Sequence
atgc intronic sequence ATGC exonic sequencegttatgagaaaaatagtattaacaacaaacataattttcccatatctataaacatgtagcagtaatatctctagcgtttgagttaacagttttgaggattggtttccagACACTGAGACGTTTGGCACAAAACAGAGAAGCAGCAAGAAAGAGTAGGCTGAGAAAGAAGGCGTATGTGCAGCAGCTAGAATCCAGTAGGATTAAGCTCA
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv06s0080g00360.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: LOC_Os05g37170.8 (Oryza sativa), 3'ss of exon 4
gttatgagaaaaatagtatt-aacaacaaacataattttcccatatctataaacatgtagcagtaatatctctagcgtttgagttaacagttttgaggattggtttccagACACTGAGACGTTTGGCACAAAACAGAGAAGCAGCAAGAAAGAGTAGGCTGAGAAAGAAGGCGTATGTGCAGCAGCTAGAATCCAGTAGGATTAAGCTCA
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-------gtgtgattgtatttggtgtcagagttatgccttgtttggccctgcatttgtacca-taat----ctaacctgt------acagttccata------ccctcagACTGAAAGGCGATTGGCTCAGAACAGAGAAGCTGCAAGAAAGAGCAGGCTGAGGAAAAAG----------------------------------------
upper sequence: Vv06s0080g00360.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA12G09430.3 (Glycine max), 3'ss of exon 6
-------gttatg-agaaaaatagtattaacaacaaa--cataatttt---cccatatctataaacatgtagcagt-----aatatctctagcgtttgagttaac----agttttgaggattggttt----ccagACACTGAGACGTTTGGCACAAAACAGAGAAGCAGCAAGAAAGAGTAGGCTGAGAAAGAAGGCGTATGTGCAGCAGCTAGAATCCAGTAGGATTAAGCTCA
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gtgttgaatgacacacacaaacacatttatgtataaattcataatattaatattatattccaaggtatgtttttgtttttgaattttttttacgtgggaggtaagtcaagatattcttgtttggtttggattcagACACTGAGACGTTTAGCTCAAAACAGAGAAGCTGCAAGGAAAAGCCGTCTCAGGAAAAAG----------------------------------------
upper sequence: Vv06s0080g00360.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA11G19030.1 (Glycine max), 3'ss of exon 3
------gttatgagaaaaatag---------tattaacaaca---aacataattttcccatatctataaacatgtagcagtaat---atctctagcgtttgagttaa----cagttttgaggattggttt----ccagACACTGAGACGTTTGGCACAAAACAGAGAAGCAGCAAGAAAGAGTAGGCTGAGAAAGAAGGCGTATGTGCAGCAGCTAGAATCCAGTAGGATTAAGCTCA
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gttttgaatatgatacaaatacatacacatttatttataatctatgatatcaatattatatattgcaaggtatgtttttgtttttggattttttaaatgggaggtaagtcaagatattcttgtttggtttggattcagACACTGAGACGTTTAGCTCAAAACAGAGAAGCTGCAAGGAAAAGCCGTCTCAGGAAAAAG----------------------------------------
upper sequence: Vv06s0080g00360.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA12G30990.1 (Glycine max), 3'ss of exon 6
gttatgagaaaaatagtattaacaacaaacataattttcccatatctataaacatgtagcagtaatatctctagcgtttgagttaacagttttgaggattggtttccagACACTGAGACGTTTGGCACAAAACAGAGAAGCAGCAAGAAAGAGTAGGCTGAGAAAGAAGGCGTATGTGCAGCAGCTAGAATCCAGTAGGATTAAGCTCA
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-----------------gttattga-----ataattttccaaactcttt---tttattaaatgattttacgtaggatctaaggtaagatttttttg--ttggcctc-agACATTGAGACGTTTGGCTCAAAACAGAGAGGCTGCAAGGAAAAGCCGTCTGAGGAAAAAG----------------------------------------
upper sequence: Vv06s0080g00360.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: AT1G08320.1 (Arabidopsis thaliana), 3'ss of exon 7
gttatgagaaaaatagtattaacaacaaacataattttcccatatctataaacatgtagcagtaatatctctagcgtttgagttaacagttttgaggattggtttccagACACTGAGACGTTTGGCACAAAACAGAGAAGCAGCAAGAA--AGAGTAGGCTGAGAAAGAAGGCGTATGTGCAGCAGCTAGAA-TCCAGTAGGATTAAGCTCA-
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-------------------------------taattcatttatgaacgtataagttccgcatttcttgttattctatatgtaatgatactagtatgaa---aataacaaatgcatatacatatggtttgagcagGCGTATGTGCAACAGCTAGAATCAAGTAGGATA-AAGCTTTCCCAATTGGAGCAAGAACTTCAGCGAGCTCGTTCTCAGMapped 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|161715403|gb|FC065830.1|FC065830EST: AGGAAAGGAGCTGGATCAACGTCAGAGAAAACGCTTGATGCCAAG ACACTGAGACGTTTGGCACAAAACAGAGAAGCAGCAAGAAAGAGTAGGCTG
genomic: AGGAAAGGAGCTGGATCAACGTCAGAGAAAACGCTTGATGCCAAGgttatgagaa ... tggtttccagACACTGAGACGTTTGGCACAAAACAGAGAAGCAGCAAGAAAGAGTAGGCTG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgtagcagtaatatctctagcgtttgagttaacagttttgaggattggtttccagACACTGAGACGTTTGGCACAAAACAGAGAAGCAGCAAGAAAGAGTAGGCTGAGAAAGAAGGCGTATGTGCAGCAGCTAGAATCCAGTAGGATTAAGCTCA
agttaac putative branch site (score: 3)
tttcc putative PPT
agtaatat 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
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gttatgagaaaaatagtattaacaacaaacataattttcccatatctataaacatgtagcagtaatatctctagcgtttgagttaacagttttgaggattggtttccagACACTGAGACGTTTGGCACAAAACAGAGAAGCAGCAAGAAAGAGTAGGCTGAGAAAGAAGGCGTATGTGCAGCAGCTAGAATCCAGTAGGATTAAGCTCA
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- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA