Sequence
atgc intronic sequence ATGC exonic sequencegtatgatgcctttcaggtgtttcatgttttagtttccaaccgctaaactatcttgctaaaaggttatcatctgtccttgtttatcacatggaatgtaaagtttgcttattgactgcagGTTAACCCAGATTATAAAGGTGTATGCCATGTTGCTCTTGCCCAAGAAGGTCATTGCAGGCCTGGAGAG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv08s0056g01640.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: LOC_Os02g03260.1 (Oryza sativa), 3'ss of exon 3
gtatgatg--cctttcaggtgtttcatgttttagtttccaaccgctaaactatcttgctaaaaggttatcatctgtcctt-------gtttatcacatggaatgtaaagtttgcttattgactgcagGTTAACCCAGATTATAAAGGTGTATGCCATGTTGCTCTTGCCCAAGAAGGTCATTGCAGGCCTGGAGAG
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gtatgccgatccattttcattatcttttctccaattgatagcttgtttgttttgtatcaaacctgttttcatgttcattttgaagaaattttttaaataaactgcaa--tttg--tgttgtttgcagGCAAATCCAGACTACAAGGGTGTTTGCCACGTTGCTCTTGCTCAAGAGGGTCATTGCAGACCAGGCGAG
upper sequence: Vv08s0056g01640.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA14G40570.1 (Glycine max), 3'ss of exon 4
gtatgatgcctttcaggtgtttcatgttttagtttccaaccgctaaactatcttgctaaaaggttatcatctgtccttgtttatcacatggaatgtaaagtttgcttattgactgcagGTTAACCCAGATTATAAAGGTGTATGCCATGTTGCTCTTGCCCAAGAAGGTCATTGCAGGCCTGGAGAG
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gtatgcattcttttgatttttttcaatcttgatttgt--tcgtttca--actcttaaagagcattgtaatgcacaatgtccaagaacattgactgtgagatt-----ataaaatacagGTAAATCCAGACTATAAGGGTGTTTGCCATGTTGCTCTTGCTCAGGAAGGTCATTGTAGGCCAGGAGAG
upper sequence: Vv08s0056g01640.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA17G37540.1 (Glycine max), 3'ss of exon 4
-gtatgatgcctttcaggtgtttcatgttttagtttccaaccgctaaactatcttgctaaaagg--ttatcatctgtccttgtttatcacatggaatgtaaagtttgcttattgactgcagGTTAACCCAGATTATAAAGGTGTATGCCATGTTGCTCTTGCCCAAGAAGGTCATTGCAGGCCTGGAGAG
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ggtatgcattcttt----tgtttttt-tttcaatcttgatttgttcttttcaattcttaaagagcattttaatgcacaatgtccaagaacattgactgtgagatt-----ataaaatacaGGTAAATCCAGACTATAAGGGTGTTTGCCATGTTGCCCTTGCTCAGGAAGGTCATTGTAGGCCTGGAGA-
upper sequence: Vv08s0056g01640.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: AT4G13430.1 (Arabidopsis thaliana), 3'ss of exon 4
gtatgatgcctttcaggtgtttcatgttttagtttccaaccgctaaactatcttgctaaaaggttatcatctgtccttgtttatcacatggaatgtaaagtttgcttattgactgcagGTTAACCCAGATTATAAAGGTGTATGCCATGTTGCTCTTGCCCAAGAAGGTCATTGCAGGCCTGGAGAG
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------------------gtatgatggtttgaattgattctgttttgcttgcattcggatgaagtttaatgcttttttgtttgt----------------ttcactcat---ctgtagGCTAATCCTGACTACAAAGGTGTTTGCCATGTTGCACTTGCACAAGAAGGTCATTGCAGGCCAGGAGAGMapped 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|161719979|gb|FC068309.1|FC068309EST: AGCAAAATATCAAGTACTTCTATGATATAAAAGATCTTGGTAATTTCGAG GTTAACCCAGATTATAAAGGTGTATGCCATGTTGCTCTTGCCCAAGAAGGT
genomic: AGCAAAATATCAAGTACTTCTATGATATAAAAGATCTTGGTAATTTCAAGgtatgatgcc ... ttgactgcagGTTAACCCAGATTATAAAGGTGTATGCCATGTTGCTCTTGCCCAAGAAGGT
EST:
gi|110688159|gb|EE066391.1|EE066391EST: AGCAAAATATCAAGTACTTCTATGATATAAAAGATCTTGGTAATTTCAAG GTTAACCCAGATTATAAAGGTGTATGCCATGTTGCTCTTGCCCAAGAAGGT
genomic: AGCAAAATATCAAGTACTTCTATGATATAAAAGATCTTGGTAATTTCAAGgtatgatgcc ... ttgactgcagGTTAACCCAGATTATAAAGGTGTATGCCATGTTGCTCTTGCCCAAGAAGGT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttatcatctgtccttgtttatcacatggaatgtaaagtttgcttattgactgcagGTTAACCCAGATTATAAAGGTGTATGCCATGTTGCTCTTGCCCAAGAAGGTCATTGCAGGCCTGGAGAG
tattgac putative branch site (score: 2)
ttgtttat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgatgcctttcaggtgtttcatgttttagtttccaaccgctaaactatcttgctaaaaggttatcatctgtccttgtttatcacatggaatgtaaagtttgcttattgactgcagGTTAACCCAGATTATAAAGGTGTATGCCATGTTGCTCTTGCCCAAGAAGGTCATTGCAGGCCTGGAGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA