Sequence
atgc intronic sequence ATGC exonic sequencegtatacctgcgattaccaatgactgtttttttcctctctctgagtggagatattgtatgaaattgtaactgactgttcatgctttgatcttagGTTCATCCAAGTGATGTTATGGGACCTTCACTCCCTGGTCCCATTGTTCTCCTTGTGGACTGTCCAACAGAGTCGCACGCTGCAGAACTGTTCTCACTTA
Basic information
species | Arabidopsis thaliana |
transcript | AT1G52160.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G52160.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA13G43270.1 (Glycine max), 3'ss of exon 6
-----------------------------------------------gtatacctgcgattaccaatgactgtttttttcctctctctgagtggagatattgtatgaaattgtaac-tgactgttcatgctttgatcttagGTTCATCCAAGTGATGTTATGGGACCTTCACTCCCTGGTCCCATTGTTCTCCTTGTGGACTGTCCAACAGAGTCGCACGCTGCAGAACTGTTCTCACTTA
| | | | | | ||| | || | |||| | | | || | | | ||||||| |||||| | | | | ||||||||||||||||||| |||| ||||| | |||||||||||||| |||||||| || || |||||||| || || | || | | || || |
gttagtctcaaaactctacattatttgcccaaagcagagtagaattagaaaaggaaacagaatttgagcctgatggatttcaatctc-aattacacatgcttcaatacattgtaaagcaactgtttgtctactaaaat-agGTTCATCCAAGTGATGTCTTGGGTCCTTCTGTTCCTGGTCCCATTGTACTCCTTGTTGATTGCCCAACAGAATCTCATTTGGAAGCATTATTGTCTGTAC
upper sequence: AT1G52160.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA15G02070.1 (Glycine max), 3'ss of exon 7
---------------------------------------------------------------------------gtatacctgcgattaccaatgactgtttttttcctctctctgagtggagatattgtatgaaattgtaactgactgttcatgctttgatcttagGTTCATCCAAGTGATGTTATGGGACCTTCACTCCCTGGTCCCATTGTTCTCCTTGTGGACTGTCCAACAGAGTCGCACGCTGCAGAACTGTTCTCACTTA
| | | ||| | ||| || | ||| || | ||| || | || || | || | |||||| | || | |||||||||||||||||||| |||| ||||| | |||||||||||||| |||||||| || || |||||||| || || | || | | || || |
gttagtcttaaaactcgacattatttgcccaaagcagagtagaattataaaaggaaacagaatttgagacagagatttcaatctcaattgcacatg-ctttagtttatttcaatttga-tgttgggcttccataccttgtaaagtaactgtttgt-ctgctacaatagGTTCATCCAAGTGATGTCTTGGGTCCTTCTGTTCCTGGTCCCATTGTACTCCTTGTTGATTGCCCAACAGAATCCCATTTGGAAGCATTATTGTCTATGC
upper sequence: AT1G52160.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: Vv09s0002g04000.t01 (Vitis vinifera), 3'ss of exon 6
gtatacctgcgattaccaatgactgtttttttcctctctctgagtggagatattgtatgaaattgtaactgactgttcatgctttgatcttagGTTCATCCAAGTGATGTTATGGGACCTTCACTCCCTGGTCCCATTGTTCTCCTTGTGGACTGTCCAACAGAGTCGCACGCTGCAGAACTGTTCTCACTTA-
|| | |||| ||| |||| | | | | || | |||| | | || || |||| | ||| | ||||||||||||||||||||| ||||||||||| | |||||||| |||| | ||||| ||||| ||||| || || | || ||| || || | |
------gtgggtttacttatgg-tgttctatgtatgtttcataccat-----ttgttttgatccatagct--ttgttt-ttcttattttttagGTTCATCCAAGTGATGTGATGGGACCTTCTATTCCTGGTCCTCTTGTATTGCTTGTAGACTGCCCAACGGAATCATAT-CTACAGGACCTTTTATCCGTGG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tctgagtggagatattgtatgaaattgtaactgactgttcatgctttgatcttagGTTCATCCAAGTGATGTTATGGGACCTTCACTCCCTGGTCCCATTGTTCTCCTTGTGGACTGTCCAACAGAGTCGCACGCTGCAGAACTGTTCTCACTTA
atattgtatgaaatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatacctgcgattaccaatgactgtttttttcctctctctgagtggagatattgtatgaaattgtaactgactgttcatgctttgatcttagGTTCATCCAAGTGATGTTATGGGACCTTCACTCCCTGGTCCCATTGTTCTCCTTGTGGACTGTCCAACAGAGTCGCACGCTGCAGAACTGTTCTCACTTA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG