Sequence
atgc intronic sequence ATGC exonic sequence...agaagaaagtagatcgttcacttggtagaaagccaaaatttcttttcacccacgtcctcatcatccaactcttatttttatgtatttaatttggaatcagGTGAGGAAGGAAAAGTTAGGTGACAGAATTACAGCCCTTCACCAGCTAGTATCCCCATTTGGGAAG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv11s0016g03560.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: LOC_Os02g17680.1 (Oryza sativa), 3'ss of exon 3
agaagaaagtagatcgttcacttggtagaaagccaaaatttcttttca--cccacgtcctcatcatcc-aactcttatttttatgtatttaatttggaatcagGTGAGGAAGGAAAAGTTAGGTGACAGAATTACAGCCCTTCACCAGCTAGTATCCCCATTTGGGAAG
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-gcatggaatc-attgtaggttaagagataaggtgagatggggttggagatggaaatgatggcgttcttaattagtatgttt-tgcttgtgctttttcttcagGTGAGGAAGGAGAAGCTAGGTGATAGAATAACTGCCCTTCACCAGCTTGTCTCCCCATTTGGGAAG
upper sequence: Vv11s0016g03560.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: LOC_Os01g13000.1 (Oryza sativa), 3'ss of exon 3
agaagaaagtagatcgttcacttgg-tagaaagccaaaatttcttttcacccacgtcct-catcatccaactcttattt-ttatgtattta--atttggaatcagGTGAGGAAGGAAAAGTTAGGTGACAGAATTACAGCCCTTCACCAGCTAGTATCCCCATTTGGGAAG
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-----agaacaaatacatcaatggaattgaagatcgtagcttgctacattgcatgcattacaatacataatttgtatctcttctataccaaacattttatttcagGTCAGGAAGGAGAGGCTTGGGGACAGAATAACAGCTCTTCACCAGATAGTTTCCCCATTTGGCAAG
upper sequence: Vv11s0016g03560.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA07G09180.3 (Glycine max), 3'ss of exon 2
agaagaaagtagatcgttcacttggtagaa--agccaaaatttcttttcacccacgtcctcatcatccaactcttatttttatgtatttaatttggaatcagGTGAGGAAGGAAAAGTTAGGTGACAGAATTACAGCCCTTCACCAGCTAGTATCCCCATTTGGGAAG
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atgagaatcgaaaccagccaaatgaaacaacaaaatataaccaaatttttagcatgtgcgtgt-acgacacatgtatattaattcctctt-ctcaatttcagGTTAGGAAGGAAAAGCTAGGTGAGAGAATTACGGCCCTTCATCAGCTCGTTTCCCCATTTGGGAAG
upper sequence: Vv11s0016g03560.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA05G35610.1 (Glycine max), 3'ss of exon 3
agaagaaagtagatcgttcacttggtagaaagccaaaatttcttttcacccacgtcct-catcatccaac-tcttatttttatgtatttaatttggaatcagGTGAGGAAGGAAAAGTTAGGTGACAGAATTACAGCCCTTCACCAGCTAGTATCCCCATTTGGGAAG
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--ctacacatgttttcttaatttttattttcttcattttatcttgatatgaaaattaaacataagccaacatattaattaagcatgtgcttgtccgtttcagGTTAGGAAGGAGAAATTAGGTGACAGAATTACCGCCCTTCATCAACTCGTTTCCCCATTCGGAAAG
upper sequence: Vv11s0016g03560.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA08G04110.1 (Glycine max), 3'ss of exon 3
agaagaaagtagatcgttcacttggtagaaagc--caaaatttcttttcacccacg-----tcctcatcatccaac-tcttatttttatgtatttaatttggaatcagGTGAGGAAGGAAAAGTTAGGTGACAGAATTACAGCCCTTCACCAGCTAGTATCCCCATTTGGGAAG
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--------atttttatttcattttattttatttttctcattttatcttgatatatgaagaattaacataagccagcatatcaattaagcatgtgtttgcccgttacagGTTAGGAAGGAGAAATTAGGTGACAGAATTACCGCCCTTCATCAACTCGTTTCCCCATTCGGAAAGMapped 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|71871899|gb|DT020954.1|DT020954EST: CACTTAAGAAAGCTAGGGTTCAAGCTTCTCCAACCCAGCCTACCTTCAAG GTGAGGAAGGAAAAGTTAGGTGACAGAATTACAGCCCTTCACCAGCTAGTA
genomic: CACTTAAGAAAGCTAGGGTTCAAGCTTCTCCAACCCAGCCTACCTTCAAGgtaagaaaca ... ttggaatcagGTGAGGAAGGAAAAGTTAGGTGACAGAATTACAGCCCTTCACCAGCTAGTA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcacccacgtcctcatcatccaactcttatttttatgtatttaatttggaatcagGTGAGGAAGGAAAAGTTAGGTGACAGAATTACAGCCCTTCACCAGCTAGTATCCCCATTTGGGAAG
atttaat putative branch site (score: 4)
tcttatttttatgtat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
agaagaaagtagatcgttcacttggtagaaagccaaaatttcttttcacccacgtcctcatcatccaactcttatttttatgtatttaatttggaatcagGTGAGGAAGGAAAAGTTAGGTGACAGAATTACAGCCCTTCACCAGCTAGTATCCCCATTTGGGAAG
-gaagaaa
- - - - - - - - - cacttgg
- - - - - - - - - - - - - - -aagccaa
- - - - - - - - - - - - - - - - - - - - - - - - - - cgtcctc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tcatcca