Sequence
atgc intronic sequence ATGC exonic sequencegtttgtcttagctgaattttatttctggtgtaatctatgtcttaggaagcttttgatattgaaatcatgttttcatgttggtttttaatttacattcaaggacatttccatttatgaatatgcatagtgatcctgtttgttcaatgctttaatatggattcatgcagGAGCAAAAATTTAAAAACAAGTGTAATTGGATGCCCTAAAACCATTGATGGTGATTTGAAATGTAAAGAAGTTCCCACAAGTTTTGGGTTTGATACAGCT
Basic information
species | Glycine max |
transcript | GLYMA09G01050.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA09G01050.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os06g13810.1 (Oryza sativa), 3'ss of exon 5
gtttgtcttagctgaattttatttctggtgtaatctatgtcttaggaagcttttgatattgaaatcatgttttcatgttggtttttaatttacattcaaggacatttccatttatgaatatgcatagtgatcctgtttgttcaatgctttaatatggattcatgcagGAGCAAAAATTTAAAAACAAGTGTAATTGGATGCCCTAAAACCATTGATGGTGATTTGAAATGTAAAGAAGTTCCCACAAGTTTTGGGTTTGATACAGCT
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--------------------------------------------------------------aattctgcaa-catagagaatctagatat-tattctcg-atagttttattggc-aatattaactatatgcttgtt-gacaagtgagtgattgtttaactttgtagGGGGAAGAACATGAAAACTCGTGTCATTGGTTGCCCAAAGACTATTGATGGAGATCTGAAATGCAAGGAGGTTCCAACAAGCTTTGGGTTTGACACTGCT
upper sequence: GLYMA09G01050.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G059151_T01 (Zea mays), 3'ss of exon 5
gtttgtcttagctgaattttatttctggtgtaatctatgtcttaggaagcttttgatattgaaatcatgttttcatgttggtttttaatttacattcaaggacatttccatttatgaatatgcatagtgatcctgtttgttcaatgctttaatatggattcatgcagGAGCAAAAATTTAAAAACAAGTGTAATTGGATGCCCTAAAACCATTGATGGTGATTTGAAATGTAAAGAAGTTCCCACAAGTTTTGGGTTTGATACAGCT
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----------gttggctgctaacgctg-tgtt-ttgacctttcaatataaggctgattgtgaa--tataacattgcgttggttgtttcttt-------------tttctgcttattcacaagcaaatcaaaattatgatttcaa-attatgaacttgctccat--agGTCAAGGAACATGAAAACCCGTGTTATTGGTTGCCCAAAGACTATCGATGGGGATCTGAAATGTAAGGAGGTTCCGACAAGCTTTGGATTTGATACAGCT
upper sequence: GLYMA09G01050.1 (Glycine max), 3'ss of exon 5
lower sequence: AT1G12000.1 (Arabidopsis thaliana), 3'ss of exon 5
gtttgtcttagctgaattttatttctggtgtaatctatgtcttaggaagcttttgatattgaaatcatgttttcatgttggtttttaatttacattcaaggacatttccatttatgaatatgcatagtgatcctgtttgttcaatgctttaatatggattcatgcagGAGCAAAAATTTAAAAACAAGTGTAATTGGATGCCCTAAAACCATTGATGGTGATTTGAAATGTAAAGAAGTTCCCACAAGTTTTGGGTTTGATACAGCT
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-----------gtaaaccttgcagttg----aatctgttatgttgaaacttatttatcttaggcgaaagta-----gttgttcttgaagatccatgtgaccagaatc---ttta-----atatttgctgattcagcat-ttgacttattatctacttgtataattagGAGTAAGAACTTGAAAACCCGAGTCATTGGGTGCCCCAAGACCATTGATGGTGATTTGAAATGCAAAGAGGTTCCTACTAGTTTTGGGTTTGATACAGCT
upper sequence: GLYMA09G01050.1 (Glycine max), 3'ss of exon 5
lower sequence: AT4G04040.1 (Arabidopsis thaliana), 3'ss of exon 5
gtttgtcttagctgaattttatttctggtgtaatctatgtcttaggaagcttttgatattgaaatcatgttttcatgttggtttttaatttacattcaaggacatttccatttatgaatatgcatagtgatcctgtttgttcaatgctttaatatggattcatgcagGAGCAAAAATTTAAAAACAAGTGTAATTGGATGCCCTAAAACCATTGATGGTGATTTGAAATGTAAAGAAGTTCCCACAAGTTTTGGGTTTGATACAGCT
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----------------------------------------------------------------------------gtaattttttgaaat-tgtttaagattaatgagactcacttctctctgttttgtgttttaatgtttggt-ttcctattcggtttt---cagAGCTAAAAACATGAAAACTCTGGTTATTGGATGCCCTAAGACAATCGATGGTGATTTAAAGAGCAAAGAAGTCCCCACGAGTTTCGGGTTTGATACTGCT
upper sequence: GLYMA09G01050.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv10s0116g00360.t01 (Vitis vinifera), 3'ss of exon 5
gtttgtcttagctgaattttatttctggtgtaatctatgtcttaggaagcttttgatattgaaatcatgttttcatgttggtttttaatttacattcaaggacatttccatttatgaatatgcatagtgatcctgtttgttcaatgctttaatatggattcatgcagGAGCAAAAATTTAAAAACAAGTGTAATTGGATGCCCTAAAACCATTGATGGTGATTTGAAATGTAAAGAAGTTCCCACAAGTTTTGGGTTTGATACAGCT
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--------------------------------------------------------tgttaaattcagaaatctac-----tatgtgatcatcagaataagaactgactctttagtaatcagtgatttgtttaactttatttgat-ctatctgacaaat-----cagGGGTAAAAATATGAAAGCTCGGGTGATTGGATGCCCAAAGACCATTGATGGTGATTTGAAATGCAAGGAGGTTCCCACAAGTTTTGGATTTGATACTGCA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tatgaatatgcatagtgatcctgtttgttcaatgctttaatatggattcatgcagGAGCAAAAATTTAAAAACAAGTGTAATTGGATGCCCTAAAACCATTGATGGTGATTTGAAATGTAAAGAAGTTCCCACAAGTTTTGGGTTTGATACAGCT
ctttaat putative branch site (score: 4)
tttaatat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtttgtcttagctgaattttatttctggtgtaatctatgtcttaggaagcttttgatattgaaatcatgttttcatgttggtttttaatttacattcaaggacatttccatttatgaatatgcatagtgatcctgtttgttcaatgctttaatatggattcatgcagGAGCAAAAATTTAAAAACAAGTGTAATTGGATGCCCTAAAACCATTGATGGTGATTTGAAATGTAAAGAAGTTCCCACAAGTTTTGGGTTTGATACAGCT
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