Sequence
atgc intronic sequence ATGC exonic sequencegtaagtgtgtgtttctcaataggaataacttagaaagatgtgagatttgttttcatgaaaacatcacattctgtgaaatttatttactattgatggttctcttttatgaattggtatttgctgatgcagCAAAGTAAGAAGATTGCAGATGCTAAACTTGCAAAGGATTTTGAAGCAGCGTTGAAAGAGTTTCAGAAAGCACAGCATATTACAGTTGAAAGAGAAACTT
Basic information
species | Arabidopsis thaliana |
transcript | AT1G32270.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G32270.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA16G08200.1 (Glycine max), 3'ss of exon 2
gtaagtgtgtgtttctcaataggaataacttagaaagatgtgagatttgttttcatgaaaacatcacattctgtgaaatttatttactattgatggttctcttttatgaattggtatttgctgatgcagCAAAGTAAGAAGATTGCAGATGCTAAACTTGCAAAGGATTTTGAAGCAGCGTTGAAAGAGTTTCAGAAAGCACAGCATATTACAGTTGAAAGAGAAACTT
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------------------------atactgtgaaaacttgtgttacgggca---atgtctttattgcattttaggg--ttccatgaccttccatgtcttttgcctcaaaaacatttcttattattgcagGCAAGCAAGAAGATTGCAGATGCTAAACTTGCGAAAGATTTTCAGGCAGTGTTGAAAGAGTTTCAGAAGGCACAACGTCTTGCAGCTGAGAGGGAAACAG
upper sequence: AT1G32270.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA16G13410.1 (Glycine max), 3'ss of exon 2
gtaagtgtgtgtttctcaataggaataacttagaaagatgtgagatttgttttcatgaaaaca-tcacattctgtga-aatttatttactattgatggttctctt--ttatgaattggtatttgctgatgcagCAAAGTAAGAAGATTGCAGATGCTAAACTTGCAAAGGATTTTGAAGCAGCGTTGAAAGAGTTTCAGAAAGCACAGCATATTACAGTTGAAAGAGAAACTT
|| || |||| |||| ||||||||| | | | ||| | | || | | || | ||| || | || | || | ||||| ||| |||||||| ||||||||||||||||| || |||||| | |||| |||||||||||||||||| ||||| | | || ||| ||| || |||||
--------------------------------ttaatctgcatcattt-ttttaatgaaaacagtgaaaacttgttacaggcaatgtctttttagtatgtcttttgcctcaaaaacatttcttatttttgcagGCAAGCAAGAAGATAGCAGATGCTAAACTTGCGAAAGATTTTCAGGCAGTGTTGAAAGAGTTTCAGAAGGCACAACGTCTTGCAGCTGAGAGGGAAACAG
upper sequence: AT1G32270.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA01G01960.1 (Glycine max), 3'ss of exon 2
gtaagtgtgtgtttctcaataggaataacttagaaagatgtgagatttgttttcatgaaaacatcacattctgtgaaatttatttactattgatggttctcttttatgaattggtatttgctgatgcagCAAAGTAAGAAGATTGCAGATGCTAAACTTGCAAAGGATTTTGAAGCAGCGTTGAAAGAGTTTCAGAAAGCACAGCATATTACAGTTGAAAGAGAAACTT
| | | || | | | | | || |||| || || | || | | | | || ||| ||| |||||| || ||||| |||||||||||| |||||||| || |||||||| |||||| | || | ||||||||| |||||||| ||||||| | || ||| || || ||||||
---------------------agctttatgtactgaattattggtggcgcgatcttgaatttatttgtttttccc---ttgaggaaaga--aaaagtgaccttcaatgtattggt---tgtatttgcagGCAAGTAAGAAGATAGCAGATGCGAAGCTTGCAAAAGATTTTCAGGCGGTGTTGAAAGAATTTCAGAAGGCACAGCGTCTTTCAGCGGAGAGGGAAACTG
upper sequence: AT1G32270.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA09G33950.1 (Glycine max), 3'ss of exon 2
gtaagtgtgtgtttctcaataggaataacttagaaagatgtgagatttgttttcatgaaaacatcacattctgtgaaatttatttactattgatggttctcttttatgaattggtatttgctgatgcagCAAAGTAAGAAGATTGCAGATGCTAAACTTGCAAAGGATTTTGAAGCAGCGTTGAAAGAGTTTCAGAAAGCACAGCATATTACAGTTGAAAGAGAAACTT
||| || | | | || || | | | | || | | || | | | | || ||| ||| ||||| || ||||| |||||||||||| |||||||| || |||||||| |||||| | || | ||||||||| |||||||| || |||| | || ||| ||| || |||||
-----------------------aatg-tttgttgtagtttatgtactgaattattagtggcgtgatttttttttcccttgaggaaaga--aaaagtgaccttcaatgtcttggt---tgtatttgcagACAAGTAAGAAGATAGCAGATGCGAAGCTTGCAAAAGATTTTCAGGCGGTGTTGAAAGAATTTCAGAAGGCTCAGCGTCTTTCAGCTGAGAGGGAAACAG
upper sequence: AT1G32270.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv02s0012g01850.t01 (Vitis vinifera), 3'ss of exon 2
gtaagtgtgtgtttctcaataggaataacttagaaagatgtgagatttgttttcatgaaaacatcacattctgtgaaatttatttactattgatggttctcttttatgaattggtatttgctgatgcagCAAAGTAAGAAGATTGCAGATGCTAAACTTGCAAAGGATTTTGAAGCAGCGTTGAAAGAGTTTCAGAAAGCACAGCATATTACAGTTGAAAGAGAAACTT
| | ||| ||||||| | | | | | | | | || | |||||| ||| || | || | || ||| | | | || | ||||| || ||||||||||||||||||||||| ||||| |||||| |||||| || |||||||||||||| || || | | ||| ||||| |||||
-------------------tttggatatgttagaaaaaggaaacagaaga------ggatgcttccagtgctgtgatcttttttgaggggtg-taattgccttgaac-attctccatctaac--tgcagGCCAGCAAGAAGATTGCAGATGCTAAACTGGCAAAAGATTTTCAAGCAGTTTTAAAAGAGTTTCAGAAGGCTCAACGGCTGGCAGCAGAAAGGGAAACGG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gaaatttatttactattgatggttctcttttatgaattggtatttgctgatgcagCAAAGTAAGAAGATTGCAGATGCTAAACTTGCAAAGGATTTTGAAGCAGCGTTGAAAGAGTTTCAGAAAGCACAGCATATTACAGTTGAAAGAGAAACTT
tgctgat putative branch site (score: 3)
ttatttactattgat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagtgtgtgtttctcaataggaataacttagaaagatgtgagatttgttttcatgaaaacatcacattctgtgaaatttatttactattgatggttctcttttatgaattggtatttgctgatgcagCAAAGTAAGAAGATTGCAGATGCTAAACTTGCAAAGGATTTTGAAGCAGCGTTGAAAGAGTTTCAGAAAGCACAGCATATTACAGTTGAAAGAGAAACTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA