Sequence
atgc intronic sequence ATGC exonic sequencegtaatcatttctcttctcctttgagctcttaaaacaaggaatatccatatatatagtcttaaagagttctgtgatttgtagAAATATTTGCAATCAACTACTGTAAGAGTTGAGGAAATGAGAGTGAAAAGGAGAGATGCAGAGCAATGGATGTCTCATCGGATGTTGCCAGACGATCTGA
Basic information
species | Arabidopsis thaliana |
transcript | AT2G46430.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT2G46430.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA19G44430.1 (Glycine max), 3'ss of exon 5
--gtaatcatttctcttctcctt---tgagctcttaaaacaaggaatatccatat-atatagtcttaaagagtt--ctgtgattt-----------gtagAAATATTTGCAATCAACTACTGTAAGAGTTGAGGAAATGAGAGTGAAAAGGAGAGATGCAGAGCAATGGATGTCTCATCGGATGTTGCCAGACGATCTGA
| | || | | || || | | ||| | | || | || | || | ||| || | || | ||| |||||||| ||||||| || ||||||||||| ||||| ||||||||||| || || ||||| || |||||||| || || ||| | || || | |||
ttacagttgactccttcgtgattacatgcccacctaacatttgaaaagttaattttatgcaacattagttagctaactattgttttgaatattgctacagAAATATCTGCAATCTACAACTGTAAGAGTGGAGGAGATGAGAGTGAAGAGACAGGACGCAGAACAGTGGATGTCCCACCGTATGCTACCTGAGAACTTGA
upper sequence: AT2G46430.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA03G41780.1 (Glycine max), 3'ss of exon 5
-----gtaatcatttctcttctcctttgagctcttaaaacaaggaatatccatat-atatagtcttaaagagtt--ctgtgattt-----------gtagAAATATTTGCAATCAACTACTGTAAGAGTTGAGGAAATGAGAGTGAAAAGGAGAGATGCAGAGCAATGGATGTCTCATCGGATGTTGCCAGACGATCTGA
|| | | | || | | ||||| | || | || | || | ||| |||| || | ||| |||||||| ||||||| || ||||| ||||| ||||| ||||||||||| || || || || || |||||||| || || ||| | || || | |||
ttacagttgacccctgcgcgattacatgcccacctaaaatttgaaaagttaattttatgcaacattagttagttaactattgttttgaatattgttacagAAATATCTGCAATCTACAACTGTTAGAGTGGAGGAGATGAGAGTGAAGAGACAGGACGCGGAACAGTGGATGTCCCACCGTATGCTACCTGAGAACTTGA
upper sequence: AT2G46430.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv15s0046g00980.t01 (Vitis vinifera), 3'ss of exon 6
---------------gtaatcatttctcttctcctt-tgagctcttaaaacaaggaatatccatatatatagtcttaaagagt-tctgtgatttgt---agAAATATTTGCAATCAACTACTGTAAGAGTTGAGGAAATGAGAGTGAAAAGGAGAGATGCAGAGCAATGGATGTCTCATCGGATGTTGCCAGACGATCTGA
| | || | || | || ||| | | || || || | | | ||||| | | |||| ||| |||||||| ||||||| || ||||| ||| | || || |||||||| |||||| ||||||||||| |||||| ||||||| || | || ||| ||||
catctagctcctactggagccaaggcactaattctcatgaaccccaccaattttagctaaa-gtactaagattactaaagcatgtttgtgtgctgttacagAAATATCTGCAATCCACAACTGTTAGAATCGAAGAGATGAGAGTAAAAAGGCAGGATGCAGAGCAGTGGATGGCTCATCGATTGCTCCCTGACCCCCTGA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcttaaaacaaggaatatccatatatatagtcttaaagagttctgtgatttgtagAAATATTTGCAATCAACTACTGTAAGAGTTGAGGAAATGAGAGTGAAAAGGAGAGATGCAGAGCAATGGATGTCTCATCGGATGTTGCCAGACGATCTGA
atatatatagtcttaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaatcatttctcttctcctttgagctcttaaaacaaggaatatccatatatatagtcttaaagagttctgtgatttgtagAAATATTTGCAATCAACTACTGTAAGAGTTGAGGAAATGAGAGTGAAAAGGAGAGATGCAGAGCAATGGATGTCTCATCGGATGTTGCCAGACGATCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA