Sequence
atgc intronic sequence ATGC exonic sequence...atagttttagcactcgctgcatcattcttaaagacacatatcttttaatttgataacatttttttaacaatcctctgttttcatgcatcatctctggcagTCATACAGCCTCTATTGCGGCTGGAAATAATGGAATTCCTGTGAGAATGCATGGCCACGAATTTGGGAGAGCGAGTGGGATGGCTCCTCGTGCTAG
Basic information
species | Glycine max |
transcript | GLYMA13G00580.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA13G00580.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os06g48650.3 (Oryza sativa), 3'ss of exon 3
----------------------------------------------------------------atagttttagcactcgctgcatca-ttcttaaagacacatatctttt-----aatttgataacatttttttaacaatcctctgttttcatgcatcatctctggcagTCATACAGCCTCTATTGCGGCTGGAAATAATGGAATTCCTGTGAGAATGCATGGCCACGAATTTGGGAGAGCGAGTGGGATGGCTCCTCGTGCTAG
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gtcatgctcctaattaatatatgttctgttctagtttcttataccaagaaaaatgccatacatgaaaattgttctgtccaaagaattagctattctggttgtgtttcatcttgagaagaatggcatgacttatctagttatctgatacaaagatgctttcccttaaacagTCATACAGCAGCAATTGCTGCTGGAAATAATGGGATTCCAGTACGAATGCATGGTCACGAATTTGGCAAAGCAAGTGGTATGGCTCCACGTGCTAG
upper sequence: GLYMA13G00580.1 (Glycine max), 3'ss of exon 3
lower sequence: AT2G19170.1 (Arabidopsis thaliana), 3'ss of exon 4
atagttttagcactcgctgcatcattcttaaagaca----catatcttttaatttgataacatttttttaacaatcctctgttttcatgcatcatctctggcagTCATACAGCCTCTATTGCGGCTGGAAATAATGGAATTCCTGTGAGAATGCATGGCCACGAATTTGGGAGAGCGAGTGGGATGGCTCCTCGTGCTAG
| | |||||| || | || ||||| | || || || | | | | |||| || | |||||||||||| |||| || ||||| ||||| || ||||| |||| |||||||| | |||||||| | |||||||||||||||||||||||| ||
-------------------gtttgtctttaaagttgtctccaggtgttagggggagataatgctgttgtactaagcaaatctgattatgctggatttt---cagTCATACAGCAGCTATAGCAGCTGGGAATAACGGTATTCCGTTGAGGATGCATGGTTATGAATTTGGAAAAGCGAGTGGGATGGCTCCTCGTGCAAG
upper sequence: GLYMA13G00580.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv11s0103g00550.t01 (Vitis vinifera), 3'ss of exon 4
---atagttttagcactcgctgcatcattcttaaagacacatatcttttaatttgataacatttttttaacaatcctctgttttcatgcatcatctctggcagTCATACAGCCTCTATTGCGGCTGGAAATAATGGAATTCCTGTGAGAATGCATGGCCACGAATTTGGGAGAGCGAGTGGGATGGCTCCTCGTGCTAG
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atgatagtttga-ttttcttttaatattttgttcccatttactctgttttatttgattgggtctggtt--catttgttgtttcttgggaatactggacaacagTCACACAGCAGCTATTGCAGCTGGAAATAATGGAATTCCAGTGAGAATGCATGGGTATGAATTTGGGAAAGCAAGTGGGATGGCTCCCCGTGCCAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.taatttgataacatttttttaacaatcctctgttttcatgcatcatctctggcagTCATACAGCCTCTATTGCGGCTGGAAATAATGGAATTCCTGTGAGAATGCATGGCCACGAATTTGGGAGAGCGAGTGGGATGGCTCCTCGTGCTAG
ttttaac putative branch site (score: 2)
tcatctct putative PPT
tgataacattttttta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
atagttttagcactcgctgcatcattcttaaagacacatatcttttaatttgataacatttttttaacaatcctctgttttcatgcatcatctctggcagTCATACAGCCTCTATTGCGGCTGGAAATAATGGAATTCCTGTGAGAATGCATGGCCACGAATTTGGGAGAGCGAGTGGGATGGCTCCTCGTGCTAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC
- - - - - - -tcgctgc
- - - - - - - - - - - - - - - - -acacata