Sequence
atgc intronic sequence ATGC exonic sequence...gggcttttctgttgtaattataaagtttctccattgaagcatggtagtggtttaattattggagattattgaggcccttatagactgtctctcatctcagGTGAAGAGCTTTCCAAAAAACAGGCTGCTCAAGAATCCACAATTAGGAAACTAAGGGCTCAG
Basic information
species | Glycine max |
transcript | GLYMA15G01980.2 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA15G01980.2 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os05g48620.1 (Oryza sativa), 3'ss of exon 5
gggcttttctgttgtaattataaagtttctccattgaagcatggtagtggtttaattattggagattattgaggcccttatagactgtctctcatct-cagGTGAAGAGCTTTCCAAAAAACAGGCTGCTCAAGAATCCACAATTAGGAAACTAAGGGCTCAG
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-tacactttagagcccatttgattttttgcccccttcatttttatgtttagtaggttttgaggcatttatttggcatcaacaatttttttacaatgaacagGTGAAGAGCTATCAAAAAAACAAGCTGCTCAAGAAGCTACTATGCGGAAACTTAGGGCACAG
upper sequence: GLYMA15G01980.2 (Glycine max), 3'ss of exon 6
lower sequence: AT1G79830.3 (Arabidopsis thaliana), 3'ss of exon 6
------------------------------------gggcttttct-gttgtaattataaagtttctcca--------ttgaagcatggtagtggtttaattattggagattattgaggcccttatag-actgtctctcatctcagGTGAAGAGCTTTCCAAAAAACAGGCTGCTCAAGAATCCACAATTAGGAAACTAAGGGCTCAG
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gtaagacagccttttggaatgcttgaattatggatcgtatttttctcgttataaaaaaatggtgttgaaagcgaacacctgaaaaatgaaaggacgtcatttcttgctcagc-ttgagctcttgatattaatgctaatcatttcagGCGAAGAGCTTTCAAAGAAACAGGCTGCTCAAGAAGCTCAGATCAGGAAGCTAAGGGCTCAG
upper sequence: GLYMA15G01980.2 (Glycine max), 3'ss of exon 6
lower sequence: Vv16s0098g00540.t01 (Vitis vinifera), 3'ss of exon 5
gggcttttctgt-tgtaattataaagtt-tctccattgaagcatggtagtggtttaattattggagattattgaggcccttatagact-gtctctcatctcagGTGAAGAGCTTTCCAAAAAACAGGCTGCTCAAGAATCCACAATTAGGAAACTAAGGGCTCAG
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--gtatgtatgtatgtatgtaggagttgatattgaccaaagggtaatga-ggcccttcttttatatgctgataattttttaagatgcttgcctcttgcttcagGTGAAGAGCTTTCAAAAAAGCAAGCTGCTCAAGAGTCTCAGATTAGGAAATTAAGGGCACAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.agtggtttaattattggagattattgaggcccttatagactgtctctcatctcagGTGAAGAGCTTTCCAAAAAACAGGCTGCTCAAGAATCCACAATTAGGAAACTAAGGGCTCAG
gtttaat putative branch site (score: 4)
ctgtctctcatctc putative PPT
tttaattatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gggcttttctgttgtaattataaagtttctccattgaagcatggtagtggtttaattattggagattattgaggcccttatagactgtctctcatctcagGTGAAGAGCTTTCCAAAAAACAGGCTGCTCAAGAATCCACAATTAGGAAACTAAGGGCTCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - -tctgttg
- - - - - - - - - - - - - ttctcca
- - - - - - - - - - - - - - - - - - - gcatggt
- - - - - - - - - - - - - - - - - - - - - - -agtggtt