Sequence
atgc intronic sequence ATGC exonic sequencegtaagcaacctctacacatatccatcactgaaatatttgaatcctttcccggtagctatagttgttaaaagctcttatctttcttccacttttctttttgttaccgcagATGTTTACTCAGCTTCACTTCTCATATGAACAAGAGAGCCACCCGGAAGAGTTTTTTATTCCATATGTTTGGCAACTAGCTTTTTCCCGATG
Basic information
species | Arabidopsis thaliana |
transcript | AT1G04200.1 |
intron # | 15 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G04200.1 (Arabidopsis thaliana), 3'ss of exon 15
lower sequence: GLYMA10G00550.1 (Glycine max), 3'ss of exon 15
gtaagcaacctctacacatatccatcactgaaatatttgaatcctttcccggtagctatagttgttaaaagctcttatctttcttccacttttctttttgttacc--gcagATGTTTACTCAGCTTCACTTCTCATATGAACAAGAGAGCCACCCGGAAGAGTTTTTTATTCCATATGTTTGGCAACTAGCTTTTTCCCGATG
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----gtaaaatgaaaatttgt--gttattcgtgc-tttacacccaata--ggtaataaca-ttaggaggattacctgtctcacttctacaagactatatcttgtttggcagATGTTTACTCAACTTCATTTCACATATGAACAAGAGAGTCACCCAGAGGAGTTTTTTATCCCATATGTCTGGCAGCTAGTACTATCCAGATG
upper sequence: AT1G04200.1 (Arabidopsis thaliana), 3'ss of exon 15
lower sequence: GLYMA15G24080.1 (Glycine max), 3'ss of exon 17
gtaagcaacctctacacatatccatcactgaaatatttgaatcctttcccggtagctatagttgttaaaag---ctcttatctttcttccact--tttctttttgttaccgcagATGTTTACTCAGCTTCACTTCTCATATGAACAAGAGAGCCACCCGGAAGAGTTTTTTATTCCATATGTTTGGCAACTAGCTTTTTCCCGATG
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----gtaaaatgaaaata-----atttgtgtgatttgtgc-tttactcccaataggtaataacattaggaggattacctgccttacttctacaagactatatcttttttggcagATGTTTACTCAACTTCACTTCACATATGAACAAGAGAGTCACCAAGAGGAGTTCTTTATCCCATATGTCTGGCAGCTAGTACTATCCAGACG
upper sequence: AT1G04200.1 (Arabidopsis thaliana), 3'ss of exon 15
lower sequence: GLYMA20G28880.1 (Glycine max), 3'ss of exon 14
gtaagcaacctctacacatatccatcactgaaatatttgaatcctttcccggtagctatagttgttaaaagctcttatctttcttccacttttctttttgttaccgcagATGTTTACTCAGCTTCACTTCTCATATGAACAAGAGAGCCACCCGGAAGAGTTTTTTATTCCATATGTTTGGCAACTAGCTTTTTCCCGATG
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----gtaagatggaaatatattttttgatttgtggtttgcttccagtgtggaataccattaggtggattatttgtcttatttctatgaggctgtatcttgtttgt-cagATGTTTACTCAACTGCGCTTCACATATGAACAAGAGAGTCATCCAGAGGAGTTTTTTATCCCATATGTCTGGCAGCTAGTTCTATCCCATTG
upper sequence: AT1G04200.1 (Arabidopsis thaliana), 3'ss of exon 15
lower sequence: GLYMA10G38920.2 (Glycine max), 3'ss of exon 15
gtaagcaacctctacacatatccatcactgaaatatttgaatcctttcccggtagctatagttgttaaaagctcttatctttcttccacttttctttttgttaccgcagATGTTTACTCAGCTTCACTTCTCATATGAACAAGAGAGCCACCCGGAAGAGTTTTTTATTCCATATGTTTGGCAACTAGCTTTTTCCCGATG
| || | | | |||| | | |||| ||| | | | || | | | | | | | ||||| | | | ||||| |||||||||||||| || | |||| |||||||||||||||| || || || ||||||||||| |||||||| ||||| |||| | ||||| ||
----gtaagatggaaatatattttttgatttgtggtttgcttccagtgtggaataccat--taggtggattttgtcttgtttctatgaggctgtatcttgtttgt-cagATGTTTACTCAACTGCGCTTCACATATGAACAAGAGAGTCATCCAGAGGAGTTTTTTATCCCATATGTCTGGCAGCTAGTGCTATCCCGTTG
upper sequence: AT1G04200.1 (Arabidopsis thaliana), 3'ss of exon 15
lower sequence: Vv05s0020g04100.t01 (Vitis vinifera), 3'ss of exon 15
-------gtaagcaacctctacacatatcca-tcactgaaatatttgaatcctttcccggtagctatagttgttaaaagctcttatctt-tcttccacttttctttttgttaccgcagATGTTTACTCAGCTTCACTTCTCATATGAACAAGAGAGCCACCCGGAAGAGTTTTTTATTCCATATGTTTGGCAACTAGCTTTTTCCCGATG
| || | || | || | | ||| |||||| | || | ||| | | |||||| | | | |||| |||| ||||||||||| || | | |||| ||||||||||||||||||| || || ||||| ||||| || ||||| ||||| |||| | | ||||| ||
gtaaaaggcaattggttgttgagcaattacagttgttccaattaatgaatcttatctgaaaggttatgttc--------cacttatcacgtaatataaatttccgtttg-----acagATGTTTACACAATTACGCTTCACATATGAACAAGAGAGCCATCCAGAGGAGTTCTTTATCCCCTATGTGTGGCAGCTAGTTCTATCCCGCTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gctatagttgttaaaagctcttatctttcttccacttttctttttgttaccgcagATGTTTACTCAGCTTCACTTCTCATATGAACAAGAGAGCCACCCGGAAGAGTTTTTTATTCCATATGTTTGGCAACTAGCTTTTTCCCGATG
ctcttatctttcttcc CT-rich tract
ttttctttttgtta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagcaacctctacacatatccatcactgaaatatttgaatcctttcccggtagctatagttgttaaaagctcttatctttcttccacttttctttttgttaccgcagATGTTTACTCAGCTTCACTTCTCATATGAACAAGAGAGCCACCCGGAAGAGTTTTTTATTCCATATGTTTGGCAACTAGCTTTTTCCCGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA