Sequence
atgc intronic sequence ATGC exonic sequencegttagtctttgcaaaggctacacagctttttaactgtttgtttacaattgcttctctctttgtgtgtactttgttctttttgattggtgtcaaatggttagagcaatgctttgattatattgggaacgcattaataagtgtatggaccttttttctatgcgttcgcggatggcagGTGAAAAGTCCAAAGATGGGGGTTCGGTTTCAAAGAAGGGGAGTAG
Basic information
species | Arabidopsis thaliana |
transcript | AT5G25060.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G25060.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: LOC_Os02g08360.1 (Oryza sativa), 3'ss of exon 3
gttagtctttgcaaaggctacacagctttttaactgtttg-tttacaattgcttctctctttgtgtgtactttgttctttttgattggtgtcaaatggt--tagagcaatgctttgattatattgggaacgcattaataagtgtatggacct-tttttctatgcgttcgcggatggcagGTGAAAAGTCCAAAGATGGGGGTTCGGTTTCAAAGAAGGGGAGTAG
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----------------------------gttagtgatatggtttacattttcatataccttgttgtagttggctttactctttgtagattgaaaatcatgatggatatatacattgtttcttct---attgctccaattaatcaagagaccggcctttttattcattcggcaatggcagGTGGAAAGTCCAAAGATGGGGGGTCTGTTCCAAAGAAGGGCAGTAG
upper sequence: AT5G25060.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G174785_T01 (Zea mays), 3'ss of exon 3
gttagtctttgcaaaggctacacagctttttaactgtttgtttacaattgc-ttctctctttgtgtgtactttgttctttttgattggtgtcaaatggttagagcaatgctttgattatattgggaacgcattaataagtgtatggaccttttttctatgcgttcgcggatggcagGTGAAAAGTCCAAAGATGGGGGTTCGGTTTCAAAGAAGGGGAGTAG
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gttagtg---gaaggggtttca----tttttgcatactttctcatagttgccttcccactctgtagtttcaatatcttccaagatggatat----------atgcattgtttcttttatc----gctccaattgatcaagagatcggccttttt---attcattcggcaatggcagGTGGAAAATCCAAAGATGGGGGGTCTGTTCCAAAGAAGGGCAGTAG
upper sequence: AT5G25060.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G133308_T02 (Zea mays), 3'ss of exon 3
gttagtctttgcaaaggctacacagctttttaactgtttgtttacaattgcttctctctttgtgtgtactttgttctttttgattggtgtcaaatggttaga-gcaatgctttgattatattgggaacgcattaataagtgtatggaccttttttctatgcgttcgcggatggcagGTGAAAAGTCCAAAGATGGGGGTTCGGTTTCAAAGAAGGGGAGTAG
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gttagtg---gcaggggtttca----tttttgcatactttctcatagttgctttccc----------actctgtagtttcaatatcttccaagatggatatatgcattgtttcttttatc----gctccaattgatcaagagatcggccttttt---attcattcggcaatggcagGTGGAAAATCCAAAGATGGGGGGTCTGTTCCAAAGAAGGGCAGTAG
upper sequence: AT5G25060.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA08G34030.2 (Glycine max), 3'ss of exon 3
gttagtct---ttgcaaaggctacacagcttttta--actgtttgt-ttacaattgcttctctctttgtgtgtactttgttctttttgattggtgtcaaatggttagagcaatgctttgattatattgggaacgcattaataagtgtatggaccttttttctatgcgttcgcggatggcagGTGAAAAGTCCAAAGATGGGGGTTCGGTTTCAAAGAAGGGGAGTAG
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gttagtatgactcttgaattctgtatttctctctcctactatttatattccttttgtttcatctcttggaagttatacatgtttttcgtgttctgg-atatacatagttttttgct---attattttatataattgttgataaaagtatggacctttttt--attccttcgtggatgacagGTGAAAAGTCTAAAGATGGGGTATCTGGTCCAAAGAAGGGAAGTAG
upper sequence: AT5G25060.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv04s0008g06810.t01 (Vitis vinifera), 3'ss of exon 2
gttagtctttgcaaagg-ctacacagctttttaactgtttgtttacaattgcttct------ctctttgtgtgtactt-tgttctttttgattggtgtcaaatggttagagcaatgctttgattatattgggaacgcattaataagtgtatggaccttttttctatgcgttcgcggatggcagGTGAAAAGTCCAAAGATGGGGGTTCGGTTTCAAAGAAGGGGAGTAG
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gttagtatggttaaggaactatgtattttccttgctttcaattattgattttttacaaagtattcttgttatgttttagtcttgtttttgtttcatacta--tggatatatgaataattttttcattatggggatccgttaataaaaatatggaccttttt---attcattcgcaaatggcagGTGAAAAGTCGAAAGATGGGGTATCTGTTCCAAAGAAGGGAAGTAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgggaacgcattaataagtgtatggaccttttttctatgcgttcgcggatggcagGTGAAAAGTCCAAAGATGGGGGTTCGGTTTCAAAGAAGGGGAGTAG
cattaat putative branch site (score: 3)
attaataagtgtat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttagtctttgcaaaggctacacagctttttaactgtttgtttacaattgcttctctctttgtgtgtactttgttctttttgattggtgtcaaatggttagagcaatgctttgattatattgggaacgcattaataagtgtatggaccttttttctatgcgttcgcggatggcagGTGAAAAGTCCAAAGATGGGGGTTCGGTTTCAAAGAAGGGGAGTAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG