Sequence
atgc intronic sequence ATGC exonic sequencegtataatagcttgtcggctggtgtcaaagacttttattttataaggggcaggaataagagtctcatgtgcattgcagATTGGGGTTCTTGAGGACACAAGGAACCGTACTCTCCACGGCATTTTACGTGTTCAAAGTTCTTTTAGAGGATACCAAGCACGCTGTCTCCTGAAGGAAC
Basic information
species | Arabidopsis thaliana |
transcript | AT3G19960.1 |
intron # | 20 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G19960.1 (Arabidopsis thaliana), 3'ss of exon 20
lower sequence: GLYMA09G42180.1 (Glycine max), 3'ss of exon 18
-------------gtataatagcttgtcggctggtgtcaaag------acttttatttt----ataaggggcagga-ataagagtctcatgtgcattgcagATTGGGGTTCTTGAGGACACAAGGAACCGTACTCTCCACGGCATTTTACGTGTTCAAAGTTCTTTTAGAGGATACCAAGCACGCTGTCTCCTGAAGGAAC
| | ||| | ||||| || | ||||||||| ||| || || | | ||| | |||||||||||| || ||||| || || || || ||||| ||||| |||||||||||||| ||||||| ||| || || ||||||||||| | || ||||| |
atttatatctgctattcctttcctttatgaaaggtgtaggagcataaaatttttatttttaaaatatatttcaatttatgctgctttgatg-gaattgcagATTGGTGTGCTTGAAGATACTAGAAATCGTACCCTCCATGGCATTTTACGTGTCCAAAGTTGTTTCAGGGGTTACCAAGCACGTCATTCTCTCAAGGATC
upper sequence: AT3G19960.1 (Arabidopsis thaliana), 3'ss of exon 20
lower sequence: GLYMA20G00320.1 (Glycine max), 3'ss of exon 20
--------------gtataatagcttgtcggctggtgt-----caaagacttttattttataaggggc-----aggaataagagtctcatgtgcattgcagATTGGGGTTCTTGAGGACACAAGGAACCGTACTCTCCACGGCATTTTACGTGTTCAAAGTTCTTTTAGAGGATACCAAGCACGCTGTCTCCTGAAGGAAC
| | ||| | ||||| || | ||||||||| ||| | || | | ||| | |||||||||||| || ||||| || || || || ||||| ||||| |||||||||||||| ||||||| ||| || || | ||||||||| || || ||||| |
tatttatatctgctattcctttcctttatgaaaggtgtaggagcataagattttattttttaaatattttccaatttatgctgctttgatg-gaattgcagATTGGTGTGCTTGAAGATACTAGAAATCGTACCCTCCATGGCATTTTACGTGTCCAAAGTTGTTTCAGGGGTTTCCAAGCACGTCGTTCTCTCAAGGATC
upper sequence: AT3G19960.1 (Arabidopsis thaliana), 3'ss of exon 20
lower sequence: Vv10s0071g00210.t01 (Vitis vinifera), 3'ss of exon 19
----------------gtataatagcttgtcggctggtgtcaaa-gacttttattttataaggggcaggaataagagtctcat---gtg-cattg--cagATTGGGGTTCTTGAGGACACAAGGAACCGTACTCTCCACGGCATTTTACGTGTTCAAAGTTCTTTTAGAGGATACCAAGCACGCTGTCTCCTGAAGGAAC
|| | | | || | | | ||| | | || |||| | | ||||| || || |||| |||||||| || |||||||| ||||| |||| |||||||| |||||||||||||||||||||| || ||||| ||||||| || |||| || | ||| |
agtttcttccagcttggttcatgatcatggttgttagcagcaatcaaaatgaataacataaatcagatattcacgagtcctattccatgtcattatacagATTGGTGTCCTTGAGGATACAAGAAACCACACTCTCCATGGCATTTTACGTGTTCAAAGTTGCTTCAGAGGTCACCAAGCTCGTTGTCATCTCAGGGATC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtcaaagacttttattttataaggggcaggaataagagtctcatgtgcattgcagATTGGGGTTCTTGAGGACACAAGGAACCGTACTCTCCACGGCATTTTACGTGTTCAAAGTTCTTTTAGAGGATACCAAGCACGCTGTCTCCTGAAGGAAC
agacttttattttata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtataatagcttgtcggctggtgtcaaagacttttattttataaggggcaggaataagagtctcatgtgcattgcagATTGGGGTTCTTGAGGACACAAGGAACCGTACTCTCCACGGCATTTTACGTGTTCAAAGTTCTTTTAGAGGATACCAAGCACGCTGTCTCCTGAAGGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA