Sequence
atgc intronic sequence ATGC exonic sequence...ttcaagtaatatgattattataatcacactcacccacaaatccttcgcgctaatcatcaccattccattccatcattaacactcttcatctctgttacagCAGGAGGTGTCCCCGCGCACTTCAGGCCGTCTCTCACACAGCAGTGGCCCCCTCAACGGAACTCAGAGTTGTGGCTCCTTAACGGACAGCCCCCCAGTCT
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv05s0020g04020.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: LOC_Os12g41140.1 (Oryza sativa), 3'ss of exon 1
ttcaagtaatatgattattat--aatcacactcacccac--aaatccttcgcgctaatcatcaccattccattccatcattaacactcttcatctc-tgttacagCAGGAGGTGTCCCCGCGCACTTCAGGCCGTCTCTCACACAGCAGTGGCCCCCTCAACGGAACTCAGAGTTGTGGCTCCTTAACGGACAGCCCCCCAGTCT---------
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-----gttcaatgattattgtgaaattgtgctgttctgcttggaacagtagctcactttgcagatagacactgagaatttactcgtttcttgtttcatggagcagCAGGAGGTGTCGCCGCTGACCTCCGGCCGCCTCTCACACAGCAGCGGCCCTCTCAACGGCG---------GCGGCTCGCTCTCCGACAGCCCACCGGTCTCGCCGGACG
upper sequence: Vv05s0020g04020.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: LOC_Os12g41140.3 (Oryza sativa), 3'ss of exon 1
ttcaagtaatatgattattat--aatcacactcacccac--aaatccttcgcgctaatcatcaccattccattccatcattaacactcttcatctc-tgttacagCAGGAGGTGTCCCCGCGCACTTCAGGCCGTCTCTCACACAGCAGTGGCCCCCTCAACGGAACTCAGAGTTGTGGCTCCTTAACGGACAGCCCCCCAGTCT------------
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--------caatgattattgtgaaattgtgctgttctgcttggaacagtagctcactttgcagatagacactgagaatttactcgtttcttgtttcatggagcagcagGAGGTGTCGCCGCTGACCTCCGGCCGCCTCTCACACAGCAGCGGCCCTCTCAACGGCG---------GCGGCTCGCTCTCCGACAGCCCACCGGTCTCGCCGGACGTCG
upper sequence: Vv05s0020g04020.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA10G38990.1 (Glycine max), 3'ss of exon 1
ttcaagtaatatgattattataatcacactcacccacaaatccttcgcgctaatcatcaccattccattccatcattaacactcttcatctctgttacagCAGGAGGTGTCCCCGCGCACTTCAGGCCGTCTCTCACACAGCAGTGGCCCCCTCAACGGAACTCAGAGTTGTGGCTCCTTAACGGACAGCCCCCCAGTCT
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tattgtttacttcactctgttttccatttaaaaaaacgctttctttatatccttcattaatctaacgcatttattgtgatgtgattttctcatttctcagCAGGAGGTATCTCCACGAACCTCAGGGAGACTCTCTCATAGCAGTGGCCCTCTTAACGGAACCCAAAGTTGTGGCTCCTTAACCGATAGTCCTCCTGTTT
upper sequence: Vv05s0020g04020.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA20G28820.1 (Glycine max), 3'ss of exon 1
--ttcaagtaatatgat-tattataatcacactcacccacaaatccttcgcgctaatcatcaccattccattccatcattaacactcttcatctctgttacagCAGGAGGTGTCCCCGCGCACTTCAGGCCGTCTCTCACACAGCAGTGGCCCCCTCAACGGAACTCAGAGTTGTGGCTCCTTAACGGACAGCCCCCCAGTCT
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ctttcttttgtcttcacgtgtttttgtttgtttagttcactctgttttggtgtgcagcaatctaaaagcattt-attgt-ggtgtgatttctctattct-cagCAGGAGGTATCTCCACGAACCTCAGGGAGACTCTCTCATAGCAGTGGCCCTCTTAACGGAACCCAAAGTTGTGGTTCCTTAACCGATAGCCCTCCTGTTTMapped 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|352773994|gb|FQ473126.1|FQ473126EST: CATCTTCCGAGACCTCCCAACTCGTTATGGAACGTATAATGTCACAGTCG CAGGAGGTGTCCCCGCGCACTTCAGGCCGTCTCTCACACAGCAGTGGCCCC
genomic: CATCTTCCGAGACCTCCCAACTCGTTATGGAACGTATAATGTCACAGTCGgtgagttgat ... tctgttacagCAGGAGGTGTCCCCGCGCACTTCAGGCCGTCTCTCACACAGCAGTGGCCCC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cgcgctaatcatcaccattccattccatcattaacactcttcatctctgttacagCAGGAGGTGTCCCCGCGCACTTCAGGCCGTCTCTCACACAGCAGTGGCCCCCTCAACGGAACTCAGAGTTGTGGCTCCTTAACGGACAGCCCCCCAGTCT
cattaac putative branch site (score: 2)
ctcttcatctctgtt CT-rich tract
atcattaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttcaagtaatatgattattataatcacactcacccacaaatccttcgcgctaatcatcaccattccattccatcattaacactcttcatctctgttacagCAGGAGGTGTCCCCGCGCACTTCAGGCCGTCTCTCACACAGCAGTGGCCCCCTCAACGGAACTCAGAGTTGTGGCTCCTTAACGGACAGCCCCCCAGTCT
-tcaagta
- - - - - - - - - - -aatcaca
- - - - - - - - - - - - - - ctcaccc
- - - - - - - - - - - - - - - - - - caaatcc
- - - - - - - - - - - - - - - - - - - - - - - - - - - catcacc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cattaac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctcttca