Sequence
atgc intronic sequence ATGC exonic sequence...atagtggctttttttggcacctatcatttgaaattgtccttttgtggggttgtgttttcttgcattttcttatgctaatatttgcatatccatgattcagGTTGTTACAAGTCTGGCCGATCCTTCAGCTAACATAATATTTGGAGCTGTTGTGGACGACCGCTACAATGGGGAGATTCATGTGACTATAATTGCAACCG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv19s0090g01320.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: LOC_Os04g56970.1 (Oryza sativa), 3'ss of exon 5
-----------------------------------------------------------------------------------atagtggctttttttggcacctatcatttgaaattgtccttttgtggggttgtgttttct-------tgcattttcttatgctaatatttgcatatccatgatt--cagGTTGTTACAAGTCTGGCCGATCCTTCAGCTAACATAATATTTGGAGCTGTTGTGGACGACCGCTACAATGGGGAGATTCATGTGACTATAATTGCAACCG
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gtgcgtgtaatatttcttgccattgtcttgaactgtctttgaagaagtatgatatagcactgtaatatgttaagtcgaaaaacttaagatgctattatcacgatcatactccacaatttagggctactggaattatgtggcctaggtgattgaagtgctttgttttgaccaatgcttatgcacgttttgcagATTGTGACAAGCTTGGCCGATCCTTCTGCAAATATAATTTTCGGGGCTGTTGTTGATGACCGGTACACTGGTGAGATTCATGTGACGATCATTGCCACAG
upper sequence: Vv19s0090g01320.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA14G02110.1 (Glycine max), 3'ss of exon 5
atagtggctttttttggcacctatcatttgaaattgtccttttgtggggttgtgttttcttgcattttcttatgctaatatttgcatatccatgattc----agGTTGTTACAAGTCTGGCCGATCCTTCAGCTAACATAATATTTGGAGCTGTTGTGGACGACCGCTACAATGGGGAGATTCATGTGACTATAATTGCAACCG
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----tgctgtattccgccttttgctgtatggtggtatacttactgggttcactcctaccttttcttcgtatttgccttgtccttaacacgtgtaatttttatagGTGGTGACTAGTTTGGCTGATCCTTCTGCTAATATTATATTTGGAGCTGTTGTTGATGATCGCTACACTGGGGAGATTCACGTGACTATAATTGCAACTG
upper sequence: Vv19s0090g01320.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA08G43500.1 (Glycine max), 3'ss of exon 6
--atagtggc-tttttttggcacctatcatttgaaattgtccttttgtggggttgtgt-tttcttgcattttcttatg-ctaatatttgcatatccatgatt----cagGTTGTTACAAGTCTGGCCGATCCTTCAGCTAACATAATATTTGGAGCTGTTGTGGACGACCGCTACAATGGGGAGATTCATGTGACTATAATTGCAACCG
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gtacctcggaattttattggcagaaagaacatttcagtattctttt-tgatcttatgaatttgttgcaaacatttgtatcctgttttcaaaacttcataactgttgtagGTTGTGACTAGTTTAGCCGACCCTTCTGCCAATATTATATTTGGCGCCGTTGTTGACGATCGCTACAATGGGGAGATTCATGTGACTATCATTGCAACTG
upper sequence: Vv19s0090g01320.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA18G10030.1 (Glycine max), 3'ss of exon 6
--atagtggctttttttggcacctatcatttgaaattgtccttttgtggggttgtgttt-tcttgcattttcttatgctaatatttgcatatccatgatt----cagGTTGTTACAAGTCTGGCCGATCCTTCAGCTAACATAATATTTGGAGCTGTTGTGGACGACCGCTACAATGGGGAGATTCATGTGACTATAATTGCAACCG-
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tacttaagaattttattgtcagaaggaacatttcagcattcttttgatcttatgaatttgttgtgaacatttgtatcctgtt-ttcaaaacttcataactgctgtaggTGGTGACAAGTTTAGCCGACCCTTCTGCCAATATTATATTTGGTGCCGTTGTTGATGATCGCTACAATGGGGAGATTCATGTGACTATCATTGCAACTGG
upper sequence: Vv19s0090g01320.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA02G46530.1 (Glycine max), 3'ss of exon 5
atagtggctttttttggcacctatcatttgaaattgtccttttgtggggttgtg---ttttcttgcattt-tcttatgctaatatttgcatatccatgattcagGTTGTTACAAGTCTGGCCGATCCTTCAGCTAACATAATATTTGGAGCTGTTGTGGACGACCGCTACAATGGGGAGATTCATGTGACTATAATTGCAACCG
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-ttgtgctgtattttgccttttgctgtatggtatatttactgggttgactcctaccttttcttcgtatttgccttgtcctta-acacgtgtaatttttat--agGTTGTGACTAGTTTGGCTGATCCTTCTGCTAATATTATATTTGGGGCTGTCGTTGATGATCGCTACACGGGGGAGATTCACGTGACTATCATTGCAACTG
upper sequence: Vv19s0090g01320.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: AT5G55280.1 (Arabidopsis thaliana), 3'ss of exon 5
atagtg-gctttttttggcacctatcatttgaaattgtccttttgtggggttgtgttttcttgcattttcttatgctaatatttgcatatccatgattcagGTTGTTACAAGTCTGGCCGATCCTTCAGCTAACATAATATTTGGAGCTGTTGTGGACGACCGCTACAATGGGGAGATTCATGTGACTATAATTGCAACCG
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---gtacggtatttttgtcttggtttactcggctttgtttcaat-tgggtatacactgtattataatgcagtcttctcatgttt-tgggggggttttgcagGTCGTGACAAGTTTGGCAGACCCATCGGCCAACATCATATTTGGAGCTGTTGTGGATGATCGCTACACCGGAGAGATTCATGTAACGATAATCGCCACAGMapped 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|71871223|gb|DT020278.1|DT020278EST: TTACTGGCGGAAAGGACATAACCTTGCAAGAAGTTAATAGAGTGTCTCAG GTTGTTACAAGTCTGGCCGATCCTTCAGCTAACATAATATTTGGAGCTGTT
genomic: TTACTGGGGGAAAGGACATAACCTTGCAAGAAGTTAATAGAGTGTCTCAGgtagtttgaa ... catgattcagGTTGTTACAAGTCTGGCCGATCCTTCAGCTAACATAATATTTGGAGCTGTT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ggggttgtgttttcttgcattttcttatgctaatatttgcatatccatgattcagGTTGTTACAAGTCTGGCCGATCCTTCAGCTAACATAATATTTGGAGCTGTTGTGGACGACCGCTACAATGGGGAGATTCATGTGACTATAATTGCAACCG
tgctaat putative branch site (score: 2)
ttatgctaatattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
atagtggctttttttggcacctatcatttgaaattgtccttttgtggggttgtgttttcttgcattttcttatgctaatatttgcatatccatgattcagGTTGTTACAAGTCTGGCCGATCCTTCAGCTAACATAATATTTGGAGCTGTTGTGGACGACCGCTACAATGGGGAGATTCATGTGACTATAATTGCAACCG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - tggcttt
- - - - - - - - gcaccta
- - - - - - - - - - - - - - - - - - - - - tgtgggg