Sequence
atgc intronic sequence ATGC exonic sequencegttaacccttttgtttgggcaactgaaaagaaatgttattgataagaatattgacttaagctttttgcattctgtcagGTGCAAGATTGGTTGTATACAGATGGTGAAGATGCCAATGCCACAGAGTTTCAAGAGCGTCTAGATCAGTTAAAAGCTGTTGGAGATCCAATTTTCTTCA
Basic information
species | Glycine max |
transcript | GLYMA13G10700.1 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA13G10700.1 (Glycine max), 3'ss of exon 7
lower sequence: LOC_Os02g48110.1 (Oryza sativa), 3'ss of exon 8
gttaacccttttgtttgggcaactgaaaagaaatgtt-attgataagaatattgacttaagctttttgcattctgtcagGTGCAAGATTGGTTGTATACAGATGGTGAAGATGCCAATGCCACAGAGTTTCAAGAGCGTCTAGATCAGTTAAAAGCTGTTGGAGATCCAATTTTCTTCA
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gtctgttcaataat--aatcttctggtgggtttcatttgtctgttgaatcctcatgctgagattgtttaagtg---cagGTACAAGATTGGTTGTATATGGATGGTGAAGATGCTCAAGCAAATGAATTCAAGGAACGCCTTGACCAACTTAAGGCCATCGGTGACCCAATTCTTTTCA
upper sequence: GLYMA13G10700.1 (Glycine max), 3'ss of exon 7
lower sequence: AT4G16660.1 (Arabidopsis thaliana), 3'ss of exon 9
-----gttaacccttttgtttgggcaactgaaaaga---aatgttattgataagaatattgacttaa-gct--------ttttgcattctgtcagGTGCAAGATTGGTTGTATACAGATGGTGAAGATGCCAATGCCACAGAGTTTCAAGAGCGTCTAGATCAGTTAAAAGCTGTTGGAGATCCAATTTTCTTCA
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gcatgaataaattttcttttgaactatataatattatttgattccaatgatgagtgtaatcgtttgacactgaggacggtcttgtgtgtt-tcagGTGCAAGATTGGCTTTACATGGATGGAGAAGATGCTAATGCCACAGAGTTTGAGAAGCGGCTTGACTCACTTAAAGCCATCGGCAGTCCCATATCTTTCC
upper sequence: GLYMA13G10700.1 (Glycine max), 3'ss of exon 7
lower sequence: Vv09s0096g00090.t01 (Vitis vinifera), 3'ss of exon 10
gttaaccc----ttttgtttgggcaactgaaaagaaatgt-tattga--taagaatattgacttaagctttttgc-attctgtcagGTGCAAGATTGGTTGTATACAGATGGTGAAGATGCCAATGCCACAGAGTTTCAAGAGCGTCTAGATCAGTTAAAAGCTGTTGGAGATCCAATTTTCTTCA
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gttagcctaagttcagagtttgttatatatttacacacgcacattcaacttaaagttttgacttgatcatcatgttatatttttagGTGCAAGAATGGTTGTATACTGATGGTGAAGATGCTACAGCTGCTGAGTTTCAAGAACGTCTAGATTTGTTAAAATCTATTGGTGACCCAATATTTTTCA
upper sequence: GLYMA13G10700.1 (Glycine max), 3'ss of exon 7
lower sequence: Vv04s0008g04410.t01 (Vitis vinifera), 3'ss of exon 8
------------gttaacccttttgtttgggcaactgaaaagaaatgttattgataagaatattgacttaagctttttgc-attctgtcagGTGCAAGATTGGTTGTATACAGATGGTGAAGATGCCAATGCCACAGAGTTTCAAGAGCGTCTAGATCAGTTAAAAGCTGTTGGAGATCCAATTTTCTTCA
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gttttatcccaagttcagagttt--gttatatatttacacacacacatt-caacttaatgttttgacttggtcatcatgttatattttcagGTGCAAGAATGGTTGTATACTGATGGTGAAGATGCTACGGCTGCTGAGTTTCAAGAACGTCTAGATTTGTTAAAATCTATTGGTGACCCGATATTTTTCA
upper sequence: GLYMA13G10700.1 (Glycine max), 3'ss of exon 7
lower sequence: Vv04s0043g00710.t01 (Vitis vinifera), 3'ss of exon 9
gttaacccttttgtttgggcaactgaaaag----aaatgt-tattga--taagaatattgacttaagctttttgcattctgtcagGTGCAAGATTGGTTGTATACAGATGGTGAAGATGCCAATGCCACAGAGTTTCAAGAGCGTCTAGATCAGTTAAAAGCTGTTGGAGATCCAATTTTCTTCA
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gttagcctaagttcagagtctgttatatatttacacatgcacattcaacttaaagttttgacttgatatcatgttatatttttagGTGCAAGAATGGTTGTATACTGATGGTGAAGATGCTACAGCTGCTGAGTTTCAAGAACGTCTAGATTTGTTAAAATCTATTGGTGACCCAATATTTTTCA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgaaaagaaatgttattgataagaatattgacttaagctttttgcattctgtcagGTGCAAGATTGGTTGTATACAGATGGTGAAGATGCCAATGCCACAGAGTTTCAAGAGCGTCTAGATCAGTTAAAAGCTGTTGGAGATCCAATTTTCTTCA
tattgac putative branch site (score: 2)
ttctgtc putative PPT
aaatgttattgataag 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttaacccttttgtttgggcaactgaaaagaaatgttattgataagaatattgacttaagctttttgcattctgtcagGTGCAAGATTGGTTGTATACAGATGGTGAAGATGCCAATGCCACAGAGTTTCAAGAGCGTCTAGATCAGTTAAAAGCTGTTGGAGATCCAATTTTCTTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC