Sequence
atgc intronic sequence ATGC exonic sequencegtattttcttttcattcctcttgcatctccaccactccattgcacagattcaggcatttgtgaagtcttcttgaatttctgcattattctttaatgagaacaaaagatctttttttttcagtgggaacttttatgacattgagtttgattatggatagGTTTGCAGCAGCACTAATTGATTTCCAAGTTGATTGCTGGGTTATGAATGTTGTTCCAGTTAGTGGATTCAACACCCTGCCTGTAATCTATGATCGTGGA
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv18s0001g01600.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: LOC_Os01g62800.1 (Oryza sativa), 3'ss of exon 6
gtattttcttttcattcctcttgcatctccaccactccattgcacagattcaggcatttgtgaagtcttcttgaatttctgcattattctttaatgagaacaaaagatctttttttttcagtgggaacttttatgacattgagtttgattatggatagGTTTGCAGCAGCACTAATTGATTTCCAAGTTGATTGCTGGGTTATGAATGTTGTTCCAGTTAGTGGATTCAACACCCTGCCTGTAATCTATGATCGTGGA
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------------------------------------------------------ttctcacaaagacaaaataaattg--gacttattttctgtttggtgcgtgatatattctgttttgcgcaatatctcattttgcttgctaattttttatg--cagGTTTGCAGCTGCATTGATTAATCGTAAACTTGATTGCTGGGTGATGAATGTTGTTCCTGTTAGTGAGCCAAACACACTGCCTGTAATCTATGACCGGGGA
upper sequence: Vv18s0001g01600.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA13G09520.1 (Glycine max), 3'ss of exon 6
gtattttcttttcattcctcttgcatctccaccactccattgcacagattcaggcatttgtgaagtcttcttgaatttctgcattattctttaatgagaacaaaagatctttttttttcagtgggaacttttatgacattgagtttgattatggatagGTTTGCAGCAGCACTAATTGATTTCCAAGTTGATTGCTGGGTTATGAATGTTGTTCCAGTTAGTGGATTCAACACCCTGCCTGTAATCTATGATCGTGGA
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gtatgagagtattacatttcttgctttctttt---tctgttatata--tt---acatttgtcgg---ttattaggtttctgtagaatgatt-------gtctaatgttgttgttatccgtgtgtgta---ttatgtcgttga---taactgcagAG----TTGCTGCTGCGCTGCATGATCTCCAGATTGACTGTTGGGTTATGAATGTTGTTCCTGTCAGTGGATTTAATACCTTGCCTGTTATATATGACCGCGGG
upper sequence: Vv18s0001g01600.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA14G24900.1 (Glycine max), 3'ss of exon 6
gtattttcttttcattcctcttgcatctccaccactccattgcacagattcaggcatttgtgaagtcttcttgaatttctgcattattctttaatgagaacaaaagatctttttttttcagtgggaacttttatgacattgagtttgattatggat--agGTTTGCAGCAGCACTAATTGATTTCCAAGTTGATTGCTGGGTTATGAATGTTGTTCCAGTTAGTGGATTCAACACCCTGCCTGTAATCTATGATCGTGGA
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gtatgggagtattacatttcttgt-tttctttctctgttttatatta-------catttgttgg---ttattaggcttctgtagttgtct--------------ggccttgctgctatctgtgtgtattatgatg----taactttcattataactgcagAGTTGCTGCTGCGCTGCATGATCTCCAGATCGACTGTTGGGTTATGAATGTTGTTCCTGTCAGTGGGTTTAATACCTTGCCTGTTATATATGACCGTGGG
upper sequence: Vv18s0001g01600.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: AT1G77260.1 (Arabidopsis thaliana), 3'ss of exon 6
gtattttcttttcattcctcttgcatctccaccactccattgcacagattcaggcatttgtgaagtcttcttgaatttctgcattattctttaatgagaacaaaagatctttttttttcagtgggaacttttatgacattgagttt---gattatggatagGTTTGCAGCAGCACTAATTGATTTCCAAGTTGATTGCTGGGTTATGAATGTTGTTCCAGTTAGTGGATTCAACACCCTGCCTGTAATCTATGATCGTGGA
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-----------------------------------------------------------------------------------gtaaccatcaatcacaccctttttttgtttctgccttaccaaagtttatttgatctagtatttcttgattttgg-tagGTTTGCAGCAGCATTAAACGATCTGGGGCTTGACTGTTGGGTTATGAACATTGTTCCCGTTAGCGGATTCAACACCTTGCCAGTTATTTATGACCGTGGAMapped 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|28968089|gb|CB347122.1|CB347122EST: AATGATTCAAAATTGAGAAATGTGATGGACATGAGAGCAGGATTTGGAGG GTTTGCAGCAGCACTAATTGATTTCCAAGTTGATTGCTGGGTTATGAATGT
genomic: AATGATTCAAAATTGAGAAATGTGATGGACATGAGAGCAGGATTTGGAGGgtattttctt ... ttatggatagGTTTGCAGCAGCACTAATTGATTTCCAAGTTGATTGCTGGGTTATGAATGT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aagatctttttttttcagtgggaacttttatgacattgagtttgattatggatagGTTTGCAGCAGCACTAATTGATTTCCAAGTTGATTGCTGGGTTATGAATGTTGTTCCAGTTAGTGGATTCAACACCCTGCCTGTAATCTATGATCGTGGA
gtttgat putative branch site (score: 5)
tttttttttca 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtattttcttttcattcctcttgcatctccaccactccattgcacagattcaggcatttgtgaagtcttcttgaatttctgcattattctttaatgagaacaaaagatctttttttttcagtgggaacttttatgacattgagtttgattatggatagGTTTGCAGCAGCACTAATTGATTTCCAAGTTGATTGCTGGGTTATGAATGTTGTTCCAGTTAGTGGATTCAACACCCTGCCTGTAATCTATGATCGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA