Sequence
atgc intronic sequence ATGC exonic sequence...gtagtctaatagaatagctagggatcgatgagaaaataaattatattaatttgattattctgaagcttatgttcttcaatttttttctccttttgactagATGGTCTGCAATAGCAAGTCACTTACCGGGTCGGACAGATAATGAAATCAAGAATTTTTGGAACACCCATCTCAAGAAGAAGCTGATTCAAATGGGATAT
Basic information
species | Glycine max |
transcript | GLYMA01G09280.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA01G09280.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os06g11780.1 (Oryza sativa), 3'ss of exon 2
gtagtctaatagaatagctagggatcgatgagaaaataaattatatta-atttgattattctgaagcttatgttcttcaatttttttctccttttgactagATGGTCTGCAATAGCAAGTCACTTACCGGGTCGGACAGATAATGAAATCAAGAATTTTTGGAACACCCATCTCAAGAAGAAGCTGATTCAAATGGGATAT
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---------------------------gtaatacctgaacctagctgacatttcataatccccaaagcaa-gtgttttggctaatctgtgagca-aaccagGTGGTCAGCTATTGCAAAGCATCTCCCTGGACGGACAGATAACGAGATCAAGAACTTCTGGAACACCCACCTCAGGAAGAAACTGATCAAGATGGGCATT
upper sequence: GLYMA01G09280.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G159547_T01 (Zea mays), 3'ss of exon 2
gtagtctaatagaatagctagggatcgatgagaaaataaattatattaatttgattattctgaagcttatgtt-------cttcaatttttttctccttttgactagATGGTCTGCAATAGCAAGTCACTTACCGGGTCGGACAGATAATGAAATCAAGAATTTTTGGAACACCCATCTCAAGAAGAAGCTGATTCAAATGGGATAT
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-------gctagtttgtttcactctaacttcaataactcgtatttttgacttgtacgtagtgcatgctatgctaatccagtgtcaactgttgtcatggtcaaaccagATGGTCAGCTATCGCAAAGCACCTCCCTGGGCGGACTGATAACGAGATCAAGAATTTCTGGAACACGCACCTGAAGAAGAAGCTCATCCAGATGGGCTTC
upper sequence: GLYMA01G09280.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv18s0001g05670.t01 (Vitis vinifera), 3'ss of exon 2
gta-gtctaatagaatagctagggatcgatgagaaaataaattatattaatttgattattctgaagcttatgttcttcaatttttttctccttttgactagATGGTCTGCAATAGCAAGTCACTTACCGGGTCGGACAGATAATGAAATCAAGAATTTTTGGAACACCCATCTCAAGAAGAAGCTGATTCAAATGGGATAT
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gtaagcctaataaact---tctgcttccatga---aacaaaaccctcaagctcatgcattactaa----------tccaatatttttgtcca--caattagATGGTCCGCAATTGCATCGCACCTCCCTGGCCGGACGGACAACGAAATTAAGAATTTCTGGAATACCCATCTAAAGAAGAAGCTCATTCAGATGGGGTTT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttaatttgattattctgaagcttatgttcttcaatttttttctccttttgactagATGGTCTGCAATAGCAAGTCACTTACCGGGTCGGACAGATAATGAAATCAAGAATTTTTGGAACACCCATCTCAAGAAGAAGCTGATTCAAATGGGATAT
cttatgttcttcaatt CT-rich tract
ttcttcaattttttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtagtctaatagaatagctagggatcgatgagaaaataaattatattaatttgattattctgaagcttatgttcttcaatttttttctccttttgactagATGGTCTGCAATAGCAAGTCACTTACCGGGTCGGACAGATAATGAAATCAAGAATTTTTGGAACACCCATCTCAAGAAGAAGCTGATTCAAATGGGATAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - - - - - - - - - - - - aaaataa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctgaagc