Sequence
atgc intronic sequence ATGC exonic sequence...tttgggtggcataaaattcttcatctcacactcacatatttccttttttaatttttaaaaccatcataggaaaattttcacatccatgtctgttaagcagGTGATAAGCCAGCTGGAAAGACGGACTGTTGCTTACCATGAATCAGGTCATGCTGTTGCTGGTTGGTTCTTGGAACATGCGGAACCCTTGTTGAAAGTGA
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv06s0004g05030.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: LOC_Os01g62500.1 (Oryza sativa), 3'ss of exon 6
-tttgggtggcataaaattcttcatctcacactcacatatttccttttttaatttttaaaaccat-catag-gaaaattttcacatccatgtctgttaagcagGTGATAAGCCAGCTGGAAAGACGGACTGTTGCTTACCATGAATCAGGTCATGCTGTTGCTGGTTGGTTCTTGGAACATGCGGAACCCTTGTTGAAAGTGA
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aattaagtgctgttgcattggatgtaaagtatt---atatggggcatgaacaattggacattcatgtgtagcggttatgtacttatcaatctgtccaccacagGTGATTAGCAAGTTGGAGCGGCGAACTGTTGCTTACCATGAATCTGGTCATGCTGTTGCTGGATGGTTTTTGGAGCATGCCGAGCCACTACTGAAGGTCA
upper sequence: Vv06s0004g05030.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: LOC_Os05g38400.2 (Oryza sativa), 3'ss of exon 6
tttgggtggcataaaattcttcatctcacactcacatatt-tccttttttaatttttaaaaccatcataggaaaattttcacatccatgtctgttaa-------gcagGTGATAAGCCAGCTGGAAAGACGGACTGTTGCTTACCATGAATCAGGTCATGCTGTTGCTGGTTGGTTCTTGGAACATGCGGAACCCTTGTTGAAAGTGA
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--------tagtaactttcttttatatgaaatgacttgttctcaacatgtgatagtcatgtttccccatttatttttcttacctcttagcctgttaatcaaattgcagGTCATCAGCAAACTGGAGCGCCGCACTGTTGCTTACCATGAATCTGGTCATGCTGTTGCTGGATGGTTTTTAGAGCATGCAGAGCCTCTTCTGAAAGTTA
upper sequence: Vv06s0004g05030.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GRMZM2G038401_T01 (Zea mays), 3'ss of exon 6
---------------------------------------------------------------------------tttgggtggcataaaattcttcatctcacactcacatatttccttttttaatttttaaaaccat--cataggaaaattttcacatccatgtctgttaagcagGTGATAAGCCAGCTGGAAAGACGGACTGTTGCTTACCATGAATCAGGTCATGCTGTTGCTGGTTGGTTCTTGGAACATGCGGAACCCTTGTTGAAAGTGA
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gtaagagaatatcatagtagtataacctatgaagctgatttgtgagatttatttcggtgccttattgggatcctaattaagttacttgacagcctttttct-atg-taatgtcattctttttgcacatgcaactattattccttatgtggcctctgagaacgttaacccttttgcagGTCATTAGCAAACTGGAGCGCCGTACTGTTGCTTACCATGAATCTGGACATGCAGTTGCTGGATGGTTCTTGGAACATGCTGAGCCTCTTCTAAAAGTTA
upper sequence: Vv06s0004g05030.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA11G14640.1 (Glycine max), 3'ss of exon 3
tttgggtggcataaaattcttcatctcacactcacatatttccttttttaatttttaaaaccatca--taggaaaattttcacatccatgtctgttaagcagGTGATAAGCCAGCTGGAAAGACGGACTGTTGCTTACCATGAATCAGGTCATGCTGTTGCTGGTTGGTTCTTGGAACATGCGGAACCCTTGTTGAAAGTGA
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-ttaaattaaaaaagttgaactaactgagttttgga-accctctctctccaccttttccactactagttagagtttctctaacacgtatgtttcttaaccagGTAATAAGCAAGCTGGAAAGGCGTACTGTTGCCTACCATGAAGCAGGCCATGCTGTTGCAGGTTGGTTCTTGGAACATGCCGAGCCCTTGTTGAAAGTAA
upper sequence: Vv06s0004g05030.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA12G06580.1 (Glycine max), 3'ss of exon 3
tttgggtggcataaaattct-tcatctcacactcacatatttccttttttaatttttaaaaccatca--taggaaaattttcacatccatgtctgttaagcagGTGATAAGCCAGCTGGAAAGACGGACTGTTGCTTACCATGAATCAGGTCATGCTGTTGCTGGTTGGTTCTTGGAACATGCGGAACCCTTGTTGAAAGTGA
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--taattaatatctaacagaactatctgagatttgga-accctctctctccaccttttcctctactagttagagtttctctaatacctatgtttcttaaccagGTAATAAGCAAGCTGGAAAGGCGGACTGCTGCCTACCATGAAGCAGGCCATGCTGTTTCAGGTTGGTTCTTGGAACATGGTGAGCCCTTGTTGAAAGTAA
upper sequence: Vv06s0004g05030.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA12G06530.1 (Glycine max), 3'ss of exon 6
tttgggtggcataaaattct-tcatctcacactcacatatttccttttttaatttttaaaaccatca--taggaaaattttcacatccatgtctgttaagcagGTGATAAGCCAGCTGGAAAGACGGACTGTTGCTTACCATGAATCAGGTCATGCTGTTGCTGGTTGGTTCTTGGAACATGCGGAACCCTTGTTGAAAGTGA
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--cgcattcgaaaatgttgaactaactgagatttgga-accctctctctccaccttttcctctactagttagagtttctctaatatctatgtttcttaaccagGTAATAAGCAAGCTGGAAAGGCGGACTGTTGCCTACCATGAAGCAGGCCATGCTGTTTCAGGTTGGTTCTTGGAGCATGTTGAGCCCTTGTTGAAAGTAA
upper sequence: Vv06s0004g05030.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: AT1G07510.1 (Arabidopsis thaliana), 3'ss of exon 6
tttgggtggcataaaattcttcatctcacactcaca-tatttccttttttaatttttaaaaccatcataggaaaattttcacatccat-------gtctgttaa--gcagGTGATAAGCCAGCTGGAAAGACGGACTGTTGCTTACCATGAATCAGGTCATGCTGTTGCTGGTTGGTTCTTGGAACATGCGGAACCCTTGTTGAAAGTGA
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---------caacaaattggtgacgt-atattatcagcacgatttttttttctttctacaacggaaacctgaatgttctacaatctcttttggtggtttcatgaccgcagGTAATAAGCAAGCTGGAGCGCCGTACAGTTGCATATCATGAATCTGGCCATGCGGTTGCTGGGTGGTTCCTGGAACATGCGGAACCGTTGCTAAAGGTGAMapped 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|110699287|gb|EE076153.1|EE076153EST: TTGAGGCAGCTATAGATACGATAATTGGTGGTCTGGAGAAGAAGA-TAAG GTGATAAGCCAGCTGGGAAGACGGACTGTTGCTTAACATGA-TCAGGTCAT
genomic: TTGAGGCAGCTATAGATAGGATAATTGGTGGTCTGGAGAAGAAGAATAAGgtaactcatt ... tgttaagcagGTGATAAGCCAGCTGGAAAGACGGACTGTTGCTTACCATGAATCAGGTCAT
EST:
gi|110365164|gb|EC928958.1|EC928958EST: TTGAGGCAGCTATAGATAGGATAATTGGTGGTCTGGAGAAGAAGAATAAG GTGATAAGCCAGCTGGAAAGACGGACTGTTGCTTACCATGAATCAGGTCAT
genomic: TTGAGGCAGCTATAGATAGGATAATTGGTGGTCTGGAGAAGAAGAATAAGgtaactcatt ... tgttaagcagGTGATAAGCCAGCTGGAAAGACGGACTGTTGCTTACCATGAATCAGGTCAT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttttaatttttaaaaccatcataggaaaattttcacatccatgtctgttaagcagGTGATAAGCCAGCTGGAAAGACGGACTGTTGCTTACCATGAATCAGGTCATGCTGTTGCTGGTTGGTTCTTGGAACATGCGGAACCCTTGTTGAAAGTGA
ttttaat putative branch site (score: 3)
atttttaaaaccat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tttgggtggcataaaattcttcatctcacactcacatatttccttttttaatttttaaaaccatcataggaaaattttcacatccatgtctgttaagcagGTGATAAGCCAGCTGGAAAGACGGACTGTTGCTTACCATGAATCAGGTCATGCTGTTGCTGGTTGGTTCTTGGAACATGCGGAACCCTTGTTGAAAGTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
- tgggtgg
- - - - - ataaaat
- - - - - - - - - - - - - cacactc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaaccat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ggaaaat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -acatcca