Sequence
atgc intronic sequence ATGC exonic sequencegtataactctaacttgtttgatcttcttcctcatttggtaaagctttagtgattgatctaacaatctgtctaatttactcatctcttgtttgtatcagGAAGAGTTTCAGTTGGCTTTGTTTAAGACAAATAAAAAAGAGAGTTTGTTTGCAGATCGG
Basic information
species | Arabidopsis thaliana |
transcript | AT5G55990.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G55990.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA08G44580.1 (Glycine max), 3'ss of exon 3
-------gtataactctaacttgtttgatcttcttcctcatttggtaaagcttt-agtgattgatctaacaatctgtctaatttactcatctcttgtttgtatcagGAAGAGTTTCAGTTGGCTTTGTTTAAGACAAATAAAAAAGAGAGTTTGTTTGCAGATCGG
||| |||| ||| | | | || ||| || ||| | || ||| | | | ||||| | | | |||| |||||||||||||||||||||||||| ||||||||||||||||| ||| ||||||| ||||||
gtaaattctattgttctattttgccatctactttctcttgaagggtttagttttcaaaaatctatcagatgttacattcaattt---tagatatcatttg---cagGAAGAGTTTCAGTTGGCTTTGTTCAAGACAAATAAAAAAGAAAGTCTGTTTGCTGATCGG
upper sequence: AT5G55990.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA18G08230.1 (Glycine max), 3'ss of exon 4
-----------------------------------------------------------------------------------gtataactctaacttgttt--gatcttcttcctcatttggtaaagctttagtgattgatctaacaatctgtctaattt---actcatctcttgtttgtat---cagGAAGAGTTTCAGTTGGCTTTGTTTAAGACAAATAAAAAAGAGAGTTTGTTTGCAGATCGG-
| ||| | | | || ||| | | | || ||| || | | | | | | | | ||||| || || | | ||| | | | || || |||||||||||||||||||| ||||| ||||||||||||||||| ||| ||||||| ||||||
tttgtcattggaaaactgtgttttgggcatattgtatttcactagttgagcctttttcaacaatgaaagaaaataaatatttcatttaagttttatttatttatagtgtagcttctatttttctattttgtcatttact--tttcaaaatctatcagatgttacattcaattttagatttcatttgcaggAAGAGTTTCAGTTGGCATTGTTCAAGACAAATAAAAAAGAAAGTCTGTTTGCTGATCGGG
upper sequence: AT5G55990.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA07G39940.1 (Glycine max), 3'ss of exon 3
-gtataactctaacttgt-ttgatcttcttcctcatttggtaaagc--tttagtgattgatctaacaatctgtctaatttactcatctcttgtttgtatcagGAAGAGTTTCAGTTGGCTTTGTTTAAGACAAATAAAAAAGAGAGTTTGTTTGCAGATCGG
|| || | | || | || | || ||| ||| | | || |||| ||| | ||| | | | | || | | |||||||| ||||||||||| ||||| ||||| || || |||||||| || ||||||||| ||
agtgta-ttatgttttatgttaaactcagaactctttttatttttttatctaaacattg-tctttttgtttgttttgatggtttccttattttccatggcagGAAGAATTTCAGTTGGCATTGTTCAAGACGAACAAGAAAGAGAGCTTATTTGCAGATAGG
upper sequence: AT5G55990.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA17G00830.1 (Glycine max), 3'ss of exon 3
gtataactc-taacttgtttgatcttcttcctcatttggtaaagctttagtgattgat-ctaacaatctgtctaatttactcatctcttgtttgtat----cagGAAGAGTTTCAGTTGGCTTTGTTTAAGACAAATAAAAAAGAGAGTTTGTTTGCAGATCGG
| ||||| ||| || || | | |||| | | | ||| | | | || | ||| | ||| | | || || || || |||||||| ||||||||||| ||||| ||||| || || |||||||| || ||||||||| ||
--agaactcacaacactttatattgtttatggcattggttgt--ttgtagatctaaacattgactttttgtttgttttgatggtttcctgattttacatggcagGAAGAATTTCAGTTGGCATTGTTCAAGACGAACAAGAAAGAGAGCTTATTTGCAGATAGG
upper sequence: AT5G55990.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv19s0015g01070.t01 (Vitis vinifera), 3'ss of exon 2
------------------------------------------------------gtataac-tctaacttgtttgatcttcttcctcatttggtaaagctttagtgattgatctaacaatctgtctaatttactcatctcttgt-ttgtat--cagGAAGAGTTTCAGTTGGCTTTGTTTAAGACAAATAAAAAAGAGAGTTTGTTTGCAGATCGG
||| | || || || | | |||| | | | | | || || || | | | | ||||| | ||| || ||| |||||||||||||| ||||||||||| || ||||| ||||| || || || ||||| ||||||
gttcatagataagctattattcaatttataggcagtattggaaatctgattgtagtaatgcacctcacatgaataaatctcttgattctctcccattccatttgttgtttcccaactatagttagtaattgatgtttctacggtaccatattacagGAAGAGTTTCAATTGGCTTTGTTCAAAACAAACAAAAAGGAAAGCTTATTTGCTGATCGG
upper sequence: AT5G55990.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv00s1569g00020.t01 (Vitis vinifera), 3'ss of exon 2
---------------------------------------------------------------------------------------------gtataactctaacttgtttgatctt----cttcctcatttggtaaagctttagtgattgatctaacaatctgtctaatttactcatctcttg---tttgtat--cagGAAGAGTTTCAGTTGGCTTTGTTTAAGACAAATAAAAAAGAGAGTTTGTTTGCAGATCGG
| | || | || | || | | | | | ||| | | | | | | || | | ||| | || || || ||| |||||||| ||||| |||| || ||||||||||| ||||| ||||||||||||||||| |||
gtgacatactgttttcctacttatactgaaagtctgtaggctatcatattgttttgcagtttcaggatgacattgctcctctgttatatcttagcacaaatttagcaatcttcttgtgaaaattccattattaatttgaagtactgatactttcttactattgtgttttgttggtggattctttaaatcccatattgcagGAAGAATTTCAACTGGCGTTATTTAAGACAAACAAAAAGGAGAGTTTGTTTGCAGACCGG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctttagtgattgatctaacaatctgtctaatttactcatctcttgtttgtatcagGAAGAGTTTCAGTTGGCTTTGTTTAAGACAAATAAAAAAGAGAGTTTGTTTGCAGATCGG
ctcatctcttgttt CT-rich tract
tctaattta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtataactctaacttgtttgatcttcttcctcatttggtaaagctttagtgattgatctaacaatctgtctaatttactcatctcttgtttgtatcagGAAGAGTTTCAGTTGGCTTTGTTTAAGACAAATAAAAAAGAGAGTTTGTTTGCAGATCGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT