Sequence
atgc intronic sequence ATGC exonic sequence...ctcctagtaatttcctcacccttttgatgggcctgcctgtatttattctatcaacatcaaaatctaagattgataataattgtgtacaaaattttggcagCGATTCTTGCCTTCAGAGTTTGGAATGGACCCAGCAAGGATGGGAGATGCACTTGAACCAGGAAGAGTAACATTTGATGAGAAGATGATTGTGAGGAGGG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv02s0033g00290.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: LOC_Os12g16220.2 (Oryza sativa), 3'ss of exon 1
ctcctagtaatttcctcacccttttgatgggcctgcctgtatttattctatca---acatcaaaatctaagattgataataattgtgtacaaaattttg---gcagCGATTCTTGCCTTCAGAGTTTGGAATGGACCCAGCAAGGATGGGAGATGCACTTGAACCAGGAAGAGTAACATTTGATGAGAAGATGATTGTGAGGAGGG
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-----aataaat-ctagacaacatcaatataaatgtgggaaatgatagaatgacttacattgtaaaacggaggaagtatttactgtgaataattctctgcgagcagCGTTTCCTGCCGTCAGAATTTGGCATGGATCCATCAAGGATGGGGAATGCTCTTGAACCTGGGAGGGTTACATTTGATGAGAAGATGGAGATAAGAAGAG
upper sequence: Vv02s0033g00290.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GRMZM2G326116_T01 (Zea mays), 3'ss of exon 2
ctcctagtaatttcctcacccttttgatgggcctgcctgtatttattctatcaacatcaaaatctaagat--tgataataatt--gtgtacaaaattttg---gcagCGATTCTTGCCTTCAGAGTTTGGAATGGACCCAGCAAGGATGGGAGATGCACTTGAACCAGGAAGAGTAACATTTGATGAGAAGATGATTGTGAGGAGGG
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------gacatgtacggactctcat-atatgtagttcaatatataaataaacaacaaaagatgaagaggtgctgagtctaaataaacttacgttattgtggatgcagCGTTTTATACCATCGGAATTCGGCATGGATCCATCCAAGATGGGGCATGCTCTTGAACCAGGAAGGGTTACATTTGATGAAAAGATGGACCTAAGGCGTG
upper sequence: Vv02s0033g00290.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA09G34470.1 (Glycine max), 3'ss of exon 1
ctcctagtaatttcctcacccttttgatgggcctgcctgtatttattctatca--acatcaaaatctaagattgataataattgtgta---caaaattttggcagCGATTCTTGCCTTCAGAGTTTGGAATGGACCCAGCAAGGATGGGAGATGCACTTGAACCAGGAAGAGTAACATTTGATGAGAAGATGATTGTGAGGAGGG
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----aaaaagttgttccaaataagaccttaattaaaatgt-tttatttcaaaattatattagaatcacatttttttaatcattatacaatttggtttttctctagCGTTTCTTGCCTTCAGAATTTGGCATGGACCCTGCACTTATGGGACATGCACTTGAACCGGGAAGAGTGACATTTGATGAGAAAATGACCGTAAGGAAAG
upper sequence: Vv02s0033g00290.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA16G17680.3 (Glycine max), 3'ss of exon 1
ctcctagtaatttcctcacccttttgatgggcctgcc--tgtatttattctatcaacatcaaaatctaagattgataataattgtgtacaaaattttg---gcagCGATTCTTGCCTTCAGAGTTTGGAATGGACCCAGCAAGGATGGGAGATGCACTTGAACCAGGAAGAGTAACATTTGATGAGAAGATGATTGTGAGGAGGG
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-----actaattactaaacaatattgcaaaacttttttttgtctttccctcttctaaacaatattgtaaaactttttttttttgtttgtttgcctttccctgtagCGTTTCTTGCCTTCTGAATTTGGCCTAGACCCAGCAAGGATGGGGCATGCATTAGAACCAGGAAGGGTAACATTTGAAGACAAAATGGCTGTAAGGAAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttctatcaacatcaaaatctaagattgataataattgtgtacaaaattttggcagCGATTCTTGCCTTCAGAGTTTGGAATGGACCCAGCAAGGATGGGAGATGCACTTGAACCAGGAAGAGTAACATTTGATGAGAAGATGATTGTGAGGAGGG
gattgat putative branch site (score: 4)
attgataataattgtg 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ctcctagtaatttcctcacccttttgatgggcctgcctgtatttattctatcaacatcaaaatctaagattgataataattgtgtacaaaattttggcagCGATTCTTGCCTTCAGAGTTTGGAATGGACCCAGCAAGGATGGGAGATGCACTTGAACCAGGAAGAGTAACATTTGATGAGAAGATGATTGTGAGGAGGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - ctcaccc
- - - - - - - - - - - -ttgatgg
- - - - - - - - - - - - - - - gcctgcc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -caaaatc