Sequence
atgc intronic sequence ATGC exonic sequence...tgcaatttttttgccagtaaacacttctgcaccactttgtgaatgcttctatttccacctaggatgaatattctctaatctttataattgtttttatcagTGGTCTGACAATCTCCAGAAGCTTGATTTCCAAGAGTTGGTAATGTTCCTTCAACACCTTCCAACTAAGAACTGGACTGACCAGGAGCTCGAGATGGTAC
Basic information
species | Glycine max |
transcript | GLYMA13G42180.1 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA13G42180.1 (Glycine max), 3'ss of exon 9
lower sequence: LOC_Os09g34040.1 (Oryza sativa), 3'ss of exon 9
---------------------------------------------------------------tgcaatttttttgccagtaaacact-tctgcaccactttgtgaatgcttctatttccacctaggatgaatattctctaatctttataattgttttta--tcagTGGTCTGACAATCTCCAGAAGCTTGATTTCCAAGAGTTGGTAATGTTCCTTCAACACCTTCCAACTAAGAACTGGACTGACCAGGAGCTCGAGATGGTAC
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gtaagttgaagtaccccttgactgttcataattatttttttcaacttcagtgtatgcaagtgttgcatgcctggtgcaggcaaatgcagttttcacaatgtttctggtgtaaatactaatgtccaagtccattgtaat-taagttctctctttatttctacctcagTGGTCAGACAAGCTGAAGAAACTTGATTTTCAAGAGATGGTCATGTTCCTTCAGCACCTTCCGACGAGGAACTGGGCTCACCATGAGCTTGAGATGGTGC
upper sequence: GLYMA13G42180.1 (Glycine max), 3'ss of exon 9
lower sequence: AT2G30710.1 (Arabidopsis thaliana), 3'ss of exon 9
---tgcaatttttttgccagtaaacacttctgcaccactttgtgaatgcttctatttccac-ctaggatgaatattctctaatctttataattgtttttatcagTGGTCTGACAATCTCCAGAAGCTTGATTTCCAAGAGTTGGTAATGTTCCTTCAACACCTTCCAACTAAGAACTGGACTGACCAGGAGCTCGAGATGGTAC
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gtaagcaaacactgaatcgaatataacttgcgt-tggtcttgaaaatgttttcttctataaaccacgagaatcaaatacaagttgtttctgtaaacaatg-cagTGGTCTGATGAGCTGAAGAAGCTAGATTTTCAAGAAATGGTAATGTTCCTGCAACACCTTCCGACACATAACTGGTCAGACCAAGAGCTCGAAATGGTTT
upper sequence: GLYMA13G42180.1 (Glycine max), 3'ss of exon 9
lower sequence: Vv05s0094g00070.t01 (Vitis vinifera), 3'ss of exon 9
----tgcaatttttttgccagtaaacacttctgcaccactttgtgaatgcttctatttccacctaggatgaatattctctaatctttataattgtttttatcagTGGTCTGACAATCTCCAGAAGCTTGATTTCCAAGAGTTGGTAATGTTCCTTCAACACCTTCCAACTAAGAACTGGACTGACCAGGAGCTCGAGATGGTAC
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tgtttgtgttttttttccttg-agatttctttgcacaattagaagctagattaagcatgaaac---acttaaccatgtgtacactgttttttgtttgttttcagTGGTCGGATACGCTTCAGAAGCTTGATTTCCAAGAGCTGGTAATGTTCCTTCAACACCTTCCAACTCATAACTGGACTCACCAAGAGCTCGAGATGGTGC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cttctatttccacctaggatgaatattctctaatctttataattgtttttatcagTGGTCTGACAATCTCCAGAAGCTTGATTTCCAAGAGTTGGTAATGTTCCTTCAACACCTTCCAACTAAGAACTGGACTGACCAGGAGCTCGAGATGGTAC
ctctaat putative branch site (score: 3)
ttgttttt putative PPT
atgaatattctctaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tgcaatttttttgccagtaaacacttctgcaccactttgtgaatgcttctatttccacctaggatgaatattctctaatctttataattgtttttatcagTGGTCTGACAATCTCCAGAAGCTTGATTTCCAAGAGTTGGTAATGTTCCTTCAACACCTTCCAACTAAGAACTGGACTGACCAGGAGCTCGAGATGGTAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - ttttgcc
- - - - - - - - - - - - - - gcaccac
- - - - - - - - - - - - - - - - - - - gtgaatg