Sequence
atgc intronic sequence ATGC exonic sequence...gaataatgatattgcaatgatcatgtatttgagattcttatgtaagaaaatgcacatatattatttccaaacttcaagaagtgaattattgttgttacagGAGTTGGGGAATACTGTCTTTAACAATAGCATATTGCTGGCAACTCTACACACTGTGGATTCTGGTTCAGTTGCACGAAGCTGTCCCCGGGAAACGCTAC
Basic information
species | Arabidopsis thaliana |
transcript | AT1G47670.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G47670.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA15G07440.1 (Glycine max), 3'ss of exon 1
gaataatgatattgcaatgatcatgtatttgagattcttatgtaagaaaatgcacatatattatttccaaacttcaagaagtgaattattgt----tgttacagGAGTTGGGGAATACTGTCTTTAACAATAGCATATTGCTGGCAACTCTACACACTGTGGATTCTGGTTCAGTTGCACGAAGCTGTCCCCGGGAAACGCTAC
| || | ||| | | || | | || | || | || | | | | | |||||| | |||| | |||| |||| ||||||||||||||| || || ||||| ||||||||||| |||||||| ||||| | ||||||||||||||| | |||||||| || || || ||| | |||
--agaaaagt-ttgtatacactatagaatatggaat-ttgtccaatttattttatgaaaaatatttcagcccacttagaaatactttatccaaatatgttgcagGAGTTGGGGAATTCTTTCCTTAACCATAGCATATTGTTGGCAACTTTACACGTTATGGATTCTGGTTCAGCTTCACGAAGCAGTTCCAGGTAAAAGATAC
upper sequence: AT1G47670.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA13G31880.1 (Glycine max), 3'ss of exon 2
gaataatgatattgcaatgatcat-gtatttgagattcttatgtaagaaaatgcacatatattatttccaaacttcaagaagtgaattattgt----tgttacagGAGTTGGGGAATACTGTCTTTAACAATAGCATATTGCTGGCAACTCTACACACTGTGGATTCTGGTTCAGTTGCACGAAGCTGTCCCCGGGAAACGCTAC
| || | ||| | | || | || ||| ||| | | || | | | | | |||||| | |||| | |||| |||| ||||||||||||||| || || ||||| ||||||||||| |||||||| ||||| | |||||| |||||||| | |||||||| || || || ||| | |||
--agaaaagt-ttgtatgcactatagaatatgaaatt--tgtccaatttattttatgaaaaatatttcaccccacttagaaatactttatccaaatatgttgcagGAGTTGGGGAATTCTTTCCTTAACCATAGCATATTGTTGGCAACTTTACACGTTATGGATTTTGGTTCAGCTTCACGAAGCAGTTCCAGGTAAAAGATAC
upper sequence: AT1G47670.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv18s0001g11300.t01 (Vitis vinifera), 3'ss of exon 1
-----gaataatgatattgcaatgatcatgtatttgagattcttatgtaagaaaatgcacatatattatttccaaacttcaagaagtgaattattgttgttacagGAGTTGGGGAATACTGTCTTTAACAATAGCATATTGCTGGCAACTCTACACACTGTGGATTCTGGTTCAGTTGCACGAAGCTGTCCCCGGGAAACGCTAC
|| |||| |||| | || | || || | || ||| || || || | || | | | | | | || | |||||||||||||||||| || ||||| ||||| || | |||||||| || ||| |||||||||| ||||| | || ||||| || || ||||| | |||
aggacaaaaaatg-cattg-ggccaagataaaaatgtgaaggaaaattagtttgatgaacttagcttgccttca---ctaattatttttgtaaatgaaaatgcagGAGTTGGGGAATACTTTCCTTAACCATAGCCTACTTTTGGCAACTTTATACATTGTGGATTCTAGTTCAACTACATGAAGCAGTTCCAGGGAAGAGGTAC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gaaaatgcacatatattatttccaaacttcaagaagtgaattattgttgttacagGAGTTGGGGAATACTGTCTTTAACAATAGCATATTGCTGGCAACTCTACACACTGTGGATTCTGGTTCAGTTGCACGAAGCTGTCCCCGGGAAACGCTAC
atatattatttccaaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gaataatgatattgcaatgatcatgtatttgagattcttatgtaagaaaatgcacatatattatttccaaacttcaagaagtgaattattgttgttacagGAGTTGGGGAATACTGTCTTTAACAATAGCATATTGCTGGCAACTCTACACACTGTGGATTCTGGTTCAGTTGCACGAAGCTGTCCCCGGGAAACGCTAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - -aagaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - cacatat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - caagaag