Sequence
atgc intronic sequence ATGC exonic sequence...cctcaatatgcttctaatatgccatgtctataatgtgtcatatatccataggcttgaatttctaataatagtggtgtaataatctctttccgatttccagATTTCCCCATCTATCACACTGCGTTCGACTCCTATAACTGGATGGCATAGTATTGAGATCCATTCTTCCACCGCCATGTTACTG
Basic information
species | Glycine max |
transcript | GLYMA12G23220.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA12G23220.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv00s0319g00060.t01 (Vitis vinifera), 3'ss of exon 4
cctcaata-tgcttctaatatgccatgtctataatgtgtcatatatccataggcttgaatttctaataatagtggtgtaataatctctttccgatttcc---agATTTCCCCATCTATCACACTGCGTTCGACTCCTATAACTGGATGGCATAGTATTGAGATCCATTCTTCCACCGCCATGTTACTG
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-gtcaataatgttagtagtaaa--atttacatcacaattaagat-ttcatgctaatcaatttggtaaaatagaacttcaactttctttttcttttgtccttgagATTTTCCAGTCTATCACACTGCTTTTGACTCCTATAACTGGATGACAAACCATGGGGATCCATTGTTTCAACGTCACGTGGCTG
upper sequence: GLYMA12G23220.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv00s0285g00060.t01 (Vitis vinifera), 3'ss of exon 5
cctcaata-tgcttctaatatgccatgtctataatgtgtcatatatccataggcttgaatttctaataatagtggtgtaataatctctttcc---gatttccagATTTCCCCATCTATCACACTGCGTTCGACTCCTATAACTGGATGGCATAGTATTGAGATCCATTCTTCCACCGCCATGTTACTG
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-gtcaataatgttagtagtaaa--atttacatcacaattaagat-ttcatgctaatcaatttggtaaaatagaacttcaactttctttttcttttgtccttcagTTTTTCCAGTCTATCACACTGCTTTTGACTCCTATAACTGGATGACAAACCATGGGGATCCATTGTTTCAACGTCATGTGGCTG
upper sequence: GLYMA12G23220.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv00s0327g00020.t01 (Vitis vinifera), 3'ss of exon 4
cctcaata-tgcttctaatatgccatgtctataatgtgtcatatatccataggcttgaatttctaataatagtggtgtaataatctctttcc---gatttccagATTTCCCCATCTATCACACTGCGTTCGACTCCTATAACTGGATGGCATAGTATTGAGATCCATTCTTCCACCGCCATGTTACTG
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-gtcaataatgttagtagtaaa--atttacatcacaattaagat-ttcatgctaatcaatttggtaaaatagaacttcaactttctttttcttttgtccttcagATTTTCCAGTCTATCACACTGCTTTTGACTCCTATAACTGGATGACAAACCATGGGGATCCATTGTTTCAACGTCACGTGGCTG
upper sequence: GLYMA12G23220.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv00s0352g00020.t01 (Vitis vinifera), 3'ss of exon 5
cctcaatatgcttctaatatgccatgtctataatgtgtcatatatccataggcttgaatttctaataatagtggtgtaataatctctttccgatttccagATTTCCCCATCTATCACACTGCGTTCGACTCCTATAACTGGATGGCATAGTATTGAGATCCATTCTTCCACCGCCATGTTACTG
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nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnaatagaacttcaactttcttttttttttgtccttcagATTTTCCAGTCTATCACACTGCTTTTGACTCCTATAACTGGATGACAAACCATGGGGATCCATTGTTTCAACGTCACGTGGCTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ccataggcttgaatttctaataatagtggtgtaataatctctttccgatttccagATTTCCCCATCTATCACACTGCGTTCGACTCCTATAACTGGATGGCATAGTATTGAGATCCATTCTTCCACCGCCATGTTACTG
ttctaat putative branch site (score: 2)
tctctttccgatttcc putative PPT
ttgaatttctaataat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
cctcaatatgcttctaatatgccatgtctataatgtgtcatatatccataggcttgaatttctaataatagtggtgtaataatctctttccgatttccagATTTCCCCATCTATCACACTGCGTTCGACTCCTATAACTGGATGGCATAGTATTGAGATCCATTCTTCCACCGCCATGTTACTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC
- - - - tgcttct
- - - - - - - - - - - catgtct
- - - - - - - - - - - - - - - - - - - - - - - - - -gcttgaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -agtggtg