Sequence
atgc intronic sequence ATGC exonic sequencegtaagtgtattatcctggtttctaaacatgcaatctcggatgagtgcggaaagaaatcacatttatgtaaatttttcatcagcaagatatgatatttatttgcagCATTTGAAGGAAGACATGAAGCTGAGTTACTTGGCTCAGGAACTAATATCAACCGATCGCTTAGCTCCTCAATCTTG
Basic information
species | Arabidopsis thaliana |
transcript | AT2G20000.1 |
intron # | 11 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT2G20000.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GLYMA13G07140.1 (Glycine max), 3'ss of exon 13
gtaagtgtattatcctggtttctaaacatgcaatctcggatgagtgcggaaagaaatcacattt-atgtaaatttttcatcagcaagata-tgatatttatttgcagCATTTGAAGGAAGACATGAAGCTGAGTTACTTGGCTCAGGAACTAATATCAACCGATCGCTTAGCTCCTCAATCTTG
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--acctagaatatccttgtatttc----tttagcttcttccccccacttaaaagtttaaaattttaaatgattactacatgacgaactgacttatatctggt-gcagCATTTAAAGGAAGATATGAAGCTAAGTTACCTGGCACAGGAACTGATTTCAACTGATCGCTTAGCTCCTCAATCTTG
upper sequence: AT2G20000.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GLYMA19G05640.1 (Glycine max), 3'ss of exon 11
gtaagtgtattatcctggtttctaaacatgcaatctcggatgagtgcggaaagaaatcacatttatgtaaatttttcatcagcaagatatgatatttatttgcagCATTTGAAGGAAGACATGAAGCTGAGTTACTTGGCTCAGGAACTAATATCAACCGATCGCTTAGCTCCTCAATCTTG
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--ctttgtatttctttagcttcttccc-tccacttaaagtttaaaattttaaatgattacttggatgtttactacatgacgaactgacttataactggt--gcagCATTTAAAGGAAGATATGAAGCTAAGTTACCTGGCACAGGAATTGATTTCAACTGATCGCTTAGCTCCTCAATCTTG
upper sequence: AT2G20000.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GLYMA08G28550.1 (Glycine max), 3'ss of exon 11
gtaagtgtattatcctggtttctaaacatgcaatctcggatgagtgcggaaagaaatcacatttatgtaaatttttcatcagcaagatatgatatttatt-tgcagCATTTGAAGGAAGACATGAAGCTGAGTTACTTGGCTCAGGAACTAATATCAACCGATCGCTTAGCTCCTCAATCTTG
||| || | | || || | | | ||| | | ||| | || | || | || ||| | | ||||||| | |||||||| |||||| | |||||| ||||||||||||| |||||||| ||||| |||||||||||||||||
-----tgtctttctttagcttgctgcttctatttcatgtctaatcattgaatacatgtctgcatgcgtag-tgcttgaccaaaagactaacttatctctggtgcagCACCTAAAGGAAGATATGAAGTTAAGTTACCTGGCTCAGGAACTGATATCAACTGATCGTTTAGCTCCTCAATCTTG
upper sequence: AT2G20000.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GLYMA18G51450.1 (Glycine max), 3'ss of exon 11
gtaagtgtattatcctggtttctaaacatgcaatctcggatgagtgcggaaagaaatcacatttatg-taaatttttcatcagcaagatatgatatttatt-tgcagCATTTGAAGGAAGACATGAAGCTGAGTTACTTGGCTCAGGAACTAATATCAACCGATCGCTTAGCTCCTCAATCTTG
||| || | | ||| || | | | ||| ||| | | | ||| | ||| || | || | || ||| | | ||||||| || |||||||| |||||| | |||||| ||||||||||||| | ||||| |||||||||||||||||||||||
-----tgtctttctttagcttcctgcttctatttcatgtctaattgctgaataca--tatctgcatgcttaatgcttgaccaaaagactaacttatctctggtgcagCACTTAAAGGAAGATATGAAGTTAAGTTACCTGGCTCAGGAACTGGTTTCAACTGATCGCTTAGCTCCTCAATCTTG
upper sequence: AT2G20000.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: Vv11s0016g03260.t01 (Vitis vinifera), 3'ss of exon 11
gtaagtgtattatcctggtttctaaacat-gcaatctcggatgagtgcggaaagaaatcacatttatgtaaatttttcatcagcaagatatgatatttatt--tgcagCATTTGAAGGAAGACATGAAGCTGAGTTACTTGGCTCAGGAACTAATATCAACCGATCGCTTAGCTCCTCAATCTTG
| | | || |||| || | ||| || | | | | | || ||| | | || || || | ||| || | | || |||||||||||| |||||| |||||||| |||||| ||||||| ||||||||||| || ||||||||||||||||| |||||
----gcaatcttgctggggttctgtttattgaaatagcgtttatattttcctacatgt---atgtatttca-ttgtttttctgtaagtcattctttcccttgttgcagCATTTGAGGGAAGATATGAAGCTAAGTTACCTGGCTCAAGAACTAATATCCACAGATCGCTTAGCTCCTCAGTCTTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aagaaatcacatttatgtaaatttttcatcagcaagatatgatatttatttgcagCATTTGAAGGAAGACATGAAGCTGAGTTACTTGGCTCAGGAACTAATATCAACCGATCGCTTAGCTCCTCAATCTTG
tttattt CT-rich tract
atcacatttatgtaaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagtgtattatcctggtttctaaacatgcaatctcggatgagtgcggaaagaaatcacatttatgtaaatttttcatcagcaagatatgatatttatttgcagCATTTGAAGGAAGACATGAAGCTGAGTTACTTGGCTCAGGAACTAATATCAACCGATCGCTTAGCTCCTCAATCTTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC