Sequence
atgc intronic sequence ATGC exonic sequencegtatctttgaaaacatttcagaaactctgagttagttagtatctctaagctttgtgttttctttttcagTCATCAGTGTTACATTCGCAACCAAAATCAACTGTTGGAACTCCTGCTTACATCGCTCCTGAGGTTTTACTAAAGAAAGAATATGATGGAAAG
Basic information
species | Arabidopsis thaliana |
transcript | AT4G33950.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G33950.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: LOC_Os03g41460.1 (Oryza sativa), 3'ss of exon 3
----------------------------------gtatctttgaaaacatttcagaaactctgagttagttagtatctctaagctttgtgttttctttttcagTCATCAGTGTTACATTCGCAACCAAAATCAACTGTTGGAACTCCTGCTTACATCGCTCCTGAGGTTTTACTAAAGAAAGAATATGATGGAAAG
| | || || | ||| |||| | | | | | || | ||| | || ||| |||||| || || | ||||||||||||||||| |||||||||||||| || |||||||||||||||||| | || ||||| |||||||||||||||
ctgtgcatgtgtcttgtttagcctttcggggaatttgtgcctggaatctttttt--aactttattctgatca-tgtcatgacttttttttcttcatttgtcagTCGTCTGTTCTTCATTCGCAACCAAAATCTACTGTTGGAACTCCGGCATACATCGCTCCTGAGGTTCTGCTGAAGAAGGAATATGATGGAAAG
upper sequence: AT4G33950.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: LOC_Os12g39630.1 (Oryza sativa), 3'ss of exon 5
------------------------------gtatctttgaaaacatttca--gaaactctgagttagttagtatctctaagctttgtgttttctttttcagTCATCAGTGTTACATTCGCAACCAAAATCAACTGTTGGAACTCCTGCTTACATCGCTCCTGAGGTTTTACTAAAGAAAGAATATGATGGAAAG
| || | | | || | | | | | || ||| | || || | | | |||| |||||||| || | ||||| |||||||||||||| ||||||||||| ||||| || ||||| || ||||| || ||||||||||| |||||||||
actttctgtagtagtgaaaagaagagagaactttcgctagatttttctcgatgtgattgctgcctggataatat-tgtactgttgctttctgattttgcagTCATCGGTTCTTCATTCACAACCAAAATCAACAGTTGGAACTCCAGCTTATATTGCTCCAGAAGTTTTGCTCAAGAAAGAATACGATGGAAAG
upper sequence: AT4G33950.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: LOC_Os03g55600.1 (Oryza sativa), 3'ss of exon 5
------------------------gtatctttgaaaacatttcagaaac--tctgagttagt-tagtatctctaagctttgtg----ttttctttttcagTCATCAGTGTTACATTCGCAACCAAAATCAACTGTTGGAACTCCTGCTTACATCGCTCCTGAGGTTTTACTAAAGAAAGAATATGATGGAAAG
||| | | | ||| || | |||| ||| | || || | | | | | || || | ||||| ||||| | ||||| ||||||||||| ||||| ||||| |||||||| || || ||||| ||| | | ||||||||||| ||||| |||
taaatttcatttgcttacaatacactatactggcattactttaggacattatctggtttactctaataagcaaatgataaaagacaatctttttctgcagTCTTCAGTTCTCCATTCACAACCAAAATCCACTGTAGGAACCCCTGCTTATATTGCACCTGAAGTTCTGTTGAAGAAAGAATACGATGGCAAG
upper sequence: AT4G33950.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G066867_T01 (Zea mays), 3'ss of exon 4
-----------------------------gtatctttgaaaacatttcagaaac---tctgagttagttagtatctctaagctttgtgttttctttttcagTCATCAGTGTTACATTCGCAACCAAAATCAACTGTTGGAACTCCTGCTTACATCGCTCCTGAGGTTTTACTAAAGAAAGAATATGATGGAAAG
|| |||| |||| || | || | ||| ||| || | || | | | |||| || ||||||||||| |||| ||||| || ||||| || || ||||||||||| ||||| |||||||||||| | || ||||| ||||| |||||||||
tctatcagtagagtagatactgttatcaggtgcctttaaaaagatgtgggacatttgtcttcaactgttggtctacttatacctctt-ttttgcattgcagTCATCAGTTCTACACTCGCAGCCGAAATCTACAGTGGGAACTCCTGCATACATTGCTCCTGAGGTTCTTCTGAAGAAGGAATACGATGGAAAG
upper sequence: AT4G33950.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G171435_T02 (Zea mays), 3'ss of exon 5
