Sequence
atgc intronic sequence ATGC exonic sequence...gtatgtatgtatgtatgtaggagttgatattgaccaaagggtaatgaggcccttcttttatatgctgataattttttaagatgcttgcctcttgcttcagGTGAAGAGCTTTCAAAAAAGCAAGCTGCTCAAGAGTCTCAGATTAGGAAATTAAGGGCACAG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv16s0098g00540.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: LOC_Os05g48620.1 (Oryza sativa), 3'ss of exon 5
gtatgtatgtatgtatgtaggagttgatattgaccaaagggtaatgag-gcccttcttttatatgctgataattttttaagatgcttgcctcttgcttcagGTGAAGAGCTTTCAAAAAAGCAAGCTGCTCAAGAGTCTCAGATTAGGAAATTAAGGGCACAG
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-tacactttagagcccatttgattttttgcccccttcatttttatgtttagtaggttttgaggcatttatttggcatcaacaatttttttacaatgaacagGTGAAGAGCTATCAAAAAAACAAGCTGCTCAAGAAGCTACTATGCGGAAACTTAGGGCACAG
upper sequence: Vv16s0098g00540.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA15G01980.2 (Glycine max), 3'ss of exon 6
--gtatgtatgtatgtatgtaggagttgatattgaccaaagggtaatga-ggcccttcttttatatgctgataattttttaagatgcttgcctcttgcttcagGTGAAGAGCTTTCAAAAAAGCAAGCTGCTCAAGAGTCTCAGATTAGGAAATTAAGGGCACAG
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gggcttttctgt-tgtaattataaagtt-tctccattgaagcatggtagtggtttaattattggagattattgaggcccttatagact-gtctctcatctcagGTGAAGAGCTTTCCAAAAAACAGGCTGCTCAAGAATCCACAATTAGGAAACTAAGGGCTCAG
upper sequence: Vv16s0098g00540.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA13G43330.1 (Glycine max), 3'ss of exon 8
-gtatgtatgtatgtatgtaggagttga--tattgaccaaagggtaatgaggcccttcttttatatgctgataattttttaagatgcttgcctcttgcttcagGTGAAGAGCTTTCAAAAAAGCAAGCTGCTCAAGAGTCTCAGATTAGGAAATTAAGGGCACAG
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ggtttttctgttgtaattaaatagtttctctattgaaccatgg-tagtggtttaattattggagattatagagaccctt--attagactgtctctcatctcagGTGAAGAGCTTTCCAAAAAACAGGCTGCTCAAGAATCCACAATTAGGAAACTAAGGGCTCAG
upper sequence: Vv16s0098g00540.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: AT1G79830.3 (Arabidopsis thaliana), 3'ss of exon 6
------------------------------------gtatgtatgtatgtatgtagga-----gttgatattgacca------aagggtaatgaggcccttcttttatatgctgataattttttaagatgcttgcctcttgcttcagGTGAAGAGCTTTCAAAAAAGCAAGCTGCTCAAGAGTCTCAGATTAGGAAATTAAGGGCACAG
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gtaagacagccttttggaatgcttgaattatggatcgtatttttctcgttataaaaaaatggtgttgaaagcgaacacctgaaaaatgaaaggacgtcatttcttgctcagct--tgagctcttgatattaatgctaatcatttcagGCGAAGAGCTTTCAAAGAAACAGGCTGCTCAAGAAGCTCAGATCAGGAAGCTAAGGGCTCAGMapped 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|34544079|gb|CF512311.1|CF512311EST: TGCCCTTTTGAAAGAAAAAGATGAAATAATCAACCAAGTTATGGCTGAGG GTGAAGAGCTTTCAAAAAAGCAAGCTGCTCAAGAGTCTCAGATTAGGAAAT
genomic: TGCCCTTTTGAAAGAAAAAGATGAAATAATCAACCAAGTTATGGCTGAGGgtgagttgcc ... cttgcttcagGTGAAGAGCTTTCAAAAAAGCAAGCTGCTCAAGAGTCTCAGATTAGGAAAT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gaggcccttcttttatatgctgataattttttaagatgcttgcctcttgcttcagGTGAAGAGCTTTCAAAAAAGCAAGCTGCTCAAGAGTCTCAGATTAGGAAATTAAGGGCACAG
tgctgat putative branch site (score: 3)
cttgcctcttgcttc putative PPT
ttcttttatatgctga 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgtatgtatgtatgtaggagttgatattgaccaaagggtaatgaggcccttcttttatatgctgataattttttaagatgcttgcctcttgcttcagGTGAAGAGCTTTCAAAAAAGCAAGCTGCTCAAGAGTCTCAGATTAGGAAATTAAGGGCACAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- -tgtatgt
- - - - - - - - - - - - - - - -gaccaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cttgcct