Sequence
atgc intronic sequence ATGC exonic sequence...tatgtcatcaactagtatacagcttattttagaatactttccttgatattggaactgaggcaccgactaagaagtttatctgtactgtggaaacatatagGTTGAATGGGATGAGATAAATGCTGCCTGGGGCCAAGCTTGCCTTCTTCTCCATACAATGGTTCAATATTTCCGACCAAAGTTCCA
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv15s0046g00950.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: LOC_Os01g48920.1 (Oryza sativa), 3'ss of exon 6
tatgtcatcaactagtatacagcttattttagaatactttccttgatattggaactgaggcaccgactaagaagtttatctgtactgtggaaacatatagGTTGAATGGGATGAGATAAATGCTGCCTGGGGCCAAGCTTGCCTTCTTCTCCATACAATGGTTCAATATTTCCGACCAAAGTTCCA
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----------gtaattatgcaaaatttacagatataccacatctcatgtttgatcc------tttgttaataaatctg---ataccctt----ttcttagGTTGAATGGGATGAGATAAATGCTGCTTGGGGTCAGGCTGCTCTTCTTTTGCATACCATGGCTCAGTACTTCACCCCAAAATTTGA
upper sequence: Vv15s0046g00950.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: LOC_Os03g44200.2 (Oryza sativa), 3'ss of exon 7
--------------tatgtcatcaactagtatacagcttattttagaatactttccttga----tattggaactg---aggcaccgactaagaagtttatctgtactgtggaaaca----------------tatagGTTGAATGGGATGAGATAAATGCTGCCTGGGGCCAAGCTTGCCTTCTTCTCCATACAATGGTTCAATATTTCCGACCAAAGTTCCA
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gtaattatgcaaaatgtgcagatatcacgtccattcactatcttttagtgctttccttgaattctattcaagatgtacatggaatgttcatgttgatcctttgtgttaatgtaacaactgtgttactcttttcttagGTGGAGTGGGATGAGATAAATGCTGCTTGGGGCCAGGCTGCTCTTCTGTTGCATACCATGGCTCAGTACTTCTTCCCAAAATTTGA
upper sequence: Vv15s0046g00950.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GRMZM2G092112_T01 (Zea mays), 3'ss of exon 6
tatgtcatcaactagtatacagcttattttagaatactttccttgatattggaactgaggcaccgactaagaagtttatctgtactgtggaaacatatagGTTGAATGGGATGAGATAAATGCTGCCTGGGGCCAAGCTTGCCTTCTTCTCCATACAATGGTTCAATATTTCCGACCAAAGTTCCA
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----------gtaattatactg---attgcaaaacgcata----gatac-aactttgtgtcactatactcggcgctt--ctg----ataataatgtacagGTTGAGTGGGATGAGATAAATGCTGCATGGGGTCAGGCTGCACTGCTGTTGCATACCATGGCTCAGTATTTCACCCCAAAATTCCA
upper sequence: Vv15s0046g00950.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA04G26840.1 (Glycine max), 3'ss of exon 6
-tatgtcatcaactagtatacagcttattttagaatactttccttgata--ttgga-actgaggcaccgactaagaagtttatctgtactgtggaaacatatagGTTGAATGGGATGAGATAAATGCTGCCTGGGGCCAAGCTTGCCTTCTTCTCCATACAATGGTTCAATATTTCCGACCAAAGTTCCA
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ttatcctagagaattttcttaatcttgaattgaataatttttcttcctagtttgaatatttaagctttgattatgatgttcacttttat----gaaatgtttagGTTGAATGGGATGAGATAAATGCTGCCTGGGGCCAAGCTTGCCTCCTTCTTCATACTATGTGCCAATATTTCCGACCGAAGTTTCA
upper sequence: Vv15s0046g00950.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA11G21490.1 (Glycine max), 3'ss of exon 6
--tatgtcatcaactagtatacagcttattttagaatactttccttgata--ttgga-actgaggcaccgactaagaagtttatctgtactgtggaaacatatagGTTGAATGGGATGAGATAAATGCTGCCTGGGGCCAAGCTTGCCTTCTTCTCCATACAATGGTTCAATATTTCCGACCAAAGTTCCA
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tttatcctagagaattttcttaatcttgaactgaatcctttttcttcctagtttgaatattgaagctttgattatgatgttact----attatg-aaatgtttagGTTGAATGGGATGAGATAAATGCTGCCTGGGGCCAAGCTTGCCTCCTTCTTCACACTATGTGCCAGTATTTCCGACCGAAGTTTCA
upper sequence: Vv15s0046g00950.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: AT3G61710.3 (Arabidopsis thaliana), 3'ss of exon 6
tatgtcatcaactagtatacagcttattttagaatactttccttg-atattggaactgaggcaccgactaagaagtttatctgtactgtg-gaaacatat--agGTTGAATGGGATGAGATAAATGCTGCCTGGGGCCAAGCTTGCCTTCTTCTCCATACAATGGTTCAATATTTCCGACCAAAGTTCCA--------------
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-----------------------gtaagttttgctactttccttgtatgtttataatctcgttctg-ctcatatttttgtctaaacaacatgaaacatatttagGTTGAGTGGGATGAGATCAATGCTGCTTGGGGCCAAGCCTGTCTTCTCCTCCATACGATGTGTAACTATTTCCGGCCAAAGTTTCAGTATCCTTATAACT
upper sequence: Vv15s0046g00950.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: AT3G61710.1 (Arabidopsis thaliana), 3'ss of exon 6
tatgtcatcaactagtatacagcttattttagaatactttccttg-atattggaactgaggcaccgactaagaagtttatctgtactgtg-gaaacata--tagGTTGAATGGGATGAGATAAATGCTGCCTGGGGCCAAGCTTGCCTTCTTCTCCATACAATGGTTCAATATTTCCGACCAAAGTTCCA
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-----------------------gtaagttttgctactttccttgtatgtttataatctcgttctg-ctcatatttttgtctaaacaacatgaaacatatttagGTTGAGTGGGATGAGATCAATGCTGCTTGGGGCCAAGCCTGTCTTCTCCTCCATACGATGTGTAACTATTTCCGGCCAAAGTTTCAMapped 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|110724261|gb|EE099932.1|EE099932EST: AATTTGGAACAATTAACAATTTTCGGCTTGGACGACTTCCTAAAATTCCA GTTGAATGGGATGAGATAAATGCTGCCTGGGGCCAAGCTTGCCTTCTTCTC
genomic: AATTTGGAACAATTAACAATTTTCGGCTTGGACGACTTCCTAAAATTCCAgtaagaaatc ... aaacatatagGTTGAATGGGATGAGATAAATGCTGCCTGGGGCCAAGCTTGCCTTCTTCTC
EST:
gi|34548484|gb|CF516716.1|CF516716EST: AATTTGGAACAATTAACAATTTTCGGCTTGGACGACTTCCTAAAATTCCA GTTGAATGGGATGAGATAAATGCTGCCTGGGGCCAAGCTTGCCTTCTTCTC
genomic: AATTTGGAACAATTAACAATTTTCGGCTTGGACGACTTCCTAAAATTCCAgtaagaaatc ... aaacatatagGTTGAATGGGATGAGATAAATGCTGCCTGGGGCCAAGCTTGCCTTCTTCTC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atattggaactgaggcaccgactaagaagtttatctgtactgtggaaacatatagGTTGAATGGGATGAGATAAATGCTGCCTGGGGCCAAGCTTGCCTTCTTCTCCATACAATGGTTCAATATTTCCGACCAAAGTTCCA
ccttgat putative branch site (score: 5)
aaacatata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tatgtcatcaactagtatacagcttattttagaatactttccttgatattggaactgaggcaccgactaagaagtttatctgtactgtggaaacatatagGTTGAATGGGATGAGATAAATGCTGCCTGGGGCCAAGCTTGCCTTCTTCTCCATACAATGGTTCAATATTTCCGACCAAAGTTCCA
- - -catcaac
- - - - - - - - - - - - - - - agaatac
- - - - - - - - - - - - - - - - - - - ttccttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - caccgac