Sequence
atgc intronic sequence ATGC exonic sequence...gcaaaagaatgtatcgaggaatcattaaattttcatgagatgtccaaatgagctcttatcatttgattggtattgattttatgtctgaattgaatttcagCCATCGATGCACCTGGTGGCTTTCTCTTTGAATGGTGGTCTGTTTTTTGGGATATATTTATAGCTAGGACAAATGAGAAACACTCGGAGGCTGCTGCATC
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv11s0016g04550.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: LOC_Os01g42260.2 (Oryza sativa), 3'ss of exon 2
--------gcaaaagaatgtatcgaggaatcattaaattttcatgagatgtccaaatgagctcttatcatttgattggtattgattttatg-----tctgaa---ttgaattt--cagCCATCGATGCACCTGGTGGCTTTCTCTTTGAATGGTGGTCTGTTTTTTGGGATATATTTATAGCTAGGACAAATGAGAAACACTCGGAGGCTGCTGCATC
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gtatgtatttcccagcaagttgagtgaagctatttg--tgtcatgagttttgcta-caattttttaccttttgttagtaaaggatgtcgcgaactttctgaactcttgtttcttgcagCGATTGATGCTCCTGGTGGTTTTCTTTTTGAGTGGTGGTCAGTTTTTTGGGATATTTTCATAGCAAGGACAAATGAGAAGCATTCAGATGTTGCGGCTTC
upper sequence: Vv11s0016g04550.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: LOC_Os01g42270.1 (Oryza sativa), 3'ss of exon 2
gcaaaagaatgtatcgaggaatcattaaattttcatgagatgtccaaatgagctc-ttatcatttgattggtattgattttatgtctgaattgaatttca----gCCATCGATGCACCTGGTGGCTTTCTCTTTGAATGGTGGTCTGTTTTTTGGGATATATTTATAGCTAGGACAAATGAGAAACACTCGGAGGCTGCTGCATC
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--taattagtgattggaagttgctatggagttatttaatttggct---tgtgtttgccacaattttaatgatattacttacttccttgaattaactttcatacagCAATTGATGCTCCTGGTGGCTTTCTTTTTGAGTGGTGGTCAATATTTTGGGATATATTCATAGCACAAACAGATCGGGAACATTCTGATGTTGCAACGTC
upper sequence: Vv11s0016g04550.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G361398_T01 (Zea mays), 3'ss of exon 2
gcaaaagaatgtatcgaggaatcattaaattttcatgagatgtccaaatgagctcttatcatttgattggtattgattttatgtctgaattgaatttcagCCATCGATGCACCTGGTGGCTTTCTCTTTGAATGGTGGTCTGTTTTTTGGGATATATTTATAGCTAGGACAAATGAGAAACACTCGGAGGCTGCTGCATC
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------gtacgcctcttg-aacagtcacaatg----gagtctttttagcctgattttatttttgtactgccat-ggttttgagcttatctttc-ttgtagCTATTGATGCTCCTGGTGGCTTTCTCTTTGAGTGGTGGTCTGTATTTTGGGATATATTCATAGCAAGAACAAATGAGAAGCATTCAGATGTTGCAGCATC
upper sequence: Vv11s0016g04550.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G022383_T01 (Zea mays), 3'ss of exon 2
-----------gcaaaagaatgtatcgaggaatcattaaattttcatgagatgtccaaatgagctct---tatcatttgattgg--tattgattttatgtctgaa-------ttgaatttcagCCATCGATGCACCTGGTGGCTTTCTCTTTGAATGGTGGTCTGTTTTTTGGGATATATTTATAGCTAGGACAAATGAGAAACACTCGGAGGCTGCTGCATC
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gtatgcatttgtctgcaagttgtgtggagttacttttc--ttttcttgagttcttcctgtccgttttgtctgttgcttgtcaagactattatttacttcccaaaaactgttcttttttttcagCCATTGATGCACCCGGTGGCTTTCTTTTCGAGTGGTGGTCGGTTTTCTGGGATATATTCATAGCAAGAACTAACGAGAAGCATTCAGATGTTGCAGCCTC
upper sequence: Vv11s0016g04550.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA05G08110.1 (Glycine max), 3'ss of exon 2
gcaaaagaatgtatcgaggaatcatta-----aattttcatgagatgtccaaatg----agctcttatcatttgattggtattgattttatgtctgaat-tgaatttcagCCATCGATGCACCTGGTGGCTTTCTCTTTGAATGGTGGTCTGTTTTTTGGGATATATTTATAGCTAGGACAAATGAGAAACACTCGGAGGCTGCTGCATC
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gtaagataata-atataggcttttttaggggaaagaaattaggtatatgcaaatgcaactgctcttctaatttactgaatttgacctttacttttggccgcatgctccagCTATAGATGCACCTGGTGGTTTTCTTTTTGAGTGGTGGTCTGTCTTCTGGGACATATATATTGCCATGGTAAATCAGAAGCACCCAGAAGCAGCAGTTTC
upper sequence: Vv11s0016g04550.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA17G12900.1 (Glycine max), 3'ss of exon 2
gcaaaagaatgtatcgaggaatcatt-----aaattttcatgagatgtccaaatga----gctcttatcatttgattggtattgattttatgtctgaattgaatttcagCCATCGATGCACCTGGTGGCTTTCTCTTTGAATGGTGGTCTGTTTTTTGGGATATATTTATAGCTAGGACAAATGAGAAACACTCGGAGGCTGCTGCATC
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gtaagataatgcatataggctttcttaggggaaagaaattaggtatatgcaaatgcaaatgctcttctaattt-attgaatttgactttttggctacat---gctccagTTATAGATGCACCTAGTGGTTTTCTTTTTGAGTGGTGGTCTGTCTTCTGGGACATATATATTGCCAGGGCAAATCAGAAGCTCCAAGATACAGCTCAGAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aaatgagctcttatcatttgattggtattgattttatgtctgaattgaatttcagCCATCGATGCACCTGGTGGCTTTCTCTTTGAATGGTGGTCTGTTTTTTGGGATATATTTATAGCTAGGACAAATGAGAAACACTCGGAGGCTGCTGCATC
tattgat putative branch site (score: 3)
tattgattttatgt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gcaaaagaatgtatcgaggaatcattaaattttcatgagatgtccaaatgagctcttatcatttgattggtattgattttatgtctgaattgaatttcagCCATCGATGCACCTGGTGGCTTTCTCTTTGAATGGTGGTCTGTTTTTTGGGATATATTTATAGCTAGGACAAATGAGAAACACTCGGAGGCTGCTGCATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- aaaagaa
- - - - - - - - -ggaatca
- - - - - - - - - - - - - - - - -catgaga
- - - - - - - - - - - - - - - - - - - - - -ccaaatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgattgg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgtctga