Sequence
atgc intronic sequence ATGC exonic sequencegtaagtctttcaatcatttcccaacagttccatttagggaacctaacatacctagtttttaatgaaggaagggctatggtttcagtatctactgattataatgaaaagcatgagttgcttatgttttcatgaaggtttaaactgttaatgttttgattttgatcagtattttatttttggttaatatattgaacagGTGAGATATCCAGTATTGCTTACACCTGCTGAAAAGCAAATGGCTAGAGAAGTTTGCATTGCATTTAGGCAAGCG
Basic information
species | Arabidopsis thaliana |
transcript | AT3G01310.2 |
intron # | 10 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G01310.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GLYMA18G49000.1 (Glycine max), 3'ss of exon 9
gtaagtctttcaatcatttcccaacagttccatttagggaacctaacatacctagtttttaatgaaggaagggctatggtttcagtatctactgattataatgaaaagcatgagttgcttatgttttcatgaaggtttaaactgttaatgttttgattttgatcagtattttatttttggttaatatattgaacagGTGAGATATCCAGTATTGCTTACACCTGCTGAAAAGCAAATGGCTAGAGAAGTTTGCATTGCATTTAGGCAAGCG
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---------------------------------------------------------------------------aagaaacaaatatttaatattcaaaa--gcaggctggagttgctggct----------ggtgtgcaacaataat-ttttcttgttgaaaaatgtctacaattt--------catttggcagGTTAGGTATCCAGTCCTCCTGACTCCTGCTGAGAAAGAAATGGCAAGAGAAGTTTGCATTGCATTCAGGCAAGCG
upper sequence: AT3G01310.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GLYMA09G37610.1 (Glycine max), 3'ss of exon 7
gtaagtctttcaatcatttcccaacagttccatttagggaacctaacatacctagtttttaatgaaggaagggctatggtttcagtatctactgattataatgaaaagcatgagttgcttatgttttcatgaaggtttaaactgttaatgttttgattttgatcagtattttatttttggttaatatattgaacagGTGAGATATCCAGTATTGCTTACACCTGCTGAAAAGCAAATGGCTAGAGAAGTTTGCATTGCATTTAGGCAAGCG
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------------------------------------------------------------------------------------gaaacaaatatttat--tcaaaaacagg-----ctggagtttctggctggtgtgcaac----aataatttaatttttcttgttgaaaaatgccta-caatttcatttggcagGTTAGGTATCCAGTCCTCCTGACTCCTGCTGAGAAAGAAATGGCAAGAGAAGTTTGCATTGCATTCAGGCAAGCG
upper sequence: AT3G01310.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GLYMA19G02260.1 (Glycine max), 3'ss of exon 7
gtaagtctttcaatcatttcccaacagttccatttagggaacctaacatacctagtttttaatgaaggaagggctatggtttcagtatctactgattataatgaaaagcatgagttgcttatgttttcatgaaggtttaaactgttaatgttttgattttgatcagtattttatttttggttaatatattgaacagGTGAGATATCCAGTATTGCTTACACCTGCTGAAAAGCAAATGGCTAGAGAAGTTTGCATTGCATTTAGGCAAGCG
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---------------------------------------------------------------------------aaggaacaaacatgtacc-attgcaaagcaggcca-gaattgcttgc-------------ttgaaacagtaa---tttaacttctgtattgaagcatgttt---atcatctcatctgacagGTTAGGTATCCAGTGTTACTGACTCCTGCTGAGAAGGAAATGGCAAGAGATGTTTGCATTGCATTCAGTCAAGCG
upper sequence: AT3G01310.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GLYMA13G05060.1 (Glycine max), 3'ss of exon 10
gtaagtctttcaatcatttcccaacagttccatttagggaacctaacatacctagtttttaatgaaggaagggctatggtttcagtatctactgattataatgaaaagcatgagttgcttatgttttcatgaaggtttaaactgttaatgttttgattttgatcagtattttatttttggttaatatattgaacagGTGAGATATCCAGTATTGCTTACACCTGCTGAAAAGCAAATGGCTAGAGAAGTTTGCATTGCATTTAGGCAAGCG
||| ||||||| | | ||| | | | || | | ||| || | | || || |||||| || |||| || | ||| || ||| | | | ||| | | ||| ||||| || |||||||| || || || |||||||| ||| ||||||| ||||| |||||||||||||| || ||||||
-----------------------------------------------gtacgaagtttttt-taatagaatgaaca-------aacatgtgcc-attgcaaagcaggcca-gaattgcttgc-------------ttgaaacagtaa---tttaacttctgaattgaagcatgttt---atcatctcatttggcaggttagGTATCCAGTGTTACTGACCCCTGCTGAGAAGGAAATGGCAAGAGATGTTTGCATTGCATTCAGTCAAGCG
upper sequence: AT3G01310.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: Vv14s0066g02540.t01 (Vitis vinifera), 3'ss of exon 9
gtaagtctttcaatcatttcccaacagttccatttagggaacctaacatacctagtttttaatgaaggaagggctatggtttcagtatctactgattataatgaaaagcatgagttgcttatgttttcatgaaggtttaaactgttaatgttttgattttgatcagtattttatttttggttaatatattgaacagGTGAGATATCCAGTATTGCTTACACCTGCTGAAAAGCAAATGGCTAGAGAAGTTTGCATTGCATTTAGGCAAGCG
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---------------------------------------------------------------------------------------------taggggaatggatagtagttccagctta-gtcctcatttttcatggggat-tgaaagaatggcctttaatacatgtttgaaatctt-ttactttgtttgacagGTAAGGTATCCTGTATTGCTGACTCCTACTGAGAAGCAAATGGCAAGGGATGTTTGCCTTGCCTTTAGGCAAGCG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctgttaatgttttgattttgatcagtattttatttttggttaatatattgaacagGTGAGATATCCAGTATTGCTTACACCTGCTGAAAAGCAAATGGCTAGAGAAGTTTGCATTGCATTTAGGCAAGCG
attttgatcagtattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagtctttcaatcatttcccaacagttccatttagggaacctaacatacctagtttttaatgaaggaagggctatggtttcagtatctactgattataatgaaaagcatgagttgcttatgttttcatgaaggtttaaactgttaatgttttgattttgatcagtattttatttttggttaatatattgaacagGTGAGATATCCAGTATTGCTTACACCTGCTGAAAAGCAAATGGCTAGAGAAGTTTGCATTGCATTTAGGCAAGCG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT