGATTATAAGAAAGgtaggagatt ... ttttgtgtagTTGTGTATCTTGATGCTGATACTATTGTGGTAAAGAACATTGAGGATCTGT
EST:
gi|125212040|gb|EL226994.1|EL226994EST: GGGTGTTTATACAAAGCTTAAGATCTTTAACATGACTGATTATAAGAAAG TTGTGTATCTTGATGCTGATACTA
genomic: GGGTGTTTATACAAAGCTTAAGATCTTTAACATGACTGATTATAAGAAAGgtaggagatt ... ttttgtgtagTTGTGTATCTTGATGCTGATACTA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tggattccggtttgagaacttaaatctcaaaagctttgtctttttttttgtgtagTTGTGTATCTTGATGCTGATACTATTGTGGTAAAGAACATTGAGGATCTGTTTAAGTGTTCTAAGTTTTGCGCAAACTTGAAGCATTCTGAGAGGCTAAA
ctttgtcttttttttt CT-rich tract
tttgtcttttttttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaggagatttcagcagtttttttcgttggattccggtttgagaacttaaatctcaaaagctttgtctttttttttgtgtagTTGTGTATCTTGATGCTGATACTATTGTGGTAAAGAACATTGAGGATCTGTTTAAGTGTTCTAAGTTTTGCGCAAACTTGAAGCATTCTGAGAGGCTAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG