Sequence
atgc intronic sequence ATGC exonic sequence...ttctcctaattggtttgttagctatttggtgaatgtagtttaagtgaacaggctcttgcaattctcgtgttggctgatgtttatagcttctttgttccagGCGCTGGATACATTTAATGCAGCAATTGTTTCTCCAATTTATTATGTCATGTTCACAACTCTGACTATAAGTGCAAGTGCAATAATGTTCAAG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv03s0038g01940.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: LOC_Os06g50180.1 (Oryza sativa), 3'ss of exon 6
-ttctcctaattggtttgtta-gctatttggtgaatgtagtttaagtgaacaggctcttgcaattctcgtgttggc-tgatgtttatagcttctttgttccagGCGCTGGATACATTTAATGCAGCAATTGTTTCTCCAATTTATTATGTCATGTTCACAACTCTGACTATAAGTGCAAGTGCAATAATGTTCAAG
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atgctaaaaaaccttgagtggtgcaatgtttctgtgctattctgatcattcagtgtatctcacttttcatgtaatcatgattttttttcccactttg---cagGCACTGGATACCTTTGATTTAGCTGTTGTTTCTCCAATTTATTATGTAATGTTTACGACTCTTACAATAGTGGCAAGTGGAATTATGTTCAAG
upper sequence: Vv03s0038g01940.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA12G03390.1 (Glycine max), 3'ss of exon 6
ttctcctaattggtttgttagctatttggtgaatgtagtttaagtgaacaggctcttgcaattctcgtgtt---ggctgatgtttatagcttctttgttccagGCGCTGGATACATTTAATGCAGCAATTGTTTCTCCAATTTATTATGTCATGTTCACAACTCTGACTATAAGTGCAAGTGCAATAATGTTCAAG
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-ggttctcactgatatcaacttctcttatcatccatctattatat-aactcccttttgcttttgacaaatcttgagcttat-tttactattcaaatatttcagGCTCTGGATACATTCAATGCCACAATTGTTTCTCCTGTATATTATGTAATGTTCACAACTCTTACTATTATTGCCAGTGCAATAATGTTTAAG
upper sequence: Vv03s0038g01940.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA11G11230.1 (Glycine max), 3'ss of exon 2
-ttctcctaattggtttgttagctatttggtgaatgtagtttaagtg-aacaggctcttgcaattctcgtgtt---ggctgatgtttatagcttctttgttccagGCGCTGGATACATTTAATGCAGCAATTGTTTCTCCAATTTATTATGTCATGTTCACAACTCTGACTATAAGTGCAAGTGCAATAATGTTCAAG
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tttcttatcatccgtctatgatgtatctgtaagac----tacaagtataactcccttttgcttttgacaaatcttgagcttat-tttactattaaactattgcagGCTCTGGATACATTCAATGCCACAATTGTTTCGCCTGTATATTATGTAATGTTCACCACTCTTACTATTATTGCCACTGCAATAAT-------
upper sequence: Vv03s0038g01940.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: PP1S49_181V6.2 (Physcomitrella patens), 3'ss of exon 6
------------------------------------ttctcctaatt--ggtttgttagctatttggtgaatgtagtttaagtgaacaggctcttgcaattctcgtgttggctgatgtttatagc-ttctttgttccagGCGCTGGATACATTTAATGCAGCAATTGTTTCTCCAATTTATTATGTCATGTTCACAACTCTGACTATAAGTGCAAGTGCAATAATGTTCAAG
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gtaataagcctagcgtgaataaccagcttgaagatgtcactcgaatttaagccagtaaggtgtgaatttggtatgccctctttttgcttgatgttttgaagcgta-gttggatcatgaagttggtactcacctgtgcagGCCCTGGACACATTTAACACGGCAATTGTTTCTCCTATATATTACGTCATGTTCACATCATTGACCATCCTGGCGAGTGCTATCATGTTCAAGMapped 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|37189643|gb|CF608992.1|CF608992EST: TTACTGTTGCAGCAGTCTGTGTCATCACGCAGTTAAACTATCTGAATAAG GCGCTGGATACATTTAATGCAGCAATTGTTTCTCCAATTTATTATGTCATG
genomic: TTACTGTTGCAGCAGTCTGTGTCATCACGCAGTTAAACTATCTGAATAAGgcaagtctag ... tttgttccagGCGCTGGATACATTTAATGCAGCAATTGTTTCTCCAATTTATTATGTCATG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gaacaggctcttgcaattctcgtgttggctgatgtttatagcttctttgttccagGCGCTGGATACATTTAATGCAGCAATTGTTTCTCCAATTTATTATGTCATGTTCACAACTCTGACTATAAGTGCAAGTGCAATAATGTTCAAG
ggctgat putative branch site (score: 4)
cttctttgttcc putative PPT
atgtttata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttctcctaattggtttgttagctatttggtgaatgtagtttaagtgaacaggctcttgcaattctcgtgttggctgatgtttatagcttctttgttccagGCGCTGGATACATTTAATGCAGCAATTGTTTCTCCAATTTATTATGTCATGTTCACAACTCTGACTATAAGTGCAAGTGCAATAATGTTCAAG
- ctcctaa
- - - - - tggtttg
- - - - - - - - - - - - - - gtgaatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gtgttgg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctgatgt