Sequence
atgc intronic sequence ATGC exonic sequence...atagtgcatgtcacctttggttccttgcagcattaacttgtttatattttcttctggaatgtttcagaaggtacttcaccattaactttctcatgaatagGTCAAGCAGATGGTAGTGGCTACGCTTGCTGAATCTGGCATGAATCTTTCAGATGATGTAATAGAAAGTATCATTGATAAG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv00s1569g00020.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: LOC_Os12g40510.1 (Oryza sativa), 3'ss of exon 6
atagtgcatgtcacctttggttccttgcagca-ttaacttgtttatatt-ttcttctgg--aatgtttcagaaggtacttcaccattaactt------tctcatgaatagGTCAAGCAGATGGTAGTGGCTACGCTTGCTGAATCTGGCATGAATCTTTCAGATGATGTAATAGAAAGTATCATTGATAAG
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----------tcaaagctaaatattttaaatagttttgttgtggatgtcattcttttgggtaggatatttccttttacttcatctatagtttataaaattgatttatcagGTTAAGCAGATGGTTGTTGCTACACTTGCTGAGTCTGGAATGAATCTTTCTGATGAAATTATAGAGAGCATAATCGATAAG
upper sequence: Vv00s1569g00020.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: LOC_Os03g42840.1 (Oryza sativa), 3'ss of exon 5
------atagtgcatgtcacctttggttccttgcagcattaacttgtttatattttcttctggaatgtttcagaaggtacttcaccattaactttctcatg-aatagGTCAAGCAGATGGTAGTGGCTACGCTTGCTGAATCTGGCATGAATCTTTCAGATGATGTAATAGAAAGTATCATTGATAAG
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tgtgtcataactcagaataccatttgccttctgcag-ataatgcaactgatcttctatctt------ttttatgttatacttaattgtttccttttttgcctattagGTTAAGCAAATGGTTGTTGCAACACTTGCTGAGTCGGGAATGAATCTTTCGGATGAAGTCATAGAGAGCATCATTGATAAG
upper sequence: Vv00s1569g00020.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GRMZM2G007555_T01 (Zea mays), 3'ss of exon 6
atagtgcatgtcacctttggttccttgcagcattaacttgtttatattttcttctggaatgtttcagaaggtacttcaccattaact--ttctcatgaatagGTCAAGCAGATGGTAGTGGCTACGCTTGCTGAATCTGGCATGAATCTTTCAGATGATGTAATAGAAAGTATCATTGATAAG
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cttttttctgaagtatttctcttgata-agaaatgccacctttggattgaattatgtccttttttggctagc-cttaatggttaattgcgtttggttttcagGTTAAGCAGATGGTTGTTGCTACACTTGCTGAGTCAGGAATGAATCTTTCAGATGAAATTGTAGAGAGTATAATTGACAAG
upper sequence: Vv00s1569g00020.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GRMZM2G112672_T02 (Zea mays), 3'ss of exon 5
atagtgcatgtcacctttggttccttgcagcattaacttgtttatattttcttctggaatgtttcagaaggtacttcaccattaactt-tctcatgaatagGTCAAGCAGATGGTAGTGGCTACGCTTGCTGAATCTGGCATGAATCTTTCAGATGATGTAATAGAAAGTATCATTGATAAG
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atca-gcatttctattattcttattaaagccagttaactactaaaaagtgaattgattttaatgcattctgtatctaataattttcttgttttgttattagGTAAAGCAAATGGTTGTTGCTACACTTGCGGAGTCAGGAATGAATCTTTTAGATGAGGTCATAGAGAGCATCATTGATAAG
upper sequence: Vv00s1569g00020.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA17G00830.1 (Glycine max), 3'ss of exon 6
atagtgcatgtcacctttggttccttgcagcattaacttgtttatattttcttctgga----atgtttcagaaggtac-ttcaccattaacttt-ctcatg-aatagGTCAAGCAGATGGTAGTGGCTACGCTTGCTGAATCTGGCATGAATCTTTCAGATGATGTAATAGAAAGTATCATTGATAAG
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-------gtttctttcctcgaaatctgttccatacgctgatatatgtttcttatagcagcatatatttgataatatacattgatgattgatgtcatttgtgtaatagGTAAAACAAATGGTAGTGGCCACTCTAGCCGAATCTGGCATGAATCTTTCAGATGATGTGATCGAAAGTATTATTGACAAG
upper sequence: Vv00s1569g00020.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA07G39940.1 (Glycine max), 3'ss of exon 6
---atagtgcatgtcacctttggttccttgcagcattaacttgtttatattttcttctggaatgtttcagaaggt-acttcaccattaac-tttctcatgaatagGTCAAGCAGATGGTAGTGGCTACGCTTGCTGAATCTGGCATGAATCTTTCAGATGATGTAATAGAAAGTATCATTGATAAG
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ttcttttctcaaaatctgtttcatactctgacatgatatgtttcttatagcagctt-----atatttggtaatatgaattgatgattgatgttatttgggtatagGTAAAACAAATGGTAGTGGCCACTCTAGCCGAATCTGGCATGAATCTTTCAGATGATGTGATCGAAAGTATTATTGACAAGMapped EST sequences
Showing partial alignments of ESTs and genomic sequences. See full alignments
ATGC EST sequence
ATGC genomic sequence (exon)
ATGC genomic sequence (truncated intron)
EST:
gi|110380717|gb|EC946005.1|EC946005EST: CATTTCAACTGTATGATCTAAAGCAACAAGGGTTCATTGAAAGACAGGAG GTCAAGCAGATGGTAGTGGCTACGCTTGCTGAATCTGGCATGAATCTTTCA
genomic: CATTTCAACTGTATGATCTAAAGCAACAAGGGTTCATTGAAAGACAGGAGgtgcccattt ... tcatgaatagGTCAAGCAGATGGTAGTGGCTACGCTTGCTGAATCTGGCATGAATCTTTCA
EST:
gi|77582686|gb|DV220332.1|DV220332EST: CATTTCAACTGTATGATCTAAAGCAACAAGGGTTCATTGAAAGACAGGAG GTCAAGCAGATGGTAGTGGCTACGCTTGCTGAATCTGGCATGAATCTTTCA
genomic: CATTTCAACTGTATGATCTAAAGCAACAAGGGTTCATTGAAAGACAGGAGgtgcccattt ... tcatgaatagGTCAAGCAGATGGTAGTGGCTACGCTTGCTGAATCTGGCATGAATCTTTCA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.attttcttctggaatgtttcagaaggtacttcaccattaactttctcatgaatagGTCAAGCAGATGGTAGTGGCTACGCTTGCTGAATCTGGCATGAATCTTTCAGATGATGTAATAGAAAGTATCATTGATAAG
cattaac putative branch site (score: 2)
ctttctcat CT-rich tract
attaacttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
atagtgcatgtcacctttggttccttgcagcattaacttgtttatattttcttctggaatgtttcagaaggtacttcaccattaactttctcatgaatagGTCAAGCAGATGGTAGTGGCTACGCTTGCTGAATCTGGCATGAATCTTTCAGATGATGTAATAGAAAGTATCATTGATAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
- - -gcatgtc
- - - - - - - - - - - ccttgca
- - - - - - - - - - - - - - - cattaac
- - - - - - - - - - - - - - - - - - - - - - - - - - - -ggaatgt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cttcacc