Sequence
atgc intronic sequence ATGC exonic sequencegttagcgtgtttttcgcttttttatcatttagtggttcagtgtcatatacctttgcccttttttccaactggtagttttaatatgttttgaatttttattaaaccacgcagATACGATCCATGGTTGAAGCAAGCACTTCTGATTATGACAAGGAGAAGTTGCAAGAAAGGTTGGCTAAGCTTTCGGGTGGTGTTGCTGTACTAAAG
Basic information
species | Arabidopsis thaliana |
transcript | AT2G33210.2 |
intron # | 11 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT2G33210.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: LOC_Os10g32550.1 (Oryza sativa), 3'ss of exon 12
gttagcgtgtttttcgcttttttatcatttagtggttcagtgtcatatacctttgcccttttttccaactggtagtt-ttaatatgttttgaatttttattaaaccacgcagATACGATCCATGGTTGAAGCAAGCACTTCTGATTATGACAAGGAGAAGTTGCAAGAAAGGTTGGCTAAGCTTTCGGGTGGTGTTGCTGTACTAAAG
| | | | |||| | | || || ||| ||| | |||| || | || ||| || ||| || || | || |||||| |||| |||| |||||||||||||||||||||||| ||| | || || ||||||| ||||| || || ||||||||||| ||||||
---------------gttcgtacaacattaattcattgcgt------tactagtgcattattttgaaaatcgtggttgttgatagatt----atataaatgctgtgttgcagATTAGATCTGCAATTGAGCTAAGCACTTCTGATTATGACAAGGAAAAGCTACAGGAGCGGTTGGCAAAGCTCTCCGGAGGTGTTGCTGTTCTAAAG
upper sequence: AT2G33210.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: LOC_Os03g04970.1 (Oryza sativa), 3'ss of exon 12
gttagcgtgtttttcgcttttttatcatttagtggttcagtgtcatatacctttgcccttttttccaactggtagttttaatatgttttgaatttttattaaaccacgcagATACGATCCATGGTTGAAGCAAGCACTTCTGATTATGACAAGGAGAAGTTGCAAGAAAGGTTGGCTAAGCTTTCGGGTGGTGTTGCTGTACTAAAG
| || | ||| |||| || || || | | | || |||||| || |||| | | | |||| || || ||| ||| | |||| |||| |||||||||||| ||||| || |||||| | || || |||| || |||||||| |||||||||||||| ||||||
----gttcattctatgctagtttacttttacatga---agccacgtgtgtctcactaaatttttctaa-tggtgacaccactgta----aaattcttttt---cca-acagCTGAGATCTGCAATTGAGCTAAGCACTTCTGACTATGATAAAGAGAAGCTTCAGGAGCGGTTAGCAAAGCTTTCTGGTGGTGTTGCTGTTCTAAAG
upper sequence: AT2G33210.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GRMZM2G416120_T01 (Zea mays), 3'ss of exon 11
gttagcgtgtttttcgcttttttatcatttagtggttcagtgtcatatacctttgcccttttttccaactggtagttttaatatgttttgaatttttattaaaccacgcagATACGATCCATGGTTGAAGCAAGCACTTCTGATTATGACAAGGAGAAGTTGCAAGAAAGGTTGGCTAAGCTTTCGGGTGGTGTTGCTGTACTAAAG
|| || | ||| ||| || || | || | | || ||| |||| | ||| || ||| || || || ||| | | |||||| |||| ||||| |||||||| |||||||||||||| ||| | || ||| ||||||| ||||| || || ||||||||||| || |||
---------gttcgtgcaatattac--ttttgttgtgctgtcttaaattgcttctaactttctggtt-ctgataattt--atggattatggattat----ggatgttgcagATTAGATCAGCAGTTGAGAACAGCACTTCAGATTATGACAAGGAAAAGCTCCAGGAACGGTTGGCAAAGCTCTCTGGAGGTGTTGCTGTTCTGAAG
upper sequence: AT2G33210.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GLYMA10G33680.1 (Glycine max), 3'ss of exon 12
gttagcgtgtttttcgcttttttatcatttagtggttcagtgtcatatacctttgcccttttttccaactggtagtt-ttaatatgttttgaattttt----------attaaaccacgcagATACGATCCATGGTTGAAGCAAGCACTTCTGATTATGACAAGGAGAAGTTGCAAGAAAGGTTGGCTAAGCTTTCGGGTGGTGTTGCTGTACTAAAG
|| | || | | | | |||| | || | | | | | | | | ||| | | ||| || || || || | |||| | ||| ||| | || |||||| |||| ||||| |||||||| |||||||||||||| ||||| || ||||| || || |||||||| || |||||||| ||||| |||
gtctgtttgaatcttccactattattaatttttattctaccattgttggtgtattctgtttcatgta-ctgatacttattgatgttttttacttgtttcttgtgatgaattttaacaagcagATTAGATCAGCAATTGAAAATAGCACTTCAGATTATGACAAGGAAAAGTTACAGGAAAGATTAGCCAAGCTTTCTGGGGGTGTTGCAGTACTGAAG
upper sequence: AT2G33210.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GLYMA20G33910.1 (Glycine max), 3'ss of exon 12
----gttagcgtgtttttcgcttttttatcatttagtggttcagtgtcatatacctttgc-ccttttttccaactggtagttttaatatgttttgaatt-tttattaaaccacgcagATACGATCCATGGTTGAAGCAAGCACTTCTGATTATGACAAGGAGAAGTTGCAAGAAAGGTTGGCTAAGCTTTCGGGTGGTGTTGCTGTACTAAAG
||| | | || |||||||| | | ||| |||| | | ||| | | | | || | |||| | ||||| | | ||| | || ||||| |||| ||||| |||||||| |||||||||||||| ||||| || ||||| || || |||||||| || |||||||| ||||| |||
gtctgtttgaatcttacattattttttattctaccattgtt-ggtgtattctgtcttcatgtactgatacttattgatgtttttgacttgtttcttgtgatgaattttaacaaacagATTAGATCAGCAATTGAAAATAGCACTTCAGATTATGACAAGGAAAAGTTACAGGAAAGATTAGCCAAGCTTTCTGGGGGTGTTGCAGTACTGAAG
upper sequence: AT2G33210.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GLYMA10G25630.1 (Glycine max), 3'ss of exon 12
gttagcgtgtttttcgcttttttatcatttagtggttcagtgtcatatacctttgccctttttt-ccaactggtagttttaatatgttttgaatttttattaaaccacgcagATACGATCCATGGTTGAAGCAAGCACTTCTGATTATGACAAGGAGAAGTTGCAAGAAAGGTTGGCTAAGCTTTCGGGTGGTGTTGCTGTACTAAAG
||| | || ||| ||| | | |||| | | ||| | || | | || | | | ||||| || | || | | ||||| | || ||||| ||||| || |||||||||||||| ||||| || ||||| || || |||||||| ||||||||||| || || |||
gtttgagttgatttatagatttggttttcccatggtattctatttccaccctaggatctgtaaggtttaatgatgcacctgacttgtttgtgatgaattttga--taaacagATTAGGTCTGCAATTGAAAACAGCACCTCAGATTATGACAAGGAAAAGTTACAGGAAAGATTAGCCAAGCTTTCTGGTGGTGTTGCCGTGCTTAAG
upper sequence: AT2G33210.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GLYMA20G19980.1 (Glycine max), 3'ss of exon 12
gttagcgtgtttttcgcttttttatcatttagtggttcagtgtcatatacctttgcccttttttccaactggtagttttaatatgttttgaatttttattaaaccacgcagATACGATCCATGGTTGAAGCAAGCACTTCTGATTATGACAAGGAGAAGTTGCAAGAAAGGTTGGCTAAGCTTTCGGGTGGTGTTGCTGTACTAAAG
||| | || ||| ||| || | || | | | ||| | | | | | || | ||| ||||| || | || | | ||||| | || ||||| || || || |||||||||||||| ||||| || ||||| || || |||||||| ||||||||||| || || |||
gtttgagttgatttatacatttggtcccgt-gtattctatttccatccaa--tgatctgtaaggtttaatgatgcacctaacttgtttgtgatgaattttga--taaacagATTAGGTCAGCAATTGAAAACAGTACCTCAGATTATGACAAGGAAAAGTTACAGGAAAGATTAGCCAAGCTTTCTGGTGGTGTTGCAGTGCTTAAG
upper sequence: AT2G33210.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: Vv05s0051g00340.t01 (Vitis vinifera), 3'ss of exon 12
----------------------------------------------gttagcgtgtttttcgcttttttatcatttagtggttcag-tgtcatatacctttgcccttttttc----caactggtagttttaatatgttttg----------aatt---tttattaaaccac---------gcagATACGATCCATGGTTGAAGCAAGCACTTCTGATTATGACAAGGAGAAGTTGCAAGAAAGGTTGGCTAAGCTTTCGGGTGGTGTTGCTGTACTAAAG
||| | ||| | ||||| | || | || || | |||| | ||| || | || | ||| || | ||| |||| |||| |||| || ||| || |||||| | || ||||| ||||||||||||||||||||||| |||||||||||||||||||| |||||||| |||||||||||||| | |||
gtccatattactttcttctcacatgttatttagaatctcctgattctttattctttttctttcttttct-tctctggatgattgatctgtcgattggtttttccttcattgcgaagcaaatgccaaattttatatatttttttcatgttgtaattggattcatttggttacattgggatggcagATTAGGTCAGCCATTGAATTGAGCACTTCTGATTATGACAAGGAAAAGTTGCAAGAAAGGTTGGCCAAGCTTTCTGGTGGTGTTGCTGTCTTGAAG
upper sequence: AT2G33210.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: PP1S52_245V6.1 (Physcomitrella patens), 3'ss of exon 12
--gttagcgtgtttttcgcttttttatcatttagtggttcagtgtcatatacctttgcccttttttccaactggtagttttaatatgttttgaatttttattaaaccacgcagATACGATCCATGGTTGAAGCAAGCACTTCTGATTATGACAAGGAGAAGTTGCAAGAAAGGTTGGCTAAGCTTTCGGGTGGTGTTGCTGTACTAAAG
| | ||| |||| | |||| | || || | | || | | | | || || | | ||| ||| ||||||| ||| | | ||||||||||| |||||||| ||||||||||| ||||||||||| | || || ||||||||||| || |||
gtgccaatatgtcccgtgcttgtggtgaattt-----tcttacaacacatttcatagcgatcgtggttatgtactaccatttg-acgaagaaaatgttttc-------cgcagATCCGAGAGGCTATCAACAGCGCAACTTCTGATTACGACAAGGAAAAGTTGCAAGAGAGGTTGGCTAAATTATCAGGGGGTGTTGCTGTGCTCAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ccttttttccaactggtagttttaatatgttttgaatttttattaaaccacgcagATACGATCCATGGTTGAAGCAAGCACTTCTGATTATGACAAGGAGAAGTTGCAAGAAAGGTTGGCTAAGCTTTCGGGTGGTGTTGCTGTACTAAAG
ttttaat putative branch site (score: 3)
tggtagttttaatatg 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttagcgtgtttttcgcttttttatcatttagtggttcagtgtcatatacctttgcccttttttccaactggtagttttaatatgttttgaatttttattaaaccacgcagATACGATCCATGGTTGAAGCAAGCACTTCTGATTATGACAAGGAGAAGTTGCAAGAAAGGTTGGCTAAGCTTTCGGGTGGTGTTGCTGTACTAAAG
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- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA