Sequence
atgc intronic sequence ATGC exonic sequence...caaacaaaggaatcgaggcagtgggttttttgtattattaattagttccgttttctatgccctgttattttgtttgttgaaatgtacttttgttttgcagTGTAATAGTTGAAGCTCTGAAGGTGGATAGTCTGCAGAAACTTTGCTCATCATTGGAACCTATTCTTCGGAGAGTT
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv00s0181g00220.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: LOC_Os02g08120.2 (Oryza sativa), 3'ss of exon 2
-caaacaaaggaatcgaggcagtgggttttttgtattattaattagttccgttttctatgcc-ctgttattttgtttgttgaaatgtacttttgttttgcagTGTAATAGTTGAAGCTCTGAAGGTGGATAGTCTGCAGAAACTTTGCTCATCATTGGAACCTATTCTTCGGAGAGTT
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ccttgcgtgttcattactgtaaagctcaacatgtgagaa-ggtgaattgcgtcttttgttcttctgtcatgattttttccgcttcgc-ctctttctctgcagTGTTATTGTTGAAGCATTAAAGGTGGATAGTCTGCAGAGGCTTTGCTCATCACTGGAACCAATTCTTCGTAGAGTG
upper sequence: Vv00s0181g00220.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: LOC_Os02g35470.3 (Oryza sativa), 3'ss of exon 2
caaacaaaggaatcgaggcagtgggttttttgtattattaat-tagttccgttttcta--tgccctgtt---attttgtttgttgaaatgtacttttgttttgcagTGTAATAGTTGAAGCTCTGAAGGTGGATAGTCTGCAGAAACTTTGCTCATCATTGGAACCTATTCTTCGGAGAGTT
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----taaattttttttgt--gtatatccttgaaattgcaaaaatatgtttgtatcttagttgctcgatttagaggttgctcacttaacaaatgacacatattgcagTGTCATTGTGGAAGCTCTTAAGGTGGATAGTTTGCAGAAGCTTTGTTCATCACTGGAGCCAATTCTTCGTAGAGTT
upper sequence: Vv00s0181g00220.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GRMZM2G018837_T04 (Zea mays), 3'ss of exon 2
caaacaaaggaatcgaggcagtgggtt-ttttgtattattaattagttccgttttctatgccctgtt--attttgtttgttgaaa------tgtacttttgttttgcagTGTAATAGTTGAAGCTCTGAAGGTGGATAGTCTGCAGAAACTTTGCTCATCATTGGAACCTATTCTTCGGAGAGTT
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--------cttgcttgcttggcgttttattttaacttattaat-aacagaataatcggtgacctatcacattctatttgttgtaaacggtctgtctgtctaccatgcagTGTTATTGTTGAAGCGTTAAAGGTGGATAGTCTGCAGAGGCTCTGCTCATCATTGGAACCAATTCTTCGTAGAGTA
upper sequence: Vv00s0181g00220.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GRMZM2G451882_T01 (Zea mays), 3'ss of exon 2
caaacaaaggaatcgaggcagtg-ggttttttgtattatta-attagttccgttttctatgccctgtt--attttgtttgt---tgaaatgtacttttgttttgcagTGTAATAGTTGAAGCTCTGAAGGTGGATAGTCTGCAGAAACTTTGCTCATCATTGGAACCTATTCTTCGGAGAGTT
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------tggctctcttgcttgtttggcgttttattttaacgtattaataacaaaata-atgacctatcacattctagttgtaaataatctctctatctaccctgcagTGTTATTGTTGAAGCTTTAAAGATGGATAGTCTGCAGAGGCTCTGCTCATCACTGGAACCAATTCTTCGTAGAGTA
upper sequence: Vv00s0181g00220.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA15G07330.2 (Glycine max), 3'ss of exon 2
-caaacaaaggaatcgaggcagtgggttttttgtattattaattagttccgttttctatgc-cctgttattttgttt-gttgaaatgtacttttgttttgcagTGTAATAGTTGAAGCTCTGAAGGTGGATAGTCTGCAGAAACTTTGCTCATCATTGGAACCTATTCTTCGGAGAGTT
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tgttattagggtattaacactaatatgttaatctgttaaagcttaatttgctgatcaatgcatttgttgtttttcttcatttattcatacc---aatttgcagTGTAATTGTTGAAGCCCTGAAGGTGGACAGTCTGCAGAAACTTTGTTCATCACTGGAGCCTATTCTTCGTAGAGTT
upper sequence: Vv00s0181g00220.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA08G06320.1 (Glycine max), 3'ss of exon 1
caaacaaaggaatcgaggca-gtgggttttttgtattattaattagttccgttttctatgccctgttattttgtttgttgaaatgtacttttgttttgcagTGTAATAGTTGAAGCTCTGAAGGTGGATAGTCTGCAGAAACTTTGCTCATCATTGGAACCTATTCTTCGGAGAGTT
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taagcagttatgtttctatatgttcaagcttaatttggtgtcttaaacttggtta-tatatctagtaatttcttatattcattgtttatgttattttgcagTGTAATTGTTGAGGCCCTGAAGGTGGACAGTCTGCAGAAACTTTGCTCATCACTGGAGCCTATTCTACGCAGAGTT
upper sequence: Vv00s0181g00220.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA07G30990.2 (Glycine max), 3'ss of exon 1
caaacaaaggaatcgaggcagtgggttttttgtattattaattagttccgtttt--ctatgccctgttattttgtttgttgaaatgtacttttgt---tttgcagTGTAATAGTTGAAGCTCTGAAGGTGGATAGTCTGCAGAAACTTTGCTCATCATTGGAACCTATTCTTCGGAGAGTT
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----gaaaggaatcacta-aggaggcagttagcttaatttggtgtcttaaacttggctatgaatttgtttattgcttttattcatttatttatgttaatttgcagTGTAATTGTTGAAGCCCTGAAGGTTGACAGTCTGCAGAAACTTTGCTCGTCACTGGAGCCTATTCTACGCAGAGTT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttccgttttctatgccctgttattttgtttgttgaaatgtacttttgttttgcagTGTAATAGTTGAAGCTCTGAAGGTGGATAGTCTGCAGAAACTTTGCTCATCATTGGAACCTATTCTTCGGAGAGTT
cttttgtttt CT-rich tract
ttattttgtttgtt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
caaacaaaggaatcgaggcagtgggttttttgtattattaattagttccgttttctatgccctgttattttgtttgttgaaatgtacttttgttttgcagTGTAATAGTTGAAGCTCTGAAGGTGGATAGTCTGCAGAAACTTTGCTCATCATTGGAACCTATTCTTCGGAGAGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
