Sequence
atgc intronic sequence ATGC exonic sequencegtaagcatctctttgaactgattgctttcttggattgtagttgatgttttcatctgctttatatgttttgcctctgtttttagGCATGATTTCCAATTCTTTAACACACAAAGGCTGAATGAGTTGTATGAGAAAGAAGTGCGGTACCTCATG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv05s0020g01780.t01 (Vitis vinifera), 3'ss of exon 17
lower sequence: LOC_Os01g27040.1 (Oryza sativa), 3'ss of exon 17
gtaagcatctctttgaactgattgctttcttgga------ttgtagttgatgttttcatctgctttata-------------tgttttgcctctgttt-ttagGCATGATTTCCAATTCTTTAACACACAAAGGCTGAATGAGTTGTATGAGAAAGAAGTGCGGTACCTCATG
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gtaagttttctcttgcctctttcattttgtgaaaaaaaaatcatgattaccttgtttgctctctttagaactactgtcagctcatattgtttttgtttgtcagACATGATTTCCAGTTCTTCAACAACCAAAGGCTCAATGAATTGTATGAAAAGGAAGTCCGGTACCTTATG
upper sequence: Vv05s0020g01780.t01 (Vitis vinifera), 3'ss of exon 17
lower sequence: 13113.m00246 (Oryza sativa), 3'ss of exon 17
gtaagcatctctttgaactgattgctttcttgga-------ttgtagttgatgttttcatctgctttata-------------tgttttgcctctgttt-ttagGCATGATTTCCAATTCTTTAACACACAAAGGCTGAATGAGTTGTATGAGAAAGAAGTGCGGTACCTCATG
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gtaagttttctcttgcctctttcattttgtgaaaaaaaaaatcatgattaccttgtttgctctctttagaactactgtcagctcatattgtttttgtttgtcagACATGATTTCCAGTTCTTCAACAACCAAAGGCTCAATGAATTGTATGAAAAGGAAGTCCGGTACCTTATG
upper sequence: Vv05s0020g01780.t01 (Vitis vinifera), 3'ss of exon 17
lower sequence: LOC_Os05g05780.1 (Oryza sativa), 3'ss of exon 17
--------gtaagcatctctttgaactgattgctttcttggattgtagttgatgttttcatctgctt---------tatatgttttgcctctgttttt---agGCATGATTTCCAATTCTTTAACACACAAAGGCTGAATGAGTTGTATGAGAAAGAAGTGCGGTACCTCATG
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gtaagcttgttcacatagtcttttttttttcatttttcaaaatttttaatatttttttcatttaattgcagtggtgtactcattttggttttgtttttgttagGCATGATTTCCAGTTCTTCAACACTCAGAGACTCAATGAATTATATGAGAAGGAAGTCAAATACCTTGTG
upper sequence: Vv05s0020g01780.t01 (Vitis vinifera), 3'ss of exon 17
lower sequence: AC235535.1_FGT001 (Zea mays), 3'ss of exon 17
gtaagcatctctttgaactgattgctttcttg-gattgtagttgatgttttcatctgctttatatgttttgcctctgtttttagGCATGATTTCCAATTCTTTAACACACAAAGGCTGAATGAGTTGTATGAGAAAGAAGTGCGGTACCTCATG
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gtaaatttcttgtttt-ttgaaagctaaccaatggctccattttatggaattatatcttacctggcttttaatttttgtattagGCATGATTTCCAGTTTTTCAATAACCAAAGGCTAAATGAATTGTACGAAAAGGAAGTGCGGTACCTCATG
upper sequence: Vv05s0020g01780.t01 (Vitis vinifera), 3'ss of exon 17
lower sequence: GRMZM2G010085_T01 (Zea mays), 3'ss of exon 14
gtaagcatctctttgaactgattgctttcttggattgtagttgatgttttcatctgctttatatgttttgcctctgtttttagGCATGATTTCCAATTCTTTAACACACAAAGGCTGAATGAGTTGTATGAGAAAGAAGTGCGGTACCTCATG
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gtaaattcttgttttctcgaatactaatcaatggttctatttcactgatttgtacctgacttggctttaattttttgtgttagACATGATTTCCAGTTTTTCAATAACCAAAGGCTAAATGAATTGTATGAAAAGGAAGTGCGGTACCTTATG
upper sequence: Vv05s0020g01780.t01 (Vitis vinifera), 3'ss of exon 17
lower sequence: GLYMA15G10370.1 (Glycine max), 3'ss of exon 17
gtaagcatctct--ttgaactgattgcttt----cttggattgtagttgatgttttcatctgctt-tatatgttttgcctctg-tttttagGCATGATTTCCAATTCTTTAACACACAAAGGCTGAATGAGTTGTATGAGAAAGAAGTGCGGTACCTCATG
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gtaagcttctacacttgatttttcttcttaacagttagcatagtacctccgttatttacttactgatatttttttgttctttgacctccagGCATGATTTCCAATTTTTCAACACACAAAGGTTGAGTGAGCTGTATGAAAAGGAAGTACGCTATCTCATG
upper sequence: Vv05s0020g01780.t01 (Vitis vinifera), 3'ss of exon 17
lower sequence: GLYMA13G28720.1 (Glycine max), 3'ss of exon 17
gtaagcatct---ctttgaactgattgcttt----cttggattgtagttgatgttttcatctgct--ttatatgttttgcctctgtttttagGCATGATTTCCAATTCTTTAACACACAAAGGCTGAATGAGTTGTATGAGAAAGAAGTGCGGTACCTCATG
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gtaagcttctacactttgatttttcttcttaacaattagcatagtacctctgttatttacttactgataattttttgttctttgacgtctagGCATGATTTCCAGTTTTTCAACACACAAAGATTGAGTGAGCTGTATGAAAAGGAAGTACGCTATCTCATG
upper sequence: Vv05s0020g01780.t01 (Vitis vinifera), 3'ss of exon 17
lower sequence: AT5G18620.1 (Arabidopsis thaliana), 3'ss of exon 17
------------gtaagcatctctttgaactgattgctttct-tggattgtagttgatgttttcatctgctttatatg-ttttgcctctgtttt-tagGCATGATTTCCAATTCTTTAACACACAAAGGCTGAATGAGTTGTATGAGAAAGAAGTGCGGTACCTCATG
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gtgagtacctcaattgtctccactctgcatttagccttttccctgtcttatttatagtacttttatcgtaaaaatctaatttcttgtccatcctgcagGCATGATTTTCAGTTCTTTAACATTCAGAGGCTGACTGAGCTGTATGAAAAAGAAGTGCGATACCTTATGMapped 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|28967912|gb|CB346945.1|CB346945EST: GGTGCTCCAGCAAAACAAAGAGAGCCTAGAATTCCGCGCATGCCCCAGCT GCATGATTTCCAATTCTTTAACACACAAAGGCTGAATGAGTTGTATGAGAA
genomic: GGTGCTCCAGCAAAACAAAGAGAGCCTAGAATACCGCGCATGCCCCAGCTgtaagcatct ... ctgtttttagGCATGATTTCCAATTCTTTAACACACAAAGGCTGAATGAGTTGTATGAGAA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cttggattgtagttgatgttttcatctgctttatatgttttgcctctgtttttagGCATGATTTCCAATTCTTTAACACACAAAGGCTGAATGAGTTGTATGAGAAAGAAGTGCGGTACCTCATG
agttgat putative branch site (score: 5)
ttttgcctctgttttt putative PPT
tttatatgtttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagcatctctttgaactgattgctttcttggattgtagttgatgttttcatctgctttatatgttttgcctctgtttttagGCATGATTTCCAATTCTTTAACACACAAAGGCTGAATGAGTTGTATGAGAAAGAAGTGCGGTACCTCATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT