Sequence
atgc intronic sequence ATGC exonic sequence...tgaatatactttctacataatttggtcagtttttctccacttagttattttacatgccaaatctcgcttaatggttattttgttgcatgtctttatgcagTCTCATCAACAGCAACCTGATACAAGTTTTGGATTAGCCCGGCCCCGGTAAGGGGCATGGGCCATGCCTGCACCCTGCCAGCTGAAACTCAAGCTTGAAA
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv13s0106g00640.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: LOC_Os09g39462.1 (Oryza sativa), 3'ss of exon 3
---tgaatatactttctacata-atttggtcagtttttc--tccacttagttattttacatgccaaatctcgcttaatg-gttattttgttgcatgtctttatgcagTCTCATCAACAGCAACCTGATACAAGTTTTGGATTAGCCCGGCCCCGGTAAGGGGCATGGGCCATGCCTGCACCCTGCCAGCTGAAACTCAAGCTTGAAA-
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gtattattgcacatacaacatctattctgatatttcttcgatgcaatttat-agattatgcattaacactcagctgatgtgttcctttttcac------ttgtgcagACTCACCAACAACAACCTGAAGCTAGTTTGCGCTTAGCCCGGCCCCGATGAGGGGCCTGGGC-ATGCCTGCACCCTGCCAGCGTGCCCTGAATGTGTAAAT
upper sequence: Vv13s0106g00640.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA10G34810.3 (Glycine max), 3'ss of exon 3
tgaatatactttctacataatttggtcagtttttctccacttagttattttacatgccaaatctcg--cttaatggttattttgttgcatgtctttatgcagTCTCATCAACAGCAACCTGATACAAGTTTTGGATTAGCCCGGCCCCGGTAAGGGGCATGGGCCATGCCTGCACCCTGCCAGCTGAAACTCAAGCTTGAAA
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--tgcatttgacataaaagaccaatcttattattctttagtttttcactttgcctttgaagtttgaatctaattgaactctttcatgtacatgatactgcagTCTCATCAGCCCCCACCTGATGCAAGTTTTGGATTGGCCCGGCCCCGGTGAGGGGCATGGGCCATGCCTGCACCCAATCAGCCAGTGGTATAAGATAAGA
upper sequence: Vv13s0106g00640.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA20G32800.2 (Glycine max), 3'ss of exon 3
tgaatatactttctacataatttggtcagtttttctccacttagttattttacatgccaaatctcg--cttaatggttattttgttgcatgtctttatgcagTCTCATCAACAGCAACCTGATACAAGTTTTGGATTAGCCCGGCCCCGGTAAGGGGCATGGGCCATGCCTGCACCCTGCCAGCTGAAACTCAAGCTTGAAA
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--tgcatttgacgtaaaagaccaatcttattattctttagtttttcactttgcctttgaagtttgaatctaattgcactctttcatgcacatcatactgcagTCTCATCAGCCCCCACCAGATGCAAGTTTTGGATTGGCCCGGCCCCGGTGAGGGGCATGGGCCATGCCTGCACCCAATCAGCCAGTGGTATAAGATAAGA
upper sequence: Vv13s0106g00640.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA10G34810.2 (Glycine max), 3'ss of exon 1
tgaatatactttctacataatttggtcagtttttctccacttagttattttacatgccaaatctcg--cttaatggttattttgttgcatgtctttatgcagTCTCATCAACAGCAACCTGATACAAGTTTTGGATTAGCCCGGCCCCGGTAAGGGGCATGGGCCATGCCTGCACCCTGCCAGCTGAAACTCAAGCTTGAAA
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--tgcatttgacataaaagaccaatcttattattctttagtttttcactttgcctttgaagtttgaatctaattgaactctttcatgtacatgatactgcagTCTCATCAGCCCCCACCTGATGCAAGTTTTGGATTGGCCCGGCCCCGGTGA-------------------------------------------------Mapped 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|71881313|gb|DT030368.1|DT030368EST: GAATGCCTTTCATCCATCCTCATGAACATGTTCACCAACCTTTTTCACAG TCTCATCAACAGCAACCTGATACAAGTTTTGGATTAGCCCGGCCCCGGTAA
genomic: GAATGCCTTTCATCCATCCTCATGAACATGTTCACCAACCTTTTTCACAGgtatggaaaa ... ctttatgcagTCTCATCAACAGCAACCTGATACAAGTTTTGGATTAGCCCGGCCCCGGTAA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tattttacatgccaaatctcgcttaatggttattttgttgcatgtctttatgcagTCTCATCAACAGCAACCTGATACAAGTTTTGGATTAGCCCGGCCCCGGTAAGGGGCATGGGCCATGCCTGCACCCTGCCAGCTGAAACTCAAGCTTGAAA
gcttaat putative branch site (score: 4)
tgtcttt putative PPT
ttaatggttatttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tgaatatactttctacataatttggtcagtttttctccacttagttattttacatgccaaatctcgcttaatggttattttgttgcatgtctttatgcagTCTCATCAACAGCAACCTGATACAAGTTTTGGATTAGCCCGGCCCCGGTAAGGGGCATGGGCCATGCCTGCACCCTGCCAGCTGAAACTCAAGCTTGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - -tctccac
- - - - - - - - - - - - - - - - - - - - - - - - - - catgcca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgcatgt