Sequence
atgc intronic sequence ATGC exonic sequence...atagcctaaatttgcttataatttccactctttagttttatagatttgatttttttctttcttaatttgaacgtgttgctggtgacatgtgaatgcatagGTTCTCACTCCAAATGTCCCTGATATAATGGTTTCTCCTCCTGAGGATGATCATCTCCATCATGTGATCGACACAATGGCTCTATACGTTCTGGATGGAG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv04s0008g06810.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: LOC_Os02g08360.1 (Oryza sativa), 3'ss of exon 10
-atagcctaaatttgcttataatttccactctttagttttat-agatttgattt-ttttctttcttaatttgaacgtgttgctggtgacatgtgaatgcatagGTTCTCACTCCAAATGTCCCTGATATAATGGTTTCTCCTCCTGAGGATGATCATCTCCATCATGTGATCGACACAATGGCTCTATACGTTCTGGATGGAG
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tcttggatgaggatatctgcagtt---agcttgaaattgaatgatatctaataagttttaaccaacattttggttattattctaatttcatttggtttaacagGTCCTCACACCAAATGTTCCTGATATAGTGGTTGCTCCGCCAGATGATGCACATGTTCGGCATGTGATTGACACAATGGCTCTGCATGTACTTGACGGGG
upper sequence: Vv04s0008g06810.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GRMZM2G133308_T02 (Zea mays), 3'ss of exon 10
--atagcctaaatttgcttataatttccactctttagttttatagatttgatttttttctttcttaatttgaacgtgttgctggtgacatgtgaatgcatagGTTCTCACTCCAAATGTCCCTGATATAATGGTTTCTCCTCCTGAGGATGATCATCTCCATCATGTGATCGACACAATGGCTCTATACGTTCTGGATGGAG
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tgatatcctgtgatactggatttcgttaaatgagtgattatct-gtttaagtaagagatcttgtagattatttcatgttaatggattcat-tgacttgatagGTCCTTACACCAAATGTTCCTGATATTGTGGTTGCTCCACCTGATGATGGGCATCTTCGGCATGTGATTGACACAATGGCTCTGCACGTACTTGATGGTG
upper sequence: Vv04s0008g06810.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GRMZM2G174785_T02 (Zea mays), 3'ss of exon 10
--atagcctaaatttgcttataatttccactctttagttttatagatttgatttttttctttcttaatttgaacgtgttgctggtgacatgtgaatgcatagGTTCTCACTCCAAATGTCCCTGATATAATGGTTTCTCCTCCTGAGGATGATCATCTCCATCATGTGATCGACACAATGGCTCTATACGTTCTGGATGGAG
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tgatatcctgtgatactgcatttcgttaaatgagtgattatct-gtttaagtaagagatcttatagattatttcatgttaatggattcat-tgacttgatagGTCCTTACACCAAATGTTCCTGATATTGTGGTTGCTCCACCTGATGATGGGCATCTTCGGCATGTGATTGACACAATGGCTCTGCACGTACTTGATGGTG
upper sequence: Vv04s0008g06810.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GLYMA08G34030.1 (Glycine max), 3'ss of exon 10
------------atagcctaaatttgcttataatttccactctttagttttatagatttgatttttttctttcttaatttgaacgtgttgctggtgacatgtgaatgcatagGTTCTCACTCCAAATGTCCCTGATATAATGGTTTCTCCTCCTGAGGATGATCATCTCCATCATGTGATCGACACAATGGCTCTATACGTTCTGGATGGAG
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ataaaaaatactagaggtagaattacttcatggttctcactcct-aatattcctgatataatggtttttactcctaatat-----------tcctgccatattcgttggtagGTTCTAACTCCTAATGTTCCTGATATAATGGTTACACCTCCTGAGGATGAACATTTAAGGCATGTAATTGATACAATGGCTTTGCATGTCCTGGATGGAG
upper sequence: Vv04s0008g06810.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GLYMA16G15820.1 (Glycine max), 3'ss of exon 6
----atagcctaaatttgcttataatttccactctttagtttta-tagatttgatttttttctttcttaatttgaacgtgttgctggtgacatgtgaatgcatagGTTCTCACTCCAAATGTCCCTGATATAATGGTTTCTCCTCCTGAGGATGATCATCTCCATCATGTGATCGACACAATGGCTCTATACGTTCTGGATGGAG
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taaaaaatactagatgtagaattacttaatgGTTCTAACTCCTAATAGGCCTGATATAATGGTTT-TTACTCTTAA--TATTCCTGCTATAATTTG--TTGGTAGGTTCTAACTCCTAATGTTCCTGATATAATGGTTACACCCCCTGAGGATGACCATTTAAGGCATGTAATTGATACAATGGCTTTGTATGTCCTGGATGGAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttgatttttttctttcttaatttgaacgtgttgctggtgacatgtgaatgcatagGTTCTCACTCCAAATGTCCCTGATATAATGGTTTCTCCTCCTGAGGATGATCATCTCCATCATGTGATCGACACAATGGCTCTATACGTTCTGGATGGAG
tcttaat putative branch site (score: 3)
ttttttctttcttaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
atagcctaaatttgcttataatttccactctttagttttatagatttgatttttttctttcttaatttgaacgtgttgctggtgacatgtgaatgcatagGTTCTCACTCCAAATGTCCCTGATATAATGGTTTCTCCTCCTGAGGATGATCATCTCCATCATGTGATCGACACAATGGCTCTATACGTTCTGGATGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - -tccactc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ttgctgg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gacatgt