Sequence
atgc intronic sequence ATGC exonic sequencegtgagcttttcttcggggcattggcttccagtaattaataagcctcatctctgtattgaacaataaattttatatcattcttcttgtcaaaagggggaaaatgaaacaatttgcttggtcttgatgaagttgaaatggctgatcttctgtctgttcatttttatcttgtatcattccagGCTGTTCGGAAACTGAATGAAGCAAAGAAACTTGAATCTAGTGCTCACTACAATGCTGATTTTGGGAAAGACTAGAACACATGTTATTCCATTTCAAGAG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv18s0001g13090.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GLYMA04G03180.1 (Glycine max), 3'ss of exon 9
gtgagcttttcttcggggcattggcttccagtaattaataagcctcatctctgtattgaacaataaattttatatcattcttcttgtcaaaagggggaaaatgaaacaatttgcttggtcttgatgaagttgaaatggctgatcttctgtctgttcatttttatcttgtatcattccagGCTGTTCGGAAACTGAATGAAGCAAAGAAACTTGAATCTAGTGCTCACTACAATGCTGATTTTGGGAAAGACTAGAACACATGTTATTCCATTTCAAGAG
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-------------------------------------gtgagt----tccttgtttagga-agtaaattttctgt-gtattgatggtcacgaaggg-------------tctacctctccttgtc--actttatggggataataa-------atttatttcttactt---cggttccagGCTGTTAGGAAACTGAACGAGGCAAAGAAACTTGAATCCAGTGCGCACTACAGTGCTGATTTTGGTAAAGACTAGAATCTATTGCAAAATTCTTGCAGAG
upper sequence: Vv18s0001g13090.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GLYMA06G03230.1 (Glycine max), 3'ss of exon 9
gtgagcttttcttcggggcattggcttccagtaattaataagcctcatctctgtattgaacaataaattttatatcattcttcttgtcaaaagggggaaaatgaaacaatttgcttggtcttgatgaagttgaaatggctgatcttctgtctgttcatttttatcttgtatcattccagGCTGTTCGGAAACTGAATGAAGCAAAGAAACTTGAATCTAGTGCTCACTACAATGCTGATTTTGGGAAAGACTAGAACACATGTTATTCCATTTCAAGAG
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-------------------------------------gtgagt----tccttgtttagga-agtaaattttctgt-gtactgatggtgacgaagag-------------tctacctctccttgtc--actttatggggataataa-------atttatttcttactt---cggttccagGCTGTTAGGAAACTGAACGAGGCAAAGAAACTTGAATCCAGTGCACACTACAGTGCTGATTTTGGTAAAGACTAGAATCTATTGCAAAATTCTTGCAGAG
upper sequence: Vv18s0001g13090.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GLYMA14G07750.1 (Glycine max), 3'ss of exon 9
gtgagcttttcttcggggcattggcttccagtaattaataagcctcatctctgtattgaacaataaattttatatcattcttcttgtcaaaagggggaaaatgaaacaatttgcttggtcttgatgaagttgaaatggctgatcttctgtctgttcatttttatcttgtatcattccagGCTGTTCGGAAACTGAATGAAGCAAAGAAACTTGAATCTAGTGCTCACTACAATGCTGATTTTGGGAAAGACTAGAACACATGTTATTCCATTTCAAGAG--
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-------------------------------------------gtgagttctttctttgaggaaagct-----atttttctgtgtatcaattatgtacaaagggattactc--ctcgttgctcat--aggcacaacaatttgacttccttct-ttggttc---------------ccagGCTGTTAGAAAACTGAATGATGCAAAGAAACTTGAATCCAGTGCTCACTACAGTGCTGATTTTGGCAAAGACTAAAGGCTAT--TATAAAATTCTGAGCCAT
upper sequence: Vv18s0001g13090.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GLYMA17G37220.1 (Glycine max), 3'ss of exon 9
gtgagcttttcttcggggcattggcttccagtaattaataagcctcatctctgtattgaacaataaattttatatcattcttcttgtcaaaagggggaaaatgaaacaatttgcttggtcttgatgaagttgaaatggctgatcttctgtctgttcatttttatcttgtatcattccagGCTGTTCGGAAACTGAATGAAGCAAAGAAACTTGAATCTAGTGCTCACTACAATGCTGATTTTGGGAAAGACTAGAACACATGTTATTCCATTTCAAGAG-
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------------------------------------ggtgagttctttctctg----aggaagctatttttgtgtg--------tatcaattatgtacaaagggattactcctccttgtc--------actcataggcacaacaatttgact-----tctttctttggt----tcccaGGCTGTTAGAAAACTGAATGATGCAAAGAAACTCGAATCCAGTGCTCACTACAGTGCTGATTTTGGCAAAGACTAAAAGCTAT--TATAAAATTCTGAGCCAMapped 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|110691706|gb|EE070112.1|EE070112EST: CTGCAATTCGTGCAGAACGTGATTATGTCATACATGAAGATTTCATGAAG GCTGTTCGGAAACTGAATGAAGCAAAGAAACTTGAATCTAGTGCTCACTAC
genomic: CTGCAATTCGTGCAGAACGTGATTATGTCATACATGAAGATTTCATGAAGgtgagctttt ... atcattccagGCTGTTCGGAAACTGAATGAAGCAAAGAAACTTGAATCTAGTGCTCACTAC
EST:
gi|110423419|gb|EC989765.1|EC989765EST: CTGCAATTCGTGCAGAACGTGATTATGTCATACATGAAGATTTCATGAAG GCTGTTCGGAAACTGAATGAAGCAAAGAAACTTGAATCTAGTGCTCACTAC
genomic: CTGCAATTCGTGCAGAACGTGATTATGTCATACATGAAGATTTCATGAAGgtgagctttt ... atcattccagGCTGTTCGGAAACTGAATGAAGCAAAGAAACTTGAATCTAGTGCTCACTAC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgaagttgaaatggctgatcttctgtctgttcatttttatcttgtatcattccagGCTGTTCGGAAACTGAATGAAGCAAAGAAACTTGAATCTAGTGCTCACTACAATGCTGATTTTGGGAAAGACTAGAACACATGTTATTCCATTTCAAGAG
ggctgat putative branch site (score: 4)
tcattcc putative PPT
atttttatcttgtat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgagcttttcttcggggcattggcttccagtaattaataagcctcatctctgtattgaacaataaattttatatcattcttcttgtcaaaagggggaaaatgaaacaatttgcttggtcttgatgaagttgaaatggctgatcttctgtctgttcatttttatcttgtatcattccagGCTGTTCGGAAACTGAATGAAGCAAAGAAACTTGAATCTAGTGCTCACTACAATGCTGATTTTGGGAAAGACTAGAACACATGTTATTCCATTTCAAGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT