Sequence
atgc intronic sequence ATGC exonic sequencegtactaatccctcttttgactataattttttcgccgtttcttgctttattttgaagttctctttattgcgtataatttatttatttcttttgtcagGTGAACTGTAGAAGGGCTGCTGCCGCTGCTTTCCAAGAGAATGTTGGAAGACAAGGAAATTACCCTCATGGGATTGACATAGTGAGCATAGCTGATTATT
Basic information
species | Arabidopsis thaliana |
transcript | AT3G60740.1 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G60740.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: LOC_Os10g36490.1 (Oryza sativa), 3'ss of exon 7
-------gtactaatccctcttttgactataattttttcgccgtttcttgctttattttgaagttctctttattgcgtataatttatttatttcttttgtcagGTGAACTGTAGAAGGGCTGCTGCCGCTGCTTTCCAAGAGAATGTTGGAAGACAAGGAAATTACCCTCATGGGATTGACATAGTGAGCATAGCTGATTATT
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ttcatttgtggca-tctagattttgtgatgcattctctagcatcttagtattttttttcttactgccgaatcatgtgtgtc-cttatacatatatgatgt-agGTTAATTGCAGAAGAGCTGCTTCTGCTGCCTTTCAAGAGAATGTTGGAAGACAGGGAAATTTTCCGCATGGCATTGATATTGTGAATGCAGCAGACTACT
upper sequence: AT3G60740.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GRMZM2G303758_T01 (Zea mays), 3'ss of exon 1
gtactaatccctcttttgactataattttttcgccgtt--tcttgctttattttgaagttctc-tttattgcgtataatttatttatttcttttgt--cagGTGAACTGTAGAAGGGCTGCTGCCGCTGCTTTCCAAGAGAATGTTGGAAGACAAGGAAATTACCCTCATGGGATTGACATAGTGAGCATAGCTGATTATT
| | | | | | | | || | | | || |||||||| || ||||| | ||| || | | | | | |||| || |||||||| |||||| | ||||| || |||||||||||||||||||| |||| || ||| ||||| ||||| || |||| | | ||||| |
-aatttacatttgtcgcacccaaatgttctgtacttctgatcccatactattttgactacatcatttatcttactgatttttattgtctatgtaatagtagGTTAATTGTAGAAGAGCTGCTTCTGCTGCCTTTCAAGAGAATGTTGGAAGACAGGGAACTTTCCCACATGGCATTGATATTGTGAATACGACAGATTACT
upper sequence: AT3G60740.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA10G42560.1 (Glycine max), 3'ss of exon 8
gtactaatccctcttttgactataattttttcgccgtttcttgctttattttgaa--gttctctttat-tgcgtataatttatttatttcttttg----tcagGTGAACTGTAGAAGGGCTGCTGCCGCTGCTTTCCAAGAGAATGTTGGAAGACAAGGAAATTACCCTCATGGGATTGACATAGTGAGCATAGCTGATTATT
||| | || | || | | | | | || ||| |||| | ||| ||| || || | ||| | | | | || | |||| ||||| ||||| || || || |||||||| ||||||||||||||||||||||| ||||| || ||||| ||||||||||||| | || |||||||
---------gtccttatatcttttatgtccttctcatgacatgatttgttttagactattcacttcatgtgaaaagaatccctaactaacctgtgatacttagGTTAACTGCAGAAGAGCAGCAGCAGCTGCTTTTCAAGAGAATGTTGGAAGACAAGGGAATTATCCACATGGAATTGACATAGTGAATACTGCGGATTATT
upper sequence: AT3G60740.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA20G24470.1 (Glycine max), 3'ss of exon 9
gtactaatccctcttttgactataattttttcgccgtttcttgctttattttgaa--gttctctttat-tgcgtataat---ttatttatttcttttg-tcagGTGAACTGTAGAAGGGCTGCTGCCGCTGCTTTCCAAGAGAATGTTGGAAGACAAGGAAATTACCCTCATGGGATTGACATAGTGAGCATAGCTGATTATT
||| | || | || | | | | | || ||| |||| | ||| ||| || || | ||| | | | | | | | | |||| ||||| ||||| || || || |||||||| ||||||||||||||||||||||| ||||| || |||| ||||||||||||| | || |||||||
---------gtccttatatcttttatgtccttctcatgacatgatttgttttagactattcacttcatgtgaaaagaatcgctaactaacctgtgatacttagGTTAACTGCAGAAGAGCAGCAGCTGCTGCTTTTCAAGAGAATGTTGGAAGACAAGGGAATTATCCAAATGGAATTGACATAGTGAATACTGCAGATTATT
upper sequence: AT3G60740.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: Vv15s0048g00470.t01 (Vitis vinifera), 3'ss of exon 8
--gtactaatccctcttttgactataattttttcgccgtttctt----gctttattttgaagttctctttattgcgtataatttatttatttctt--ttgtcagGTGAACTGTAGAAGGGCTGCTGCCGCTGCTTTCCAAGAGAATGTTGGAAGACAAGGAAATTACCCTCATGGGATTGACATAGTGAGCATAGCTGATTATT
||| ||| | ||| | | | | | || |||| || | ||| | | | | | | | ||| | || |||||| ||||||||||| || ||||| ||||| |||||||||||||||||||||||||| || ||||| ||||| ||||||||||||| ||||| ||||
gtgtattaaattttgttt--gttttgttccatacacctcctctttgagatattgtcatgattatgttgtacctccatgcgaagcttttgacatgtaattctcagGTTAACTGTAGAAGAGCAGCTGCAGCTGCCTTCCAAGAGAATGTTGGAAGACAAGGGAACTACCCACATGGAATTGACATAGTGAATGCCGCTGACTATT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgctttattttgaagttctctttattgcgtataatttatttatttcttttgtcagGTGAACTGTAGAAGGGCTGCTGCCGCTGCTTTCCAAGAGAATGTTGGAAGACAAGGAAATTACCCTCATGGGATTGACATAGTGAGCATAGCTGATTATT
tttatttatttctttt CT-rich tract
tttattgcgtataatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtactaatccctcttttgactataattttttcgccgtttcttgctttattttgaagttctctttattgcgtataatttatttatttcttttgtcagGTGAACTGTAGAAGGGCTGCTGCCGCTGCTTTCCAAGAGAATGTTGGAAGACAAGGAAATTACCCTCATGGGATTGACATAGTGAGCATAGCTGATTATT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT