Sequence
atgc intronic sequence ATGC exonic sequence...cagcatatctcaattcctgccttttaccatttccaatagggaattacatggactttgagctgaaccccctgttcttgttttatatgcatttttggtgcagCCGAGAACGGTTTGGAGAGATGCATGCTAGACTTTGGTGGGAGGAGAACCGGGCAAGAATACATGAACAGTACTTGTGAAGGAGCTAACCAGGGATCATC
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv11s0016g01460.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: LOC_Os08g36020.1 (Oryza sativa), 3'ss of exon 4
cagcatatctcaattcctgccttttaccatttccaatagggaattacatggactttgagctgaaccccctgttcttgttttatatg--catttttggtgcagCCGAGAACGGTTTGGAGAGATGCATGCTAGACTTTGGTGGGAGGAGAACCGGGCAAGAATACATGAACAGTACTTGTGAAGGAGCTAACCAGGGAT-CATC
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tggcagagattcatgagcatctgct--catttggtttcgcaatacacttagtcgttcctctaaagaacatgtatttatctgttttggctgttctgcgtgcagCCGGGAGAAATTCAGCGAGATGCACGCCAGGCTATGGTGGGAAGAGAACCGGGCAAGGATACATGATCAGTATCTCTGAGAAGACATGCTAATCATGTAT-
upper sequence: Vv11s0016g01460.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: LOC_Os09g27230.1 (Oryza sativa), 3'ss of exon 4
cagcatatctcaattcctgccttttaccatttccaatagg---gaattacatgg-actttgagctgaaccccctgttcttgttttatatgcatttttggt-gcagCCGAGAACGGTTTGGAGAGATGCATGCTAGACTTTGGTGGGAGGAGAACCGGGCAAGAATACATGAACAGTACTTGTGAAGGAGCTAACCAGGGATCATC
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-----tgcttgaatctccatgatcgaagaatttggaagcaactgaattgctagctactagcagatgatcatggaaagagacttaattattctctcttgcttgcagCCGAGAGAGGTTCAGCGAGATGCATGCCAGGCTATGGTGGGAAGAAAACCGAGCGAGGATACATGAACAGTATCTCTGA---------------------
upper sequence: Vv11s0016g01460.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA15G18980.1 (Glycine max), 3'ss of exon 3
cagcatatctcaa--ttcctgccttttaccatttccaatagggaattacatggactttgagctgaaccccctgttcttgttttatatgcatttttggtgcagCCGAGAACGGTTTGGAGAGATGCATGCTAGACTTTGGTGGGAGGAGAACCGGGCAAGAATACATGAACAGTACTTGTGAAGGAGCTAACCAGGGATCATC-
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--gcatgttataaatttacgaacggggattgatgcgcatatttgagtttatttttgtgactgtatttttatttcttttggtgtttcctcgtatttggtgcagTCGAGAAAAGTTTGGGGAGATGCATGCTAGACTATGGTGGGAAGAGAACCGTGCCAGAATACATGAACAATACTTGTGAGCTAGATGCCTAGAT-TTATCA
upper sequence: Vv11s0016g01460.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA09G07930.1 (Glycine max), 3'ss of exon 3
--------cagcata-tctcaattcc--tgccttttaccatttccaatagggaattacatggactttgagctgaaccccctgttcttgttttatatgcatttttggtgcagCCGAGAACGGTTTGGAGAGATGCATGCTAGACTTTGGTGGGAGGAGAACCGGGCAAGAATACATGAACAGTACTTGTGAAGGAGCTAACCAGGGATCATC-
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ctgttagccattctgctctcaatttcattagcatgttataattctcatgtagaactgtatgaaattta--------tttcttttggtgtttcct---catatttgatgcagTCGAGAAAAGTTTGGTGAGATGCATGCTAGACTGTGGTGGGAAGAGAACCGTGCCAGAATACATGAACAATACTTGTGAGAATTCTCAA-AGGGGTGGCTG
upper sequence: Vv11s0016g01460.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA17G05900.1 (Glycine max), 3'ss of exon 4
cagcatatctcaattcctgccttttacc-atttccaatagggaattacatggactttgagctgaaccccctgttcttgttt-tatatgcatttttggtgcagCCGAGAACGGTTTGGAGAGATGCATGCTAGACTTTGGTGGGAGGAGAACCGGGCAAGAATACATGAACAGTACTTGTGAAGGAGCTAACCAGGGATCATC
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atacatacataaacatatacattgtgcttgtttttcatggttga--attttgatgtagaagtctatggaatttatttcttggtgttctcatgtgttacatagCCGAGAAAAGTTTGGGGAGATGCATGCTAGATTATGGTGGGAAGAGAACCGTGCCAGAATACATGAACAATACTTGTGA---------------------
upper sequence: Vv11s0016g01460.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA13G16800.1 (Glycine max), 3'ss of exon 5
cagcatatctcaattcctgccttttaccatttccaatagggaattacatggactttgagctgaaccccctgttcttgttt-tatatgcatttttggtgcagCCGAGAACGGTTTGGAGAGATGCATGCTAGACTTTGGTGGGAGGAGAACCGGGCAAGAATACATGAACAGTACTTGTGAA-----GGAGCTAACCAGGGATCATC
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-gatacacacacacacatatatatagtgcttgttttcatggtagaattttgatgtagaagtcaatggaatttatttcttggtgttctcatgtgttacacagCCGAGAAAAATTTGGGGAGATGCATGCTAGATTATGGTGGGAAGAGAACCGTGCCAGAATACATGAACAATACTTGTGAGTTGTGAGATTTTACAAAGGG-----
upper sequence: Vv11s0016g01460.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: AT5G20540.1 (Arabidopsis thaliana), 3'ss of exon 4
cagcatatctcaattcctgccttttaccatttccaa-tagggaatta--catggactttgagctgaaccccctgttcttgttttatatgcatttttggtgcagCCGAGAACGGTTTGGAGAGATGCATGCTAGACTTTGGTGGGAGGAGAACCGGGCAAGAATACATGAACAGTACTTGTGAAGGAGCTAACCAGGGATCATC-
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--gtactgttaaacttc---cttacattgtctcaaaacccgggtttatccatcggttctgaactaaacatc--actcaaactgtgttttcttttgcattgcagCCGAGAGAGATTCGGGGAGATGCACGCGAGATTATGGTGGGAAGAGAACAGGGCAAGGATACATGAACAATACTTGTGATCATAA-ATCTAAGAGTTTTGTMapped 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|110424952|gb|EC991327.1|EC991327EST: ATCAGAGCACTTCCAGGTGGTACACGGGAGCTTAGACGTGTCAGATTCAG CCGAGAACGGTTTGGAGAGATGCATGCTAGACTTTGGTGGGAGGAGAACCG
genomic: ATCAGAGCGCTTCCAGGTGGTACACGGGAGCTTAGACGTGTCAGATTCAGgcaagtgaac ... tttggtgcagCCGAGAACGGTTTGGAGAGATGCATGCTAGACTTTGGTGGGAGGAGAACCG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.acatggactttgagctgaaccccctgttcttgttttatatgcatttttggtgcagCCGAGAACGGTTTGGAGAGATGCATGCTAGACTTTGGTGGGAGGAGAACCGGGCAAGAATACATGAACAGTACTTGTGAAGGAGCTAACCAGGGATCATC
cattttt CT-rich tract
ttttatatgcattttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
cagcatatctcaattcctgccttttaccatttccaatagggaattacatggactttgagctgaaccccctgttcttgttttatatgcatttttggtgcagCCGAGAACGGTTTGGAGAGATGCATGCTAGACTTTGGTGGGAGGAGAACCGGGCAAGAATACATGAACAGTACTTGTGAAGGAGCTAACCAGGGATCATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - tcctgcc
- - - - - - - - - - - - - ccatttc
- - - - - - - - - - - - - - - - - - - - - - - catggac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tatgcat