Sequence
atgc intronic sequence ATGC exonic sequence...ttctagggagtttcatggttatatgcatagactattgttctccataatttgttacataactagctcaaattttcacttttcaatgttatttttcatgcagGGCTTGTATTGTGGTTGATGATCGGTTACTTGTTATTGGTGGTCAAGAGGGCGATTTTATGGCAAAACCTGGATCACCTATTTTTAAGTGCTCCCGTAGG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv09s0054g00620.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: LOC_Os04g41020.1 (Oryza sativa), 3'ss of exon 4
ttctagggagtt-tcatg-gttatatgcatagactattgttctccataatttgttacataactagctcaaattttcacttttcaatgttat-ttttcatgc-agGGCTTGTATTGTGGTTGATGATCGGTTACTTGTTATTGGTGGTCAAGAGGGCGATTTTATGGCAAAACCTGGATCACCTATTTTTAAGTGCTCCCGTAGG
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----acaaagttcttatgtggcatataagtatataacctgtttccgagaatggtcctgttgttagcttagcagcttaatcatgatttttctcttttgataccagGGCTTGTGTTGTTGCTAATGATAAGCTACTTGTTATTGGTGGCCAAGAAGGAGATTTTATGGCGAAACCTGGATCACCTATATTTAAATGTGTTAGAAGA
upper sequence: Vv09s0054g00620.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G007981_T02 (Zea mays), 3'ss of exon 4
--------------------------------------------------------ttctagggagtttcatggttat---atgcataga--ctattgttctccataatttgttacataactagctcaaattttca-----------cttttcaatgttatttttca------tgcagGGCTTGTATTGTGGTTGATGATCGGTTACTTGTTATTGGTGGTCAAGAGGGCGATTTTATGGCAAAACCTGGATCACCTATTTTTAAGTGCTCCCGTAGG
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gtatgtcggagtatacttgtgtcatttgcatgtagtcgccatgaggtaatgcctgatttcagggatgattgttggtatctagtgcttagacactgataccgtttatcctttgttgcgtcaattgtagatatttctaaatgaacaataccttataatttctgactccaactttttgcagGGCGTGTATTGTAGCTAATGATAAACTATTTGTGATTGGTGGACAAGAGGGAGACTTTATGGCTAAACCAGGATCACCTATTTTTAAATGTGTACGGAGG
upper sequence: Vv09s0054g00620.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G030598_T02 (Zea mays), 3'ss of exon 4
ttctagggagtttcatggttatatg---catagactattgttctccataatttgttacataactagctcaaattttcacttttcaatgttatttttcatgcagGGCTTGTATTGTGGTTGATGATCGGTTACTTGTTATTGGTGGTCAAGAGGGCGATTTTATGGCAAAACCTGGATCACCTATTTTTAAGTGCTCCCGTAGG
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---gggcaacatttatgcttctaggaaatgttttctatatttggttgcatcatactttataagaagttgctgaagttataaagaaattgccttttacttccagGGCTTGTGTAGTTGCAAATGATAAACTCCTTGTTATTGGTGGTCAAGAAGGTGATTTCATGGCCAAGCCTGGGTCTCCTATATTTAAATGTGTTAGAAGA
upper sequence: Vv09s0054g00620.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA08G23660.1 (Glycine max), 3'ss of exon 3
ttctagggagtttcatg-gttatatgcatagactattgttctccata--atttgttacata-actagctcaaattt-tcacttttcaatgttatttttcatgcagGGCTTGTATTGTGGTTGATGATCGGTTACTTGTTATTGGTGGTCAAGAGGGCGATTTTATGGCAAAACCTGGATCACCTATTTTTAAGTGCTCCCGTAGG
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-gtttggggttccaacacattataatctaggtttattgaaatgcattttattaagtgtatatgctaccttcaatttattacatattaatgtc----ttcgttcagGGCTTGTGTTGTGGTTGATGATCGTCTTTATGTTCTTGGTGGTCAAGAAGGAGATTTTATGGCCAAACCTGGGTCACCTATTTTCAAGTGCTCACGCAGA
upper sequence: Vv09s0054g00620.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: AT1G51540.1 (Arabidopsis thaliana), 3'ss of exon 3
ttctagggagtttcatggttatatgcatagactattgttct-ccataatttgttacataactagctcaaattttcacttttcaatgttatttttcatgcagGGCTTGTATTGTGGTTGATGATCGGTTACTTGTTATTGGTGGTCAAGAGGGCGATTTTATGGCAAAACCTGGATCACCTATTTTTAAGTGCTCCCGTAGG
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-----------gttattatcttaca-atgatctttagaccaactattatggataaaacatttgacgaaatagcatcgtgttctgtgtgccatt----gtagGGCATGTGTAGTAGTTGATGACCGACTATTTGTAATTGGTGGTCAAGAAGGTGATTTCATGGCTAAACCTGGATCTCCAATCTTCAAATGCTCACGCCGTMapped 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|34544466|gb|CF512698.1|CF512698EST: GAGAAGGAGTGGAGGTCTGAAATACCTATTCCTCGAGGAGGGCCTCATAG GGCTTGTATTGTGGTTGATGATCGGTTACTTGTTATTGGTGGTCAAGAGGG
genomic: GAGAAGGAGTGGAGGTCTGAAATACCTATTCCTCGAGGAGGGCCTCATAGgtatgtagtt ... tttcatgcagGGCTTGTATTGTGGTTGATGATCGGTTACTTGTTATTGGTGGTCAAGAGGG
EST:
gi|34546528|gb|CF514760.1|CF514760EST: GAGAAGGAGTGGAGGTCTGAAATACCTATTCCTCGAGGAGGGCCTCATAG GGCTTGTATTGTGGTTGATGATCGGTTACTTGTTATTGGTGGTCAAGAGGG
genomic: GAGAAGGAGTGGAGGTCTGAAATACCTATTCCTCGAGGAGGGCCTCATAGgtatgtagtt ... tttcatgcagGGCTTGTATTGTGGTTGATGATCGGTTACTTGTTATTGGTGGTCAAGAGGG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aatttgttacataactagctcaaattttcacttttcaatgttatttttcatgcagGGCTTGTATTGTGGTTGATGATCGGTTACTTGTTATTGGTGGTCAAGAGGGCGATTTTATGGCAAAACCTGGATCACCTATTTTTAAGTGCTCCCGTAGG
acataac putative branch site (score: 3)
ttatttttc putative PPT
aaattttcacttttca 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttctagggagtttcatggttatatgcatagactattgttctccataatttgttacataactagctcaaattttcacttttcaatgttatttttcatgcagGGCTTGTATTGTGGTTGATGATCGGTTACTTGTTATTGGTGGTCAAGAGGGCGATTTTATGGCAAAACCTGGATCACCTATTTTTAAGTGCTCCCGTAGG
- - - - - -ttcatgg
- - - - - - - - - - - -tgcatag
- - - - - - - - - - - - - - - - - - - tctccat
- - - - - - - - - - - - - - - - - - - - - - - - - - -acataac