Sequence
atgc intronic sequence ATGC exonic sequence...tataattgtcccatgtttgatctataaagcaaattgtaagcttttttgatcttctgtttgcattttgttttcttaatattatttctttcaaattccttagGCTACCTGCGGAATACCTGAAATAGCTTTTGCAACATTTGAGAACATGGAATATGGAGAAG
Basic information
species | Glycine max |
transcript | GLYMA20G36340.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA20G36340.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os10g32540.1 (Oryza sativa), 3'ss of exon 3
tataattgtcccatgtttgatctataaagcaaattgtaagcttttttgatcttctgttt-gcattttgttttcttaatattatttctttcaaattccttagGCTACCTGCGGAATACCTGAAATAGCTTTTGCAACATTTGAGAACATGGAATATGGAGAAG---
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-aaaactaggtttggtttattttaagaacatacttattgcggttcatatttacaaatatagtcacttttttcctttacataaaagtttgtatttcattcagGCTACTTGTGGAATTCCTGAGATTGCTTTTGCAACATTCGAAAACATGGAATATGGAGGTGAAG
upper sequence: GLYMA20G36340.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G116526_T01 (Zea mays), 3'ss of exon 3
---tata-attgtcccatgtttgatctataaagca-aattgtaagcttttttgatcttctgtttgcattttgttttcttaatattatttctttcaaattccttagGCTACCTGCGGAATACCTGAAATAGCTTTTGCAACATTTGAGAACATGGAATATGGAGAAG---
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ttacatacatggtttgttgaattagcattaaggttcggtttttggatatatcaataacaataccgtaatccttgttttaaataaaagctcttt-----ttgtcagGCTACTTGTGGAATTCCTGAAGTTGCCTTTGCAACATTTGAAAACATGGAATATGGAGGTGAAG
upper sequence: GLYMA20G36340.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv04s0043g00700.t01 (Vitis vinifera), 3'ss of exon 3
tataattgtcccatgtttgatctataaagcaaattgta-agcttttttgatcttctgtttgcattt--tgttttcttaatattatttctttcaaattccttagGCTACCTGCGGAATACCTGAAATAGCTTTTGCAACATTTGAGAACATGGAATATGGAGAAG
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--ttactttttcaggaaagctctttcctgtggttactatagacctgctcctgttttcctaacatctaacatctgactgatatc-ttttgtttattgcatgtagGCAACTTGTGGAATACCTGAAATAGCTTTTGCAACATTTGAGAATATGGAATATGGAGAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttgatcttctgtttgcattttgttttcttaatattatttctttcaaattccttagGCTACCTGCGGAATACCTGAAATAGCTTTTGCAACATTTGAGAACATGGAATATGGAGAAG
tcttaat putative branch site (score: 3)
ttcctt putative PPT
attttgttttcttaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tataattgtcccatgtttgatctataaagcaaattgtaagcttttttgatcttctgtttgcattttgttttcttaatattatttctttcaaattccttagGCTACCTGCGGAATACCTGAAATAGCTTTTGCAACATTTGAGAACATGGAATATGGAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - tgtccca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgcattt