Sequence
atgc intronic sequence ATGC exonic sequence...ataaatttaggtttcaaaatgtctagtggttactttgtgatattttattctagatggttgacgtatgtacatcgttactatgtgttggccacatttttagGTACTATGGAGGATGGGCAGCGCCTAACATATACTTCTTGGGGTTTGCTGGAGTAGTCAAGTTTGGAAATATTCGTATTGGTGGGCTCTCTGGAATTTAT
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv18s0001g08180.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: LOC_Os03g51540.1 (Oryza sativa), 3'ss of exon 3
ataaatttaggtttcaaaatgtctagtggttactttgtgatattttattctagatggttgacgtatgtacatcgttactatgtgt-tggccacattttta---gGTACTATGGAGGATGGGCAGCGCCTAACATATACTTCTTGGGGTTTGCTGGAGTAGTCAAGTTTGGAAATATTCGTATTGGTGGGCTCTCTGGAATTTAT
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--aagtcaacatcgtcatacattta-taaatagagggagtatcattgttgctaattttaaaaatgta-actttgctactttttttgtggtcaaacatctaatagGTATTATGGAGGATGGGCAGCACCCAACATCTACTTTTTGGGGTTCGCTGGTGTTGTTAAGTTTGGAAACATTCGAATTGGTGGACTATCAGGAATATAT
upper sequence: Vv18s0001g08180.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GRMZM2G461145_T01 (Zea mays), 3'ss of exon 4
ataaatttaggtttcaaaatgt-ctagtggttactttgtgatattttat-tctagatggt-tgacgtatgtacatcgtt--actatgtgttggccacatttttagGTACTATGGAGGATGGGCAGCGCCTAACATATACTTCTTGGGGTTTGCTGGAGTAGTCAAGTTTGGAAATATTCGTATTGGTGGGCTCTCTGGAATTTAT
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-caag---aagattaacaatgtactttgagcaacctttcggtgctttatctatagttgatgtttttttttttgctcattggaaaatgtaatgactat-ttatcagGTACTATGGAGGATGGGCAGCACCTAACATATACTTTTTGGGGTTTGCTGGTGTTGTTAAGTTTGGAAACATACGAATTGGTGGATTGTCAGGAATACAT
upper sequence: Vv18s0001g08180.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA04G06310.1 (Glycine max), 3'ss of exon 1
-ataaatttaggtttcaaaatgtctagtggttactttgtgatattttattctagatggttgacgtatgtacatcgttactatgtgttggccacatttttagGTACTATGGAGGATGGGCAGCGCCTAACATATACTTCTTGGGGTTTGCTGGAGTAGTCAAGTTTGGAAATATTCGTATTGGTGGGCTCTCTGGAATTTAT
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ccaaaatcacagccgcggactgttttttt-ttataaaaaaaaccttaacttttgcaatgtgatctagggttttgacaagtgtttgattatgtttgttgtagGTACTATGGAGGATGGGCTGCTCCTAATATCTACTTCTTGGGAGCTGCTGGGGTGGTGAGGTTTGGGAATGTTCGAATTGGTGGCCTCTCTGGGATCTAT
upper sequence: Vv18s0001g08180.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA06G06360.1 (Glycine max), 3'ss of exon 3
ataaatttaggtttcaaaatgtctagtggttactttgtgatattttattctagatggttgacgtatgtacatcgttactatgtgttggccacatttttagGTACTATGGAGGATGGGCAGCGCCTAACATATACTTCTTGGGGTTTGCTGGAGTAGTCAAGTTTGGAAATATTCGTATTGGTGGGCTCTCTGGAATTTAT
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----gttttttttttaaaaaaaacattggccg--ttgcaatgt---gatttagggttttgataagtgtttg-----attatgtgtttg------ttgtagGTACTATGGAGGATGGGCTGCTCCTAATATATACATCTTGAGAGCTGCTGGGGTGGTGAGGTTTGGGAATTTTCGAATTGGTGGCCTCTCTGGGATTTAT
upper sequence: Vv18s0001g08180.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: AT4G31770.1 (Arabidopsis thaliana), 3'ss of exon 2
ataaatttaggtttcaaaatgtctagtggtt-actttgtgatattttattctagatggttgacgtatgtacatcgttactatgtgttggccacatttttagGTACTATGGAGGATGGGCAGCGCCTAACATATACTTCTTGGGGTTTGCTGGAGTAGTCAAGTTTGGAAATATTCGTATTGGTGGGCTCTCTGGAATTTAT
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-------------gtaagttatctagtatttgagtttaggattccgaggcttaaaaaatgtgttcttg---atggttgctggttgttgtgc-----tatagGTATTATGGGGGTTGGGCTGCCACCAATATTTACTTTTTGGGTTTTGCTGGAGTTGTCAAGTTTGGTAATGTGCGAATTGGTGGCCTTTCTGGTATATACMapped 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|37188542|gb|CF607891.1|CF607891EST: ACTATATTCATTGGTGGGAATCATGAAGCATCCAATTACCTGTGGGAATT GTACTATGGAGGATGGGCAGCGCCTAACATATACTTCTTGGGGTTTGCTGG
genomic: ACTATATTCATTGGTGGGAATCATGAAGCATCCAATTACCTGTGGGAATTgtgagtaact ... acatttttagGTACTATGGAGGATGGGCAGCGCCTAACATATACTTCTTGGGGTTTGCTGG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tattctagatggttgacgtatgtacatcgttactatgtgttggccacatttttagGTACTATGGAGGATGGGCAGCGCCTAACATATACTTCTTGGGGTTTGCTGGAGTAGTCAAGTTTGGAAATATTCGTATTGGTGGGCTCTCTGGAATTTAT
ggttgac putative branch site (score: 4)
cattttt putative PPT
acattttta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ataaatttaggtttcaaaatgtctagtggttactttgtgatattttattctagatggttgacgtatgtacatcgttactatgtgttggccacatttttagGTACTATGGAGGATGGGCAGCGCCTAACATATACTTCTTGGGGTTTGCTGGAGTAGTCAAGTTTGGAAATATTCGTATTGGTGGGCTCTCTGGAATTTAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - -tcaaaat
- - - - - - - - - - - - - - - - - - - - - - - - - - - tggttga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tatgtac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gtgttgg