Sequence
atgc intronic sequence ATGC exonic sequence...atctttgtgttcatattactcctatttctgcaacttcctttttatttatttattattattattaatcctaaagccgtgcatgttgtccaattttcttcagGACACCAACAGACTGGAATACCTCATCCCAAAAAAGACATCCTTGAGGCACCGGTTGCCAATGGGGGACCAAGGCTTCATCGACTTTGTTTCTCATATGC
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv01s0011g01590.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: LOC_Os03g51020.1 (Oryza sativa), 3'ss of exon 6
------atctttgtgttcatattactcctatttctgcaacttcct---ttttattta--tttatta-----ttattattaatcctaaagccgtgcatgttg----tccaatt-----ttcttcagGACACCAACAGACTGGAATACCTCATCCCAAAAAAGACATCCTTGAGGCACCGGTTGCCAATGGGGGACCAAGGCTTCATCGACTTTGTTTCTCATATGC
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gtttgaattcttctatagatgttttttttgttttcccagtcacacagatgtaactgaattttatagcagatttatccttaaactttagcccttctgtgttaacctttcaattcattgttccccagGAAAGCAACAGACTGGAGTACTTGATTCCAAAAAAGACATCTTTGCGGCACCGCTTGCCCATGGCTGACCAAGGTTTTATCGAGTTTGTTGCATACCTTC
upper sequence: Vv01s0011g01590.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: GLYMA05G33560.1 (Glycine max), 3'ss of exon 6
---atctttgtgttcatattactcctatttctgcaacttcctt-tttatttatttattattattattaatcctaaagccgtgcatgttgtccaattttcttcagGACACCAACAGACTGGAATACCTCATCCCAAAAAAGACATCCTTGAGGCACCGGTTGCCAATGGGGGACCAAGGCTTCATCGACTTTGTTTCTCATATGC
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ttgacattttagttcttaccg-tgctatattaaaattgtgtttgcctctgcattttttact-tgaatgattgtcag--taaatttattgtttattaatctacagGAAACCAACCGGTTAGAATACTTGGTACCAAAAAAGACATCCTTGAGGCATAGATTGCCAATGGGAGACCAAGGCTTCATTGACTTTGTTGCTCACTTGC
upper sequence: Vv01s0011g01590.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: GLYMA09G29970.1 (Glycine max), 3'ss of exon 6
-atctttgtgttcatattactcctatttctgcaacttcctttttatttatttattattattattaatcctaaagccgtgcatgttgtccaat-tttcttcagGACACCAACAGACTGGAATACCTCATCCCAAAAAAGACATCCTTGAGGCACCGGTTGCCAATGGGGGACCAAGGCTTCATCGACTTTGTTTCTCATATGC
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taacacacaatatttaaagttcttgccattacctctgcattttactttcttga--aataatttgaagctactatttattaataattaataatatatatacagGAAAGCAACAGGTTAGAATACCTGATTCCTAAAAAGACATCATTGAGGCATAGATTACCGATGGGGGACCAAGGCTTCATCGACTTTGTTGCTCATTTGC
upper sequence: Vv01s0011g01590.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: GLYMA08G06160.1 (Glycine max), 3'ss of exon 8
atctttgtgttcatattactcctatttctgcaacttcctttttatttatttattattattattaatc-ctaaagccgtgcatgttgtccaattttcttcagGACACCAACAGACTGGAATACCTCATCCCAAAAAAGACATCCTTGAGGCACCGGTTGCCAATGGGGGACCAAGGCTTCATCGACTTTGTTTCTCATATGC
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-cttgacttttaattcttaccatgttgtattaaatttgtgtttgcctttgcattgtttacttgaatgattgtcagtaaatttattgtttattaatctacagGAAACCAACCGGTTAGAATACTTGATTCCGAAAAAGACATCCCTGAGGCATAGATTGCCAATGGGAGACCAAGGCTTCATTGACTTTGTTGCTCACTTGC
upper sequence: Vv01s0011g01590.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: GLYMA16G34510.1 (Glycine max), 3'ss of exon 6
atctttgtgttcatattactcctatttctgcaacttcctttttatttatttattattattattaatcctaaagccgtgcatgttgtccaat-tttcttcagGACACCAACAGACTGGAATACCTCATCCCAAAAAAGACATCCTTGAGGCACCGGTTGCCAATGGGGGACCAAGGCTTCATCGACTTTGTTTCTCATATGC
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-cacttctacacacaatatttaaattcttgccactacctctgcattttacttgaaataatttgaagctactatttattaatacttaataatatatatacagGAAAGCAACAGGTTAGAATACCTGATTCCTAAAAAGACATCATTAAGGTATAGATTACCGATGGGGGACCAAGGCTTCATCGACTTTGTTGCTCATTTGCMapped 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|34542404|gb|CF510636.1|CF510636EST: ATACATATAAATATTTCACCAAAAATCACATGCTCTATGAACGGAATCAG GACACCAACAGACTGGAATACCTCATCCCAAAAAAGACATCCTTGAGGCAC
genomic: ATACATATAAATATTTCACCAAAAATCACATGCTCTATGAACGGAATCAGgtaacagttt ... ttttcttcagGACACCAACAGACTGGAATACCTCATCCCAAAAAAGACATCCTTGAGGCAC
EST:
gi|34542494|gb|CF510726.1|CF510726EST: ATACATATAAATATTTCACCAAAAATCACATGCTCTATGAACGGAATCAG GACACCAACAGACTGGAATACCTCATCCCAAAAAAGACATCCTTGAGGCAC
genomic: ATACATATAAATATTTCACCAAAAATCACATGCTCTATGAACGGAATCAGgtaacagttt ... ttttcttcagGACACCAACAGACTGGAATACCTCATCCCAAAAAAGACATCCTTGAGGCAC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttatttattattattattaatcctaaagccgtgcatgttgtccaattttcttcagGACACCAACAGACTGGAATACCTCATCCCAAAAAAGACATCCTTGAGGCACCGGTTGCCAATGGGGGACCAAGGCTTCATCGACTTTGTTTCTCATATGC
tcctaaa putative branch site (score: 2)
ttttcttc putative PPT
tattattattattaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
atctttgtgttcatattactcctatttctgcaacttcctttttatttatttattattattattaatcctaaagccgtgcatgttgtccaattttcttcagGACACCAACAGACTGGAATACCTCATCCCAAAAAAGACATCCTTGAGGCACCGGTTGCCAATGGGGGACCAAGGCTTCATCGACTTTGTTTCTCATATGC
- - -tgtgttc
- - - - - - - - - - - - - - - caacttc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - taaagcc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gcatgtt