Sequence
atgc intronic sequence ATGC exonic sequence...tcttttttctttatacttttttctttgttttgatttcagattcttccatctagaattggaaaaagtggggtcttatttctaattggtttgtttgctgcagTGGCCACTCCAAAGCAGATTAGAGAACTGATGCAGGTGGTAGGCCTCACAAATGATGAAGTGAAAAGCCATTTGCAAGTGA
Basic information
species | Glycine max |
transcript | GLYMA17G20520.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA17G20520.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os12g39640.1 (Oryza sativa), 3'ss of exon 3
tcttttttctttatacttttttctttgttttgatttcagattcttccatctagaattgga---aaaagtggggtcttatttctaattggtttgtt--tgctgcagTGGCCACTCCAAAGCAGATTAGAGAACTGATGCAGGTGGTAGGCCTCACAAATGATGAAGTGAAAAGCCATTTGCAAGTGA
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----atttgtggtcacattgttgattgctcctagta-aaattgtttgattaattttttgattggtgcgctgaaacttgcttaatgtttttttattgttgatgcagCTGCAACTCCCAAGCAGATTAGGGAGCTGATGAAGGTTGATGGCCTCACTAATGATGAAGTCAAAAGCCACCTGCAG----
upper sequence: GLYMA17G20520.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G173882_T01 (Zea mays), 3'ss of exon 3
---------------------------------------------tcttttttctttatacttttttct-ttgttttgatttcagattcttccatctagaattggaaaaagtggggtc--ttatttctaattggtttgtttgctgcagTGGCCACTCCAAAGCAGATTAGAGAACTGATGCAGGTGGTAGGCCTCACAAATGATGAAGTGAAAAGCCATTTGCAAGTGA
| | | | | || || | ||| | | | | | |||| |||||| | | | || | || ||| |||| | | ||||||| ||||| ||||||||||| || || |||||| |||||| ||||||||||| || |||||||||||||| | ||
gtgagccttgctcttcagatgcaaattatttcttgccggttttgggcggcctgcagcgtgttcttacctacttgcttgcctgccgtattagatacgtagagttggaattaacgagttcattcatgtctgattg---tctgcactgcagTTGCCACCCCAAAGCAGATCAGGGAGCTGATGAAGGTGGACGGCCTCACAAACGACGAAGTGAAAAGCCACCTTCAG----
upper sequence: GLYMA17G20520.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv07s0197g00060.t01 (Vitis vinifera), 3'ss of exon 3
tcttttttctttatacttttttctttgttttgatttcagattcttccatctagaattggaaaaagtg-gggtcttatttctaattggtttgtttgctgcagTGGCCACTCCAAAGCAGATTAGAGAACTGATGCAGGTGGTAGGCCTCACAAATGATGAAGTGAAAAGCCATTTGCAAGTGA
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-agatttctaatggaaaagttttcagaaaacaatttgagatcatggatccttgaattgaattccatctgggacatgctactgaaattttccttttctgcagCAGCCACTCCTAAACAGATTCGAGAACTCATGCAAGTGGAAGGTCTCACTAACGATGAAGTAAAAAGCCATTTACAG---- atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ccatctagaattggaaaaagtggggtcttatttctaattggtttgtttgctgcagTGGCCACTCCAAAGCAGATTAGAGAACTGATGCAGGTGGTAGGCCTCACAAATGATGAAGTGAAAAGCCATTTGCAAGTGA
ttctaat putative branch site (score: 2)
tttgttt putative PPT
tcttatttctaatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tcttttttctttatacttttttctttgttttgatttcagattcttccatctagaattggaaaaagtggggtcttatttctaattggtttgtttgctgcagTGGCCACTCCAAAGCAGATTAGAGAACTGATGCAGGTGGTAGGCCTCACAAATGATGAAGTGAAAAGCCATTTGCAAGTGA
- - - - - - - - - - - - -tgttttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gtggggt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tggtttg