Sequence
atgc intronic sequence ATGC exonic sequence...ccttattttaaatttctttgtttgtttgcttaataatttagtatttttggtgattaattataaatgttacatgtttgtgctttgtatttgcactgcacagAGCAACAATGAAAAACTGTTAGAGAATCCTTACCTTCAAATGTGTGGCATACTTCAATTGGAAAATGATCTTGGATTTGACTTGTGA
Basic information
species | Glycine max |
transcript | GLYMA20G23240.1 |
intron # | 19 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA20G23240.1 (Glycine max), 3'ss of exon 19
lower sequence: LOC_Os01g74310.5 (Oryza sativa), 3'ss of exon 6
--------------------------------------------------------------------------ccttattttaaatt--tctttgtttgtttgcttaataattta-gtatttttggtgatt-------aattataaatgttac-------atgtttgtgct----ttgtatttgcactgca--cagAGCAACAATGAAAAACTGTTAGAGAATCCTTACCTTCAAATGTGTGGCATACTTCAATTGGAAAATGATCTTGGATTTGACTTGTGA-------------
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gtggagcctcttttttcctatctcattatgggggtgaaatttgaagtattacatgaatgccatccatatgcatcggtttatctagattagtttctggtttcacgccaggtgcttcaagtgtcgtaggaggtttcatttcatgcatatctgatatctcaattatgtcggtactgacatgttatttacattgttgccagTGTAACAATGAAAAACTGCTGGAGAACCCATACCTTCAAATGCGTGGGATACTGCAGTTGTCAAACGATCTAGGAGTTCAATAATCACTCGAATGTGCTA
upper sequence: GLYMA20G23240.1 (Glycine max), 3'ss of exon 19
lower sequence: Vv13s0019g00680.t01 (Vitis vinifera), 3'ss of exon 16
ccttattttaaatttctttgtttgtttgcttaataatttagtatttttg---gtgat-taattataaatg-ttacatgtttgtgctttgtatttgcactgcacagAGCAACAATGAAAAACTGTTAGAGAATCCTTACCTTCAAATGTGTGGCATACTTCAATTGGAAAATGATCTTGGATTTGACTTGTGA-------------
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----tttttaaagatcctaactt-ttgtcataattcattagccctttagtacgtggcataatcacatgtaactaaaattttctatgttgtgttgctattgtgcagAGCAACAATGAAAAGCTGTTAGAGAATCCATACCTTCAGATGCGTGGCATAATTCAGCTGTCAAATGATCTTGGGACTGGGTTATAATCTGATGTTTTTT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttggtgattaattataaatgttacatgtttgtgctttgtatttgcactgcacagAGCAACAATGAAAAACTGTTAGAGAATCCTTACCTTCAAATGTGTGGCATACTTCAATTGGAAAATGATCTTGGATTTGACTTGTGA
gattaat putative branch site (score: 3)
attaattataaatgtt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ccttattttaaatttctttgtttgtttgcttaataatttagtatttttggtgattaattataaatgttacatgtttgtgctttgtatttgcactgcacagAGCAACAATGAAAAACTGTTAGAGAATCCTTACCTTCAAATGTGTGGCATACTTCAATTGGAAAATGATCTTGGATTTGACTTGTGA
- - - - - - - - - - - tgtttgc
- - - - - - - - - - - - - - - - - - - - - - - - ggtgatt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tttgtgc