Sequence
atgc intronic sequence ATGC exonic sequencegtaatggttttgtatcttcttctgtgacttgctttctgtattcttctgtatgcttgatgcctccaaggaacatcttcattacctataattataaagttaatttgccccacatgtctgtgttactgtgtgagcagGAACATGTTGAAGGTTACCTCGAACTGTCTGCCAAGACAAAGATATATTTTGCTACTGCTGTTGCTTTGTGGGATGCAGAGTTCTACATTAAAGTTGATG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv12s0059g00640.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: LOC_Os06g46570.2 (Oryza sativa), 3'ss of exon 6
gtaatggttttgtatcttcttctgtgacttgctttctgtattcttctgtatgcttgatgcctccaaggaacatcttcattacctataattataaagttaat-ttgccccacatgtctgtgttactg--tgtgagcagGAACATGTTGAAGGTTACCTCGAACTGTCTGCCAAGACAAAGATATATTTTGCTACTGCTGTTGCTTTGTGGGATGCAGAGTTCTACATTAAAGTTGATG
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gtaatattctgcttatgtggtttacgaagaactagctgc--tccattacctttttgaactcatgttggagtactttcgaagtttgaacttcataccttattgctgtgcctaatgtcagtcctgtccacttctgttagGACCATGTTGAAGGATACCTTGAATTGTCTGGCAAAACCAAGACATACTTTGCTACAGCTGTTTCTTTATGGGATGCTGACTTCTATGTGAAGGTTGACG
upper sequence: Vv12s0059g00640.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: LOC_Os02g06840.2 (Oryza sativa), 3'ss of exon 7
gtaatggttttgtatcttcttctgtgacttgctttctgtattcttctgtatgcttgatgcctccaaggaacatcttcattacctataattataaagttaatttgccccacatgtctgtgttactgtg----tgagcagGAACATGTTGAAGGTTACCTCGAACTGTCTGCCAAGACAAAGATATATTTTGCTACTGCTGTTGCTTTGTGGGATGCAGAGTTCTACATTAAAGTTGATG
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------gtaagacaagcacttgcttaa-ttgcttattggtttttcatggatcgt--atttatcaagtgactgtttctcctagaatcactgggaatgctatttcgcccc-cttatttattgtggtctaactttattcagGATCATGTTGAAGGATACCTTGCACTATCTGGCAAAACCAAGACATACTTTGCTACGGCTGTTTCATTGTGGGATGCAGACTTTTATGTGAAGGTTGATG
upper sequence: Vv12s0059g00640.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: LOC_Os03g38050.1 (Oryza sativa), 3'ss of exon 6
gtaatggttttgtatcttcttctgtgacttgctttctgtattcttctgtatgcttgatgcctccaaggaacatcttcattacctataattataaagttaatttgccccacatgtctgtgttactgtgtgagcagGAACATGTTGAAGGTTACCTCGAACTGTCTGCCAAGACAAAGATATATTTTGCTACTGCTGTTGCTTTGTGGGATGCAGAGTTCTACATTAAAGTTGATG
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-----------------------gtaattaccataggacttactctagctggcatatagtacagtattactggcttgtttatttgt--ctgtaaagctgaaatatcttggaatattttttgatcact----cagGATCATGTTGAAGGGTATCTGGAATTGGCTGCAAAGACGAAATCGTTCTTTGTGACAGCCTTGTCCATGTGGGATGCAGAGTACTACATTAAAGTGGATG
upper sequence: Vv12s0059g00640.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA12G31980.1 (Glycine max), 3'ss of exon 6
------------gtaatggttttg-tatcttcttctgtgacttgctttctgtattcttctgtatgcttgatgcctccaaggaacatcttcattacctataatta----taaagttaatt-------------tgcccca-----catgtctgtgttactgtgtgagcagGAACATGTTGAAGGTTACCTCGAACTGTCTGCCAAGACAAAGATATATTTTGCTACTGCTGTTGCTTTGTGGGATGCAGAGTTCTACATTAAAGTTGATG
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gtaatgatcctctttgtcttattgctgttttccccgttgtctcttctatcatttgtctctacttgaataatcacttgataagatatcatggtcacatttatttgaaggaaaaattaaataaaaaaaaagaaatgcaacaagtttcaaacctctgtt-ttgatttttcagGATCATGTTGAAGGATACCTTGAATTGTCAGCAAAGACAAAGACATACTTTGCCACTGCTGTTAACTTATGGGATGCTGACTTCTATATCAAAGTTGATGMapped 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|30137885|gb|CB923223.1|CB923223EST: ACAGAGCTATCGAAGCAGAGGACAAAAAACATGGAGACTTCTTGAGGCTG GAACATGTTGAAGGTTACCTCGAACTGTCTGCCAAGACAAAGATATATTTT
genomic: ACAGAGCTATCGAAGCAGAGGACAAAAAACATGGAGACTTCTTGAGGCTGgtaatggttt ... gtgtgagcagGAACATGTTGAAGGTTACCTCGAACTGTCTGCCAAGACAAAGATATATTTT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tacctataattataaagttaatttgccccacatgtctgtgttactgtgtgagcagGAACATGTTGAAGGTTACCTCGAACTGTCTGCCAAGACAAAGATATATTTTGCTACTGCTGTTGCTTTGTGGGATGCAGAGTTCTACATTAAAGTTGATG
agttaat putative branch site (score: 4)
ataattataaagttaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaatggttttgtatcttcttctgtgacttgctttctgtattcttctgtatgcttgatgcctccaaggaacatcttcattacctataattataaagttaatttgccccacatgtctgtgttactgtgtgagcagGAACATGTTGAAGGTTACCTCGAACTGTCTGCCAAGACAAAGATATATTTTGCTACTGCTGTTGCTTTGTGGGATGCAGAGTTCTACATTAAAGTTGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT