Sequence
atgc intronic sequence ATGC exonic sequencegtacctctttcttcttccaattgtgtttcatgtttcgaattctctgtagctcttgattttgaggtgtgttctcttgggtcttcttcagGGCTTTTGTTCTCTGTACTTATAACCGGTGTCATAACCGATGCTATAAAGGACGCTGTTGGTCGACCTCGTCCTGATTTCTTTTGGCGTTGTTTCCCTGA
Basic information
species | Arabidopsis thaliana |
transcript | AT1G15080.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G15080.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: LOC_Os08g27040.1 (Oryza sativa), 3'ss of exon 4
--gtacctctttctt-cttccaattgtgtttcatgtttcgaattctctgtagctcttgattttgaggtgtgttctcttgggtcttcttcagGGCTTTTGTTCTCTGTACTTATAACCGGTGTCATAACCGATGCTATAAAGGACGCTGTTGGTCGACCTCGTCCTGATTTCTTTTGGCGTTGTTTCCCTGA
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gtatacgatgctctcatttgtagatatctattgaagttacatctttggttcatgctgaaccatataatttaacca--tagagtttgtgcagGGATTCTATATTCGGTACTTATAACTGCTGTGATTACTGATGCAATTAAGGATGGTGTTGGTCGTCCTCGCCCAGATTTCTTTTGGCGTTGTTTCCCTGA
upper sequence: AT1G15080.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: LOC_Os08g27030.2 (Oryza sativa), 3'ss of exon 3
--gtacctctttcttct-tccaattgtgtttcatgtttcgaattctctgtagctcttgattttgaggtgtgttctcttgggtcttcttcagGGCTTTTGTTCTCTGTACTTATAACCGGTGTCATAACCGATGCTATAAAGGACGCTGTTGGTCGACCTCGTCCTGATTTCTTTTGGCGTTGTTTCCCTGA
|| ||| | | | | | | ||| || | ||| || | || || ||| || || || | ||||| || | | || || |||||||| | ||| || || ||||| || ||| | | ||||||||| || || || ||||||||||||||||||||||||||
gtatatggtactctcatatgtagatatctatcaaattacactttcacttttttagttcatgctgaactggacact--------ttgtacagGGATTCTATATTCGGTGCTTATAACTGCTGTGATTACTGATGCAATTAAGAATGGTGTTGGTCGCCCACGCCCAGATTTCTTTTGGCGTTGTTTCCCTGA
upper sequence: AT1G15080.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: LOC_Os01g49820.1 (Oryza sativa), 3'ss of exon 3
gtacctctttcttcttccaattgtgtttcatgtttcgaattctctgtagctcttgattt-tgaggtgtgttctcttgggtcttcttcagGGCTTTTGTTCTCTGTACTTATAACCGGTGTCATAACCGATGCTATAAAGGACGCTGTTGGTCGACCTCGTCCTGATTTCTTTTGGCGTTGTTTCCCTGA
|| | ||||| | ||| ||||| | || | | | || | | | |||| | | || || | | |||| || | || || || ||||| || | || ||||| ||||| || || || | ||||||||||| ||||| |||||||||||||| ||||| |||||
gtgagctcatgttctttctattctgttttgttttgctagt-ctacacattttgtaatttcttatctgaaacctagcaatgcccttgcagGTCTCCTATTTTCAGTTCTTATCACGGCGGTAATAACTGATGCCATTAAAGATGGGGTTGGTCGACCGCGTCCAGATTTCTTTTGGCGCTGTTTTCCTGA
upper sequence: AT1G15080.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G077187_T01 (Zea mays), 3'ss of exon 3
gtacctctttcttcttccaattgtgtttcatgtttcgaattctctgtagctcttgattttgaggtgtgttctcttgggtcttcttcagGGCTTTTGTTCTCTGTACTTATAACCGGTGTCATAACCGATGCTATAAAGGACGCTGTTGGTCGACCTCGTCCTGATTTCTTTTGGCGTTGTTTCCCTGA
|||| | |||| | | | |||| ||| | || | | ||| ||| | | | ||| | |||| || | || || |||||||| || | ||| |||| ||||| |||||||| | |||||| ||||| |||||||||||||| |||||||| ||||||||
gtacattcactttctcgcca----gattcactattctactttatcaatattacttattctgaaatctaactt-----gtcctgg-cagGTCTCCTATTTTCAGTACTTATTACTGCTGTTTTAACTGATGCGATAAAGGATGGTGTTGGGCGACCACGTCCTGATTTCTTCTGGCGTTGCTTCCCTGA
upper sequence: AT1G15080.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G447433_T08 (Zea mays), 3'ss of exon 5
gtacctctttcttcttccaattgtgtttcatgtttcgaa----ttctctgt-agctcttgattttgaggtgtgttct-cttgggtcttcttcagGGCTTTTGTTCTCTGTACTTATAACCGGTGTCATAACCGATGCTATAAAGGACGCTGTTGGTCGACCTCGTCCTGATTTCTTTTGGCGTTGTTTCCCTGA
|| | | || || || | ||| | | |||| | | |||| ||| | | ||| | |||| || || |||||||| | ||| || || ||||| || ||||| | ||||||||| ||||| || |||||||||||||||||||| |||||
----------------------gtacctgacattctaaacatgttatttgtcaattgacagttttaatttatgttgaacttaaaaaatatgtagGTATCTTGTATTCAGTGCTTATAACTGCTGTGATCACTGATGCAATTAAGGATGGTGTTGGTCGCCCTCGGCCAGATTTCTTTTGGCGTTGTTTTCCTGA
upper sequence: AT1G15080.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA09G18450.2 (Glycine max), 3'ss of exon 3
gtacctctttcttcttccaattgtgtttcatgtttcgaattctctgtagct---cttgattttgaggtgtgttctcttgggt-cttcttcagGGCTTTTGTTCTCTGTACTTATAACCGGTGTCATAACCGATGCTATAAAGGACGCTGTTGGTCGACCTCGTCCTGATTTCTTTTGGCGTTGTTTCCCTGA
|||| | | | | || | | || | | || | | || || | | | | ||| | | | | |||||| ||||| || |||||||| || || | || ||||| |||||||| || || | |||||| || || || || |||||||| |||||||||||||||||
gtacttttctgtcttttagaaacttttcctaaccttattttgcatatcactttgctatagcctaacctatgtattgccaaatgcatattcagGCCTTTTATTTTCTGTACTCATTACTGCGGTGATAACGGATGCTATCAAAGATGGTGTTGGACGGCCACGCCCAGATTTCTTCTGGCGTTGTTTCCCTGA
upper sequence: AT1G15080.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv01s0011g04180.t01 (Vitis vinifera), 3'ss of exon 2
gtacctctttcttc-ttccaattgtgtttcatgtttcgaattctctgtagctcttgatt--ttgaggtgtgttctcttgggtcttcttcagGGCTTTTGTTCTCTGTACTTATAACCGGTGTCATAACCGATGCTATAAAGGACGCTGTTGGTCGACCTCGTCCTGATTTCTTTTGGCGTTGTTTCCCTGA
||| | |||| | | |||| | | || || | | | | | || || | ||| || | | | | | || ||| ||| | ||||||||||| || || | || ||||| ||||| || || || |||||||| ||||||||||| || ||||||||||||||||||||| |
gtatcactttttcccttcctagatttctttgagtcaggtactgttgtttccttgtggtgcattgcttaatggattatgtgtgcatgtttagGCCTTCTATTCTCTGTACTGATCACGGCAGTTATAACTGATGCAATTAAAGATGCTGTTGGCCGACCTCGTCCAGACTTCTTTTGGCGTTGTTTCCCTAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttcgaattctctgtagctcttgattttgaggtgtgttctcttgggtcttcttcagGGCTTTTGTTCTCTGTACTTATAACCGGTGTCATAACCGATGCTATAAAGGACGCTGTTGGTCGACCTCGTCCTGATTTCTTTTGGCGTTGTTTCCCTGA
tcttgat putative branch site (score: 4)
tcttcttc putative PPT
ttgatttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtacctctttcttcttccaattgtgtttcatgtttcgaattctctgtagctcttgattttgaggtgtgttctcttgggtcttcttcagGGCTTTTGTTCTCTGTACTTATAACCGGTGTCATAACCGATGCTATAAAGGACGCTGTTGGTCGACCTCGTCCTGATTTCTTTTGGCGTTGTTTCCCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT