Sequence
atgc intronic sequence ATGC exonic sequence...ttgcctttccaaatttctctgtcatgatgttgcttgatcatgctcttcttctaggttgaattgttaattgttaattgaaatctccattcttttgttgcagACTATGCTTGCAAAGGCTGTCGCAACCGAGTGCAAAACCACATTTTTCAATATTTCTGCATCCTCTGTTGTCAGCAAATGGCGAG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv10s0003g03500.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: LOC_Os01g55260.1 (Oryza sativa), 3'ss of exon 6
----ttgcctttccaaatttctctgtcatgatgttgcttgatcatgctcttcttctaggttgaattgttaattgttaattgaaatctccattcttttgttgcagACTATGCTTGCAAAGGCTGTCGCAACCGAGTGCAAAACCACATTTTTCAATATTTCTGCATCCTCTGTTGTCAGCAAATGGCGAG
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atatttgcattgtgagtactttgaaattttctgattttgcaatatctctgtctattactatatact-tcggtagtcagtttcaagca--attcctat-ttgcagACAATGCTGGCAAAGGCTGTTGCTACTGAGTGTAAAACTACATTCTTCAACATTTCAGCATCATCAATTGTTAGCAAATGGCGTG
upper sequence: Vv10s0003g03500.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: LOC_Os01g48270.1 (Oryza sativa), 3'ss of exon 6
ttgcctttccaaatttctctgtcatgatgttgcttgatcatgctcttc--ttctaggttg--aattgttaattgttaattgaa--atctccat-tcttttgttgcagACTATGCTTGCAAAGGCTGTCGCAACCGAGTGCAAAACCACATTTTTCAATATTTCTGCATCCTCTGTTGTCAGCAAATGGCGAG
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---caactccg--tttccattccat-atgttgcttg-tcgtgctatacgaactcaaattgctgatcatgtatgcttgatgtaactgttttgatatattttgtttcagACAATGCTAGCAAAAGCTGTGGCTACTGAGTGCAAAACAACCTTCTTCAATATTTCAGCCTCATCAATTGTCAGTAAATGGCGTG
upper sequence: Vv10s0003g03500.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GRMZM2G022777_T01 (Zea mays), 3'ss of exon 6
---ttgcctttccaaatttctctgtcatgatgttgcttgatcatgctcttcttctaggttgaattgttaattgttaattgaaatctccattcttttgttgcagACTATGCTTGCAAAGGCTGTCGCAACCGAGTGCAAAACCACATTTTTCAATATTTCTGCATCCTCTGTTGTCAGCAAATGGCGAG
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ggttcagagtcactattatgttgagcatt-tggtatattctcatgcacttatccctgtacaaagacatgcctctcagttttaa-ctggatcctgttctt-tagACAATGCTGGCAAAAGCGGTCGCTACTGAGTGCAAAACCACCTTCTTCAACATTTCAGCATCATCAATTGTCAGCAAATGGCGTG
upper sequence: Vv10s0003g03500.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GRMZM2G115766_T02 (Zea mays), 3'ss of exon 5
--------ttgcctttccaaatttctctgtcatgatgttgcttgatcatgctcttcttctaggttgaattgttaattgttaattgaaatctccattcttttgttgcagACTATGCTTGCAAAGGCTGTCGCAACCGAGTGCAAAACCACATTTTTCAATATTTCTGCATCCTCTGTTGTCAGCAAATGGCGAG
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agttgcagttgatctgtttcttttctcagtatttattgtattcagttatactgaatctccgagtgcaaccgtttaacctcctcagta--------tatttaatttcagACAATGCTAGCTAAAGCTGTGGCTACTGAGTGCAAAACAACTTTTTTCAATATTTCTGCCTCGTCGATTGTAAGCAAGTGGCGCG
upper sequence: Vv10s0003g03500.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA08G09050.1 (Glycine max), 3'ss of exon 6
--ttgcctttccaaatttctctgtcatgatgttgcttgatcatgctcttcttctaggttgaattgttaattgttaattgaaatctccattcttttgttgcagACTATGCTTGCAAAGGCTGTCGCAACCGAGTGCAAAACCACATTTTTCAATATTTCTGCATCCTCTGTTGTCAGCAAATGGCGAG
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ttttatattttaatgattgtgaat-atagcattttatttttatttttttatt-tattttgaataatttaataacttccaaacatttggtttgattgttgtagACAATGCTTGCAAAGGCAGTTGCGACAGAGTGCAATACAACTTTTTTTAATATTTCAGCCTCATCTGTAGTCAGCAAATGGCGAG
upper sequence: Vv10s0003g03500.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA05G26100.1 (Glycine max), 3'ss of exon 6
-ttgcctttccaaatttctctgtcatgatgttgcttgatcatgctcttcttctaggttgaattgttaattgttaattgaaatctccattcttttgttgcagACTATGCTTGCAAAGGCTGTCGCAACCGAGTGCAAAACCACATTTTTCAATATTTCTGCATCCTCTGTTGTCAGCAAATGGCGAG
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ttttcatattttaatgattgtga-atatagcagtttctttttcttttttatttattttgaataattaaataacttcctaacatttggtttgattgttgtagACAATGCTTGCAAAGGCAGTTGCGACAGAGTGCAAGACTACTTTTTTTAATATTTCAGCCTCATCTGTAGTCAGCAAATGGCGAG
upper sequence: Vv10s0003g03500.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: AT2G34560.1 (Arabidopsis thaliana), 3'ss of exon 6
--------------------------------------------------------------ttgcctttccaaatttctctgtcatgatgttgcttgatcatgctcttcttctaggttgaattgttaattgt--taat---tgaaatctccattcttttgttgcagACTATGCTTGCAAAGGCTGTCGCAACCGAGTGCAAAACCACATTTTTCAATATTTCTGCATCCTCTGTTGTCAGCAAATGGCGAG
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gtgcgatgattctatctcgaatgtgtttttacttttgaactcttactctcttttgcatttcaattcatatgcacaccaaaccattaactaatttcttgagcctagctcaattagatcttgtaaagtttattttcttgatgcataacagtcttattcgtcttgtgcagACTATGCTTGCAAAGGCTGTTGCTACAGAGTGCAATACAACATTCTTCAACATCTCAGCCTCATCTGTTGTTAGCAAATGGAGAGMapped 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|27586367|gb|CB009062.1|CB009062EST: TATCACCATGGAAAGGTATTCTCCTTTTTGGTCCTCCAGGAACAGGAAAG ACTATGCTTGCAAAGGCTGTCGCAACCGAGTGCAAAACCACATTTTTCAAT
genomic: TATCACCATGGAAAGGTATTCTCCTTTTTGGTCCTCCAGGAACAGGAAAGgtttgtgttc ... tttgttgcagACTATGCTTGCAAAGGCTGTCGCAACCGAGTGCAAAACCACATTTTTCAAT
EST:
gi|110732627|gb|EE108077.1|EE108077EST: TATCACCATGGAAAGGTATTCTCCTTTTTGGTCCTCCAGGAACAGGAAAG ACTATGCTTGCAAAGGCTGTCGCAACCGAGTGCAAAACCACATTTTTCAAT
genomic: TATCACCATGGAAAGGTATTCTCCTTTTTGGTCCTCCAGGAACAGGAAAGgtttgtgttc ... tttgttgcagACTATGCTTGCAAAGGCTGTCGCAACCGAGTGCAAAACCACATTTTTCAAT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttcttctaggttgaattgttaattgttaattgaaatctccattcttttgttgcagACTATGCTTGCAAAGGCTGTCGCAACCGAGTGCAAAACCACATTTTTCAATATTTCTGCATCCTCTGTTGTCAGCAAATGGCGAG
tgttaat putative branch site (score: 3)
tctccattcttttgtt putative PPT
aattgttaattgttaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttgcctttccaaatttctctgtcatgatgttgcttgatcatgctcttcttctaggttgaattgttaattgttaattgaaatctccattcttttgttgcagACTATGCTTGCAAAGGCTGTCGCAACCGAGTGCAAAACCACATTTTTCAATATTTCTGCATCCTCTGTTGTCAGCAAATGGCGAG
- -cctttcc
- - - - - - - - - ctgtcat
- - - - - - - - - - - - - - - tgcttga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aattgaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ccattct