Sequence
atgc intronic sequence ATGC exonic sequence...aagcttgttgtggccccaatttggtctgatatattgatatgtgtgtgcaatttgtcatcttgtttttttttcttgataagcatggtaaatcttgtttcagGATATGGCAGGGTTGATAAGCAAGATAAACCGTTCCTCTATTGGCCCTTTGCCTCCCTGTTATTCCCCATCTTT
Basic information
species | Glycine max |
transcript | GLYMA12G31330.1 |
intron # | 10 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA12G31330.1 (Glycine max), 3'ss of exon 10
lower sequence: LOC_Os01g64490.1 (Oryza sativa), 3'ss of exon 11
-aagcttgttgtggccc-caatttggtctgatatattgatatgtgtgtgcaatttgtcatcttgtttttttttcttgataagcatggtaaatcttgtttcagGATATGGCAGGGTTGATAAGCAAGATAAACCGTTCCTCTATTGGCCCTTTGCCTCCCTGTTATTCCCCATCTTT
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tatatttgttttcttccgtagtgtttaccaaattgatggtgtttgactcaaagttgtcaaa--gttcagttaatcttaagtttactcccatgtttgtttcagGATATGGCTGGACTAATTAGTAAGATAAATCGCTCCTCCATTGGCCCTTTGCCTCCATGCTACTCTCCATCTAT
upper sequence: GLYMA12G31330.1 (Glycine max), 3'ss of exon 10
lower sequence: LOC_Os05g36960.1 (Oryza sativa), 3'ss of exon 10
aagcttgttgtggccccaatttggtctgatatattgatatgtgtgtgcaatttgtcatcttgtttttttttcttgataagcatg---gtaaatcttgttt-cagGATATGGCAGGGTTGATAAGCAAGATAAACCGTTCCTCTATTGGCCCTTTGCCTCCCTGTTATTCCCCATCTTT
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aaatatggaacattggaattcttgtgtgctatttaacaatgc---tactatttgt-atttgccttttaagtttcagtgatcttatgaatcaacaatacctgcagGATATGGCTGGATTAATAAGTAAGATAAATAGGTCCTCCATTGGCCCCTTGCCTGCCTGTTACTCTTCTTCTAT
upper sequence: GLYMA12G31330.1 (Glycine max), 3'ss of exon 10
lower sequence: GRMZM2G074262_T01 (Zea mays), 3'ss of exon 11
aagcttgttgtggccccaatttggtctgatatattgatatgtgtgtgcaatttgtcatcttgtttttttttcttga---taagcatggtaaat-cttgtttcagGATATGGCAGGGTTGATAAGCAAGATAAACCGTTCCTCTATTGGCCCTTTGCCTCCCTGTTATTCCCCATCTTT
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----atctcatctctcagcctttgcatattttactatgtagtgttattaatttcaaaagtatagaagttgaggtaagcttgagcttactccatgtttctttcagGATATGGCTGGACTGATAAGTAAGATAAATCGCTCCTCCATTGGCCCTTTGCCTACTTTCTATTCTTCATCTAT
upper sequence: GLYMA12G31330.1 (Glycine max), 3'ss of exon 10
lower sequence: GRMZM2G137118_T01 (Zea mays), 3'ss of exon 11
---aagcttgttgtggccccaatttggtctgatatattgatat-gtgtgtgcaatttgtcatcttgtttttttttcttgataagcatggtaaatcttgtttcagGATATGGCAGGGTTGATAAGCAAGATAAACCGTTCCTCTATTGGCCCTTTGCCTCCCTGTTATTCCCCATCTTT
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cttggaccttttcctctcttaatataatgacgtgtagtcctcccgcgcgttcgagaaaaaaaaatttctgatgatct-gacctgaatttcattgcctg---cagGATATGGCTGGATTAATAAGCAAGATAAATCGGTCTTCCATGGGTCCTTTGCCTGCCTGTTACTCAGTGTCTAT
upper sequence: GLYMA12G31330.1 (Glycine max), 3'ss of exon 10
lower sequence: AT3G44200.1 (Arabidopsis thaliana), 3'ss of exon 10
aagcttgttgtggcc--ccaatttggtctgatatattgatatgtgtgtgcaatttgtcatcttgtttttttttcttgataagcatggtaaatcttgtttcagGATATGGCAGGGTTGATAAGCAAGATAAACCGTTCCTCTATTGGCCCTTTGCCTCCCTGTTATTCCCCATCTTT
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-atatcactgaagttaatggatggagtattcttggttcccctgcatttg-atctcttcaaagtatcttatggcatttgcttttatgttatatatgatttcagGATATGGCAGGGCTTATAAGCAAGGTTAATCGCTCCTCAATTGGTCCGTTGCCTCCGTGCTATTCACCATCTTT
upper sequence: GLYMA12G31330.1 (Glycine max), 3'ss of exon 10
lower sequence: Vv06s0009g00690.t01 (Vitis vinifera), 3'ss of exon 10
aagcttgttgtggccccaatttggtctgatatattgatatgtgtgtgcaatttgt------catcttgtttttttttcttgataagcatggtaaatcttgtttcagGATATGGCAGGGTTGATAAGCAAGATAAACCGTTCCTCTATTGGCCCTTTGCCTCCCTGTTATTCCCCATCTTT
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----tatatgtgattttaatttgttatcaccca--aatatgaattctgaaactgtttactccattttatttgtattctaacattggcattctacatctggtttcagGATATGGCTGGATTAATAAGTAAAATAAACCGTTCTTCTATTGGTCCTTTGCCCTCATGCTATTCCCCTTCTTT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgcaatttgtcatcttgtttttttttcttgataagcatggtaaatcttgtttcagGATATGGCAGGGTTGATAAGCAAGATAAACCGTTCCTCTATTGGCCCTTTGCCTCCCTGTTATTCCCCATCTTT
tcttgat putative branch site (score: 4)
tcttgtttc putative PPT
tttttttttcttgata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
aagcttgttgtggccccaatttggtctgatatattgatatgtgtgtgcaatttgtcatcttgtttttttttcttgataagcatggtaaatcttgtttcagGATATGGCAGGGTTGATAAGCAAGATAAACCGTTCCTCTATTGGCCCTTTGCCTCCCTGTTATTCCCCATCTTT
- gcttgtt
- - - - - tggcccc
- - - - - - - - - - - - - - - - - - - - gtgtgtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gcatggt