Sequence
atgc intronic sequence ATGC exonic sequence...aaatatgcccccatgctttctagttctcttcgacttttgatgtttccttcattgtcaatgtataggaccttggtttactcctttacatattaatctacagGTACAAAGACGTCTTGCACAAAACCGTGAGGCTGCTCGTAAAAGCCGTCTGAGGAAAAAG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv07s0031g01320.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA11G36010.1 (Glycine max), 3'ss of exon 3
aaatatgcccccatgctttctagttctcttcgacttttgatgtttccttcattgtcaatgtatag---gaccttggtttactcctttacatattaatctacagGTACAAAGACGTCTTGCACAAAACCGTGAGGCTGCTCGTAAAAGCCGTCTGAGGAAAAAG
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gaatctgtattcaatttcaatatatggcttgaattc---atactctcttttatgcctatatatggtggaaacaaataggaatctaatatggtcaaacatgcagATACAAAGACGTCTTGCACAAAATCGAGAGGCTGCTCGTAAGAGCCGATTGAGGAAAAAG
upper sequence: Vv07s0031g01320.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA18G02430.3 (Glycine max), 3'ss of exon 3
aaatatgcccccatgctttctagttctcttcgacttttgatgtttccttcattgtcaatgtatag-gaccttggtttactcctttacatatt--aatctacagGTACAAAGACGTCTTGCACAAAACCGTGAGGCTGCTCGTAAAAGCCGTCTGAGGAAAAAG
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gaatctgtatttaatttggatgtatggcttggattc---atactctcttttatgcctatatatggtggaaacaattagggatctaatatggtcaaacatgcagATACAAAGACGTCTTGCACAAAATCGAGAGGCTGCTCGTAAGAGTCGGTTGAGGAAAAAG
upper sequence: Vv07s0031g01320.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA08G14840.1 (Glycine max), 3'ss of exon 3
aaatatgcccccatgctttctagttc---tcttcgacttttgatgtttccttcattgtcaatgtatag-gaccttggtttactcctttacatatt--aatctacagGTACAAAGACGTCTTGCACAAAACCGTGAGGCTGCTCGTAAAAGCCGTCTGAGGAAAAAG
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------ggtcctctgcttccaattttggatttctggctcgtattcatacttcttttatgcttttaaggagaaaaaaagaaagtatttaacatgttgaaacatgcagACACAAAGACGTCTTGCACAAAATCGAGAGGCCGCTCGCAAGAGTCGTTTGAGGAAAAAG
upper sequence: Vv07s0031g01320.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: EFJ28227 (Selaginella moellendorffii), 3'ss of exon 2
aaatatgcccccatgctttctagttctcttcgacttttgatgtttccttcattgtcaatgtataggaccttggtttactcctttacatattaatctacagGTACAAAGACGTCTTGCACAAAACCGTGAGGCTGCTCGTAAAAGCCGTCTGAGGAAAAAG
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-----------------------------------------------------------------------------------------gtgattta--gacacttcgacgtcttgcacagAACCGCGAGGCCGCACGGAAAAGCCGCTTGAGGAAAAAG
upper sequence: Vv07s0031g01320.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: EFJ29724 (Selaginella moellendorffii), 3'ss of exon 2
aaatatgcccccatgctttctagttctcttcgacttttgatgtttccttcattgtcaatgtataggacc--ttggtttactcctttacatattaatc-tacagGTACAAAGACGTCTTGCACAAAACCGTGAGGCTGCTCGTAAAAGCCGTCTGAGGAAAAAG
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----------------------gtacgcct-ggcactacat-ttcgctgcaacagcaacttcagggtttgatcgtgtcattgtttctcgtgctggtgatttagACACTTCGACGTCTTGCACAGAACCGCGAGGCCGCGCGGAAAAGCCGCTTGAGGAAAAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ccttcattgtcaatgtataggaccttggtttactcctttacatattaatctacagGTACAAAGACGTCTTGCACAAAACCGTGAGGCTGCTCGTAAAAGCCGTCTGAGGAAAAAG
tattaat putative branch site (score: 2)
tttacatattaatcta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
aaatatgcccccatgctttctagttctcttcgacttttgatgtttccttcattgtcaatgtataggaccttggtttactcctttacatattaatctacagGTACAAAGACGTCTTGCACAAAACCGTGAGGCTGCTCGTAAAAGCCGTCTGAGGAAAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - -tgccccc
- - - - - - -tgctttc
- - - - - - - - - - - - tctcttc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gaccttg