Sequence
atgc intronic sequence ATGC exonic sequence...atattagaaatttggtgtacgtatgaagtgcacaatttgttggaccaatttgatgtgttgccatgcaatgtaacatgggtgatcattggtttatttgcagGAACTGGAGAAAAGCCTCAAAGCCACTTGTGAGGAGTTTATTATGTCGGTCACTAAGCTAGTTGTGGATCCCATGCTTTCATTTGTTACTAAG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv11s0016g00350.t01 (Vitis vinifera), 3'ss of exon 22
lower sequence: LOC_Os08g34970.1 (Oryza sativa), 3'ss of exon 21
atattagaaatttggtgtacgtatgaagtgcacaatttgttgg-accaat----ttgatgtgttgccatgcaatgtaacatgggtgatcattggtttatttgcagGAACTGGAGAAAAGCCTCAAAGCCACTTGTGAGGAGTTTATTATGTCGGTCACTAAGCTAGTTGTGGATCCCATGCTTTCATTTGTTACTAAG
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----ataaaataaggcagcagtctaatgtgattgctttgtagatgcccatatcctcgattttttaatatttttt-cagctaattttgttactactattttttcagGAATTGGAAAAAAGCCTCAAATCTACCTGTGAAGAGTTTATAATGTCCATTACAAAATTAGTAGTGGATCCAATGCTTTCTTTTGTTACTAAG
upper sequence: Vv11s0016g00350.t01 (Vitis vinifera), 3'ss of exon 22
lower sequence: GRMZM5G825854_T01 (Zea mays), 3'ss of exon 21
atattagaaatttggtgtacgtatgaagtgcacaatttgttggaccaatttgatgtgt-----tgccatgcaatgtaacatgggtgatcattggtttatttgcagGAACTGGAGAAAAGCCTCAAAGCCACTTGTGAGGAGTTTATTATGTCGGTCACTAAGCTAGTTGTGGATCCCATGCTTTCATTTGTTACTAAG
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----gcgacattcagataaagtaggggattacctatctttaatattttctagttgctcccatctttctttgatttcagcttattttgctattgttctattt-cagGAGTTGGAGAAAAGCCTTAAAGCTACCTGTGAAGAGTTTATAATGTCCATAACTAAATTAGTAGTTGACCCAATGCTTTCTTTTGTTACTAAG
upper sequence: Vv11s0016g00350.t01 (Vitis vinifera), 3'ss of exon 22
lower sequence: GLYMA17G04990.1 (Glycine max), 3'ss of exon 21
atattagaaatttggtgtacgtatgaagtgcacaatttgttggaccaatttgatgtgttgccatgcaatgtaacatgg-gtgatcattggtttatttgcagGAACTGGAGAAAAGCCTCAAAGCCACTTGTGAGGAGTTTATTATGTCGGTCACTAAGCTAGTTGTGGATCCCATGCTTTCATTTGTTACTAAG
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-ttttcctcgtcttcagtgattcttctttaatcattttattccatatgttgcattgtctaatttagaccattatctagcgcctttgacatttttttttcagGAGCTGGAAAAGAGCCTTAAAGCCACTTGTGAGGAGTTCATCATGTCAGTTACTAAGCTTGTTGTGGATCCTTTGCTTTCATTCGTTACAAAG
upper sequence: Vv11s0016g00350.t01 (Vitis vinifera), 3'ss of exon 22
lower sequence: AT1G73430.1 (Arabidopsis thaliana), 3'ss of exon 21
atattagaaatttggtgta-cgtatgaagtgcacaatt-tgttggaccaatttgatgtgttgccatgcaatgtaac-atgggtgatcattggtttatttgcagGAACTGGAGAAAAGCCTCAAAGCCACTTGTGAGGAGTTTATTATGTCGGTCACTAAGCTAGTTGTGGATCCCATGCTTTCATTTGTTACTAAG
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-tgctagtaggctcaagtaatatggcaagttgttggttgtatctggctccttgcattacttgatatgaatgggaatgatgcatagacctttattt--tcgcagGAACTGGAAAAATGTCTTAAGACAACTTGTGAGGAGTTCATCATGTCAGTAACTAAGCTAGTTGTGGATCCTATGCTTTCATTTGTGACGAAGMapped 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|110701225|gb|EE078568.1|EE078568EST: CAAGGACCTTATCACCTCGAGTTTTGGAAAGTCAAATAGATGCCAAGAAG GAACTGGAGAAAAGCCTCAAAGCCACTTGTGAGGAGTTTATTATGTCGGTC
genomic: CAAGGACCTTATCACCTCGAGTTTTGGAAAGTCAAATAGATGCCAAGAAGgtttgtgaca ... ttatttgcagGAACTGGAGAAAAGCCTCAAAGCCACTTGTGAGGAGTTTATTATGTCGGTC
EST:
gi|349827691|gb|FQ422559.1|FQ422559EST: CAAGGACCTTATCACCTCGAGTTTTGGAAAGTCAAATAGATGCCAAGAAG GAACTGGAGAAAAGCCTCAAAGCCACTTGTGAGGAGTTTATTATGTCGGTC
genomic: CAAGGACCTTATCACCTCGAGTTTTGGAAAGTCAAATAGATGCCAAGAAGgtttgtgaca ... ttatttgcagGAACTGGAGAAAAGCCTCAAAGCCACTTGTGAGGAGTTTATTATGTCGGTC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.caatttgatgtgttgccatgcaatgtaacatgggtgatcattggtttatttgcagGAACTGGAGAAAAGCCTCAAAGCCACTTGTGAGGAGTTTATTATGTCGGTCACTAAGCTAGTTGTGGATCCCATGCTTTCATTTGTTACTAAG
atgtaac putative branch site (score: 3)
tttattt putative PPT
tttattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
atattagaaatttggtgtacgtatgaagtgcacaatttgttggaccaatttgatgtgttgccatgcaatgtaacatgggtgatcattggtttatttgcagGAACTGGAGAAAAGCCTCAAAGCCACTTGTGAGGAGTTTATTATGTCGGTCACTAAGCTAGTTGTGGATCCCATGCTTTCATTTGTTACTAAG
- - -agaaatt
- - - - - - tggtgta
- - - - - - - - - - - - - - - - - - ttgttgg
- - - - - - - - - - - - - - - - - - - - - - - - - tgatgtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ccatgca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - acatggg