Sequence
atgc intronic sequence ATGC exonic sequence...ctttaaaatgcttgtgttagtgcaacttgcttcctctggaaattgcgatcagttaatcttgtgattctaaaatcatgtgatgtccaaatcttaatgacagGGGAGTTGAACCATCTGCCTCGGCATCAGATATTAAGAAGGCATATCGGAAAGCTGCACTTAGACATCATCCTGACAAG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv06s0061g00090.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: LOC_Os05g31062.1 (Oryza sativa), 3'ss of exon 5
-ctttaaaatgct--tgtgttagtgcaacttgct---tcctctggaaattgcgatcagttaatcttgtgattctaaaatcatgtgatgtccaaatcttaatgacagGGGAGTTGAACCATCTGCCTCGGCATCAGATATTAAGAAGGCATATCGGAAAGCTGCACTTAGACATCATCCTGACAAG
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tcatctatattttaatgagacgaagcaaattaataatctcttattatgtggagatagcttaattagttgtttctc---ttctctcctgccc---cctcttttgcagGGGAATTGAACCATCTTCATCTCCAGCAGATATTAAGAAGGCATACCGGAAGGCTGCACTGAGGCATCACCCAGATAAG
upper sequence: Vv06s0061g00090.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GRMZM2G110587_T01 (Zea mays), 3'ss of exon 2
-ctttaaaatgct--tgtgttagtgcaacttgcttcctctggaaattgcgatcagttaatcttgtgattctaaaatcatgtgatgtccaaa-tcttaatgacagGGGAGTTGAACCATCTGCCTCGGCATCAGATATTAAGAAGGCATATCGGAAAGCTGCACTTAGACATCATCCTGACAAG
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actcttaacttctgatgaattatcctgacatgaggcatattctatttt--gctggc--attatgtggagataaacttaattactgattaccctttctgtatcagGGGAGTGGAGCCATCCTGCTCTTCAGCAGATATTAAGAAGGCATACCGGAAAGCTGCATTGAGACATCACCCAGACAAG
upper sequence: Vv06s0061g00090.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GRMZM2G348697_T02 (Zea mays), 3'ss of exon 8
ctttaaaatgcttgtgttagtgcaacttgcttcctctggaaattgcgatcagttaatcttgtgattctaaaatcatgtgatgtccaaa--tcttaatgacagGGGAGTTGAACCATCTGCCTCGGCATCAGATATTAAGAAGGCATATCGGAAAGCTGCACTTAGACATCATCCTGACAAG
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ctcttagtttctgatg--aattatcctgatgtgaggcagattctattttccgggtattatgtggagataaacttaattactaattatccttttctgtatcagGGGAGTGGAGCCATCCTGCTCTTCAGAAGATATTAAGAAGGCATACCGGAAAGCAGCATTGAGACATCACCCAGACAAG
upper sequence: Vv06s0061g00090.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GLYMA12G02420.1 (Glycine max), 3'ss of exon 10
---ctttaaaatgcttg-tgttagtgcaacttgcttcctctggaaattgcgatcagttaatcttgtgattctaaaatcatgtgatgtccaa-atcttaatgacagGGGAGTTGAACCATCTGCCTCGGCATCAGATATTAAGAAGGCATATCGGAAAGCTGCACTTAGACATCATCCTGACAAG
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gtatgacagaaaacataatgccagctaaacttatgttcct-----aatgtagggaaatattatcattcatttaaggctatcagctaactgacattatgatgacagGGGAGTTGAACCATCTGTTTCGATATCTGAAATCAAGAAGGCCTATCGGAAAGCTGCACTTAGACACCACCCAGACAAG
upper sequence: Vv06s0061g00090.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GLYMA11G10100.1 (Glycine max), 3'ss of exon 11
ctttaaaatgcttgtgttagt--gcaacttgcttcctctggaaattgcgatcagttaatcttgtgattctaaaatcatgtgatgtccaa-atcttaatgacagGGGAGTTGAACCATCTGCCTCGGCATCAGATATTAAGAAGGCATATCGGAAAGCTGCACTTAGACATCATCCTGACAAG
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gacagaaaacataatgccagctaaaaagttatttgttcctaatgtaggga---aataatatcattcatttaaggctatcagctaactgacattatgatggcagGGGAGTTGAACCATCTGTTTCGATATCTGAAATCAAGAAGGCCTATCGGAAAGCTGCACTGAGACACCACCCGGACAAG
upper sequence: Vv06s0061g00090.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GLYMA01G43690.1 (Glycine max), 3'ss of exon 9
-ctttaaaatgct--tgtgttagtgcaacttg-cttcctctggaaattgcgatcagttaatcttgtgattctaaaatcatgtgatgtccaaatcttaatgacagGGGAGTTGAACCATCTGCCTCGGCATCAGATATTAAGAAGGCATATCGGAAAGCTGCACTTAGACATCATCCTGACAAG
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gaaatagcatgctgttacattagagaaccctggctgtgtctaattaatgccaatatt--atcaatcatttaaggcatcagctgat--tcagattatgatggcagAGGAGTTGAACATTCTGTTTCGTCATCTGAAATCAAGAAGGCCTATCACAAAGCTGCACTTAGACATCATCCAGACAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cgatcagttaatcttgtgattctaaaatcatgtgatgtccaaatcttaatgacagGGGAGTTGAACCATCTGCCTCGGCATCAGATATTAAGAAGGCATATCGGAAAGCTGCACTTAGACATCATCCTGACAAG
attctaaaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ctttaaaatgcttgtgttagtgcaacttgcttcctctggaaattgcgatcagttaatcttgtgattctaaaatcatgtgatgtccaaatcttaatgacagGGGAGTTGAACCATCTGCCTCGGCATCAGATATTAAGAAGGCATATCGGAAAGCTGCACTTAGACATCATCCTGACAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - -gcttgtg
- - - - - - - - - - tgcaact
- - - - - - - - - - - - - - -cttcctc
- - - - - - - - - - - - - - - - - - -ggaaattg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaaatca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ccaaatc