Sequence
atgc intronic sequence ATGC exonic sequence...ccggttatctattttagatttcaacgagtcaagtaatcttataactgctactttccatggagattatctatgttgatattaaaagagattttcatgacagGCTGTTCATGATGGAGTTGATATCCTGAGCCTCTCAGTTGGTCCAAATAGTCCTCCCACAACTACCAAGACAACGTTCTTGAATCCATTTGATGCTACCC
Basic information
species | Arabidopsis thaliana |
transcript | AT2G19170.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT2G19170.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA15G17830.1 (Glycine max), 3'ss of exon 5
ccggttatctattttagatt--tcaacgagtcaagtaatcttataactgc---tactttccatggagattatcta--tgttgatattaaaagagattttcatgacagGCTGTTCATGATGGAGTTGATATCCTGAGCCTCTCAGTTGGTCCAAATAGTCCTCCCACAACTACCAAGACAACGTTCTTGAATCCATTTGATGCTACCC
| ||| || || | | |||| || | || ||| || || ||| | |||| || | || ||||| || | ||||||||| |||||||| || ||||| || ||||| |||||||| |||||||||||||| ||| ||||| || || || |||||||| ||||||||||| |
ctagttcaacataaacaatcagttatacagtcttatatttttctaagtgttagtattttatctcaagatgccttaattatttatatttgaaaacg-------aacagGCTGTGCATGATGGGGTGGATATACTCAGCCTTTCAGTTGGACCAAATAGTCCTCCATCAAACACCAAAACTACATTTTTGAATCCTTTTGATGCTACAC
upper sequence: AT2G19170.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA09G06640.1 (Glycine max), 3'ss of exon 6
ccggttatctattttagatttcaacgagtcaagtaatcttataactgctactttccatggagattatctatgttgatattaaaa----gagattttcatg---acagGCTGTTCATGATGGAGTTGATATCCTGAGCCTCTCAGTTGGTCCAAATAGTCCTCCCACAACTACCAAGACAACGTTCTTGAATCCATTTGATGCTACCC
| | | || | ||| ||| | | | |||||| | | | | ||| | | | ||| | || | |||| | ||||||||| ||||||||||| ||||| || ||||| |||||||| |||||||||||||| ||| ||||| || || || ||||| || ||||||||||| |
----tagttcaacataaa---caatcagttatacagttttataattttttaaaagcgttagtattttatctcaagatgtctaattatttaaatttgaaaatgaacagGCTGTGCATGATGGAGTGGATATACTCAGCCTTTCAGTTGGACCAAATAGTCCTCCGTCAAACACCAAAACTACATTTTTGAACCCTTTTGATGCTACAC
upper sequence: AT2G19170.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA13G00580.1 (Glycine max), 3'ss of exon 5
ccggttatctattttagatttcaacga---gtcaagtaatcttataactgctactttccatggagattatctatgttgatattaaaagagattttcatg---acagGCTGTTCATGATGGAGTTGATATCCTGAGCCTCTCAGTTGGTCCAAATAGTCCTCCCACAACTACCAAGACAACGTTCTTGAATCCATTTGATGCTACCC
|| || || | |||||| | |||| ||||| || | ||||| | | | | || || | | | |||| || ||||||||| |||||||||| ||||| || ||||| |||||||| || || |||||||| || |||||||||| ||||| ||||| || ||||||||||| |
-----catttaacataaaattcaacaaattgtcacacaatctcattttt-ttacttctggtattctatctaaaattttctaatttacaaaatttgggtgtctacagGCTGTGTATGATGGAGTGGATATACTCAGCCTTTCAGTTGGACCCAACAGTCCTCCAGCAGCTACCAAGACTACGTTTTTGAACCCTTTTGATGCTACAC
upper sequence: AT2G19170.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: Vv11s0103g00550.t01 (Vitis vinifera), 3'ss of exon 6
--ccggttatctattttagatttcaacgagtcaagtaatcttataactgctactttccatggagattatctatgttgatattaaaagagattttcatga-cagGCTGTTCATGATGGAGTTGATATCCTGAGCCTCTCAGTTGGTCCAAATAGTCCTCCCACAACTACCAAGACAACGTTCTTGAATCCATTTGATGCTACCC
| || ||| || | || | |||| | | |||| | | || | | | ||| || || ||| ||||||||||||||||| || || || || | ||||| || || |||||||||||||| |||| |||||||| ||||| || || || ||||||||| | |
ttttgcccatgaattaagcatctttttaggtga---tatctgttggggtattctttgttttttgttttttcgtttattaattgaagacttcttctgtgaacagGCTGTTCATGATGGTGTGGACATTCTCAATCTCTCTGTGGGGCCAAATAGTCCTCCAGCAACCACCAAGACCACGTTTTTAAACCCTTTTGATGCTGCAC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgctactttccatggagattatctatgttgatattaaaagagattttcatgacagGCTGTTCATGATGGAGTTGATATCCTGAGCCTCTCAGTTGGTCCAAATAGTCCTCCCACAACTACCAAGACAACGTTCTTGAATCCATTTGATGCTACCC
tgttgat putative branch site (score: 4)
ttttcat putative PPT
attatctatgttgata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ccggttatctattttagatttcaacgagtcaagtaatcttataactgctactttccatggagattatctatgttgatattaaaagagattttcatgacagGCTGTTCATGATGGAGTTGATATCCTGAGCCTCTCAGTTGGTCCAAATAGTCCTCCCACAACTACCAAGACAACGTTCTTGAATCCATTTGATGCTACCC
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