Sequence
atgc intronic sequence ATGC exonic sequence...acatttacttatctcaggtttctgtttggtctttggtttctataatttaagtttggtggtgttgatatcatgatcctcttttcctgaatgatgttcccagTTAATAAGTGGGAGGAATTCCTATGACTATAAATCTGTTAGAAGATGGACTACGCAAAGGAAGTTGGGATACAGCCTTAGTGAATGTGACAAA
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv05s0020g01220.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: LOC_Os03g22400.1 (Oryza sativa), 3'ss of exon 4
acatttacttatctcaggtttctgtttggtctttggtttctataatttaagtttggtggtg-ttgatatcatgatcctcttttcctgaatgatgttcccagTTAATAAGTGGGAGGAATTCCTATGACTATAAATCTGTTAGAAGATGGACTACGCAAAGGAAGTTGGGATACAGCCTTAGTGAATGTGACAAA
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-aattttaccatttcattttcatttgtgaatgctgaattgctgatcaccaagtaaatgctaatcttcattgactccctgaattgttggtcgtttggttcagCTTGCTTGCGGAAAAAATGGCTATGACTACAAATCTGTTAAAAGATGGACTACCCGCAGGAGGTTGGGTTATGAGCTTATTGAGTGTGATAAA
upper sequence: Vv05s0020g01220.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G088653_T03 (Zea mays), 3'ss of exon 4
acatttacttatctcaggtttctgtttggtctttggtttctataatttaagtttggtggtgttgatatcatgatcctcttttcctgaatgatgttcccagTTAATAAGTGGGAGGAATTCCTATGACTATAAATCTGTTAGAAGATGGACTACGCAAAGGAAGTTGGGATACAGCCTTAGTGAATGTGACAAA
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------attttgttgcgattgtgacatg--cgttgtattttagcgcaatgttgtgttaattataat-tcataactcatctctcattactgtc--tatcagctgatttccagTGGG------TATGATTATAAAGCTGTTAGAAGATGGACAACAAAAAGGAAGTTAGGGTACAGTCTAATTGATTGTGACAAG
upper sequence: Vv05s0020g01220.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G088653_T01 (Zea mays), 3'ss of exon 4
-acatttacttatctcaggtttctgtt-tggtctttggtttctataatttaagtttggtggtgttgata--tcatgatcctcttttcctgaatgatgttcccagTTAATAAGTGGGAGGAATTCCTATGACTATAAATCTGTTAGAAGATGGACTACGCAAAGGAAGTTGGGATACAGCCTTAGTGAATGTGACAAA
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ttcattaccatatttt--gttgcgattgtgacatgcgttgtattttagcgcaatgttgtgttaattataattcataactcatctctcattactgtc--tatcagCTGATTTCCAGTGGG------TATGATTATAAAGCTGTTAGAAGATGGACAACAAAAAGGAAGTTAGGGTACAGTCTAATTGATTGTGACAAG
upper sequence: Vv05s0020g01220.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM5G849959_T01 (Zea mays), 3'ss of exon 4
--acatttacttatctcaggtttctgt-ttggtctttggtttctataatttaagtttggtggtgttgatatcatgatcctcttttcctgaatgatgttcccagTTAATAAGTGGGAGGAATTCCTATGACTATAAATCTGTTAGAAGATGGACTACGCAAAGGAAGTTGGGATACAGCCTTAGTGAATGTGACAAA
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atggacttctgccttgcatgtatctgccttcgtttattgttcatg-gatttttttttgcctatgaatgttgatccttactgacttcctgaatgttactc--agCTTGCTTGTGGAAAAAATGGTTATGATTACAAATCTGTTAAAAGATGGACCTCCCAAAGGAAGTTGGGATATGAACTCATTGAATGCGATAAA
upper sequence: Vv05s0020g01220.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM5G849959_T02 (Zea mays), 3'ss of exon 4
--acatttacttatctcaggtttctgt-ttggtctttggtttctataatttaagtttggtggtgttgatatcatgatcctcttttcctgaatgatgttcccagTTAATAAGTGGGAGGAATTCCTATGACTATAAATCTGTTAGAAGATGGACTACGCAAAGGAAGTTGGGATACAGCCTTAGTGAATGTGACAAA-------
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atggacttctgccttgcatgtatctgccttcgtttattgttcatg-gatttttttttgcctatgaatgttgatccttactgacttcctgaatgttactc--agCTTGCTTGTGGAAAAAATGGTTATGATTACAAATCTGTTAAAAGATGGACCTCCCAAAGGAAGTTGGGATATGAACTCATTGAATGCGATAAAGTAATGTMapped 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|351032678|gb|FQ462392.1|FQ462392EST: CGAAAAAGTTTTTGAAATGTCATTTCTTCAACACATTCTTTTATAAAAAG TTAATAAGTGGGAGGAATTCCTATGACTATAAATCTGTTAGAAGATGGACT
genomic: CGAAAAAGTTTTTGAAATGTCATTTCTTCAACACATTCTTTTATAAAAAGgttagttact ... atgttcccagTTAATAAGTGGGAGGAATTCCTATGACTATAAATCTGTTAGAAGATGGACT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttaagtttggtggtgttgatatcatgatcctcttttcctgaatgatgttcccagTTAATAAGTGGGAGGAATTCCTATGACTATAAATCTGTTAGAAGATGGACTACGCAAAGGAAGTTGGGATACAGCCTTAGTGAATGTGACAAA
tgttgat putative branch site (score: 4)
tgttccc putative PPT
ttgatat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
acatttacttatctcaggtttctgtttggtctttggtttctataatttaagtttggtggtgttgatatcatgatcctcttttcctgaatgatgttcccagTTAATAAGTGGGAGGAATTCCTATGACTATAAATCTGTTAGAAGATGGACTACGCAAAGGAAGTTGGGATACAGCCTTAGTGAATGTGACAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
-catttac
- - - - - - - - - - - tgtttgg
- - - - - - - - - - - - - - - - - - - - - - - - - - - ggtggtg