-----------------------------------gtatctttgaaaacatttcagaaactctgagttagttagtatctctaagctttgtgttttctttttcagTCATCAGTGTTACATTCGCAACCAAAATCAACTGTTGGAACTCCTGCTTACATCGCTCCTGAGGTTTTACTAAAGAAAGAATATGATGGAAAG
||| || | | |||| | | ||| || | | | || || | |||| | |||||||| || | ||||| ||||| || |||||||||||||| |||||||| || || ||||| ||| | | || |||||||||||||| |||
ggcttaatgtttacacgatagtagtagaatgatgaatatgttcatagggttgtcagtttcctt---ttaactaacaataccatgcattcttcattctctg-cagTCATCTGTTCTTCATTCCCAACCGAAGTCAACTGTTGGAACACCTGCTTATATTGCACCTGAAGTTCTGTTGAAAAAAGAATATGATGGCAAG
upper sequence: AT4G33950.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA02G15330.1 (Glycine max), 3'ss of exon 5
-----------------------------gtatctttgaaaacatttcagaaactctgagttagtt---agtatctctaagctttgtgttttctttttcagTCATCAGTGTTACATTCGCAACCAAAATCAACTGTTGGAACTCCTGCTTACATCGCTCCTGAGGTTTTACTAAAGAAAGAATATGATGGAAAG
| | ||| | || | | | |||||| | || || | | ||| || | |||||||||| |||||| ||||||| ||||||||||| || ||||| || ||||| || |||||||| || ||||| || ||||| ||||||||||| |||
taggtttctccatgtccaagatcaagcaaatttttttatctgaaatttgtagataacggattagtttgcaatacctatgcaccttg-attgtatttttcagTCTTCAGTGCTACATTCACAACCAAAATCTACAGTTGGTACCCCTGCATATATCGCTCCAGAAGTTTTGCTTAAGAAGGAATATGATGGCAAG
upper sequence: AT4G33950.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA07G33120.1 (Glycine max), 3'ss of exon 5
--------------------------------gtatctttgaaaacatttcagaaactctgagttagttagtatctctaagctttgtgttttctttttcagTCATCAGTGTTACATTCGCAACCAAAATCAACTGTTGGAACTCCTGCTTACATCGCTCCTGAGGTTTTACTAAAGAAAGAATATGATGGAAAG
| | | || | || | || | | | || | | || || | | ||| || |||||||||||| |||||| ||||||| ||||||||||| || ||||| || ||||| || || ||||| || ||||| || ||||| ||||||||||| |||
taggtttctccatgtccaagatcaagaaatttttttatctgtcatttgttgataacgtattaatttgctgatacctatgcaccttg-attgtctttttcagTCCTCAGTGCTACATTCACAACCAAAATCTACAGTTGGTACCCCTGCATATATTGCTCCAGAAGTTTTGCTTAAGAAGGAATATGATGGCAAG
upper sequence: AT4G33950.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv03s0063g01080.t01 (Vitis vinifera), 3'ss of exon 5
-------------------gtatctttgaaaacatttcagaaactctgagttagttagtatctcta-agctttgtgttt-----------tctttttcagTCATCAGTGTTACATTCGCAACCAAAATCAACTGTTGGAACTCCTGCTTACATCGCTCCTGAGGTTTTACTAAAGAAAGAATATGATGGAAAG
|| | || | | || | || || ||| | | | || | | ||| | ||| |||||| |||||| | ||||| ||||||||||| ||||||||||| ||||| ||||| |||||||| || ||||| |||||||||||||| || |||
ataaaacaattgttttgatgttcatctgttgctgcccctgcctcttcatgctattttttattttgatatctatatatttaactttggctgtttttctcagTCCTCAGTGCTGCATTCACAACCAAAATCGACTGTTGGAACCCCTGCATACATTGCTCCTGAAGTCTTACTTAAGAAAGAATATGACGGGAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atttcagaaactctgagttagttagtatctctaagctttgtgttttctttttcagTCATCAGTGTTACATTCGCAACCAAAATCAACTGTTGGAACTCCTGCTTACATCGCTCCTGAGGTTTTACTAAAGAAAGAATATGATGGAAAG
ctttgtgttttctttt CT-rich tract
ttttcttttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatctttgaaaacatttcagaaactctgagttagttagtatctctaagctttgtgttttctttttcagTCATCAGTGTTACATTCGCAACCAAAATCAACTGTTGGAACTCCTGCTTACATCGCTCCTGAGGTTTTACTAAAGAAAGAATATGATGGAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA