Sequence
atgc intronic sequence ATGC exonic sequencegtacgtgttctttcttttagaaatcatgaaatttgaggtgcttcagccatttttgttaaaacgagaagaaagaagaggggaaaggggacatatgggcttgattcataagtgattcatgcatgcagTGGTTTGAAGTCCTTGATGGGCTTTTGGGGAAGCACTGGAGGAATGTAGGCCTACTTTTCAACTGCACTTTCCTTCTCTTTGGCTCCGTGATACAGCTGA
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv18s0001g03540.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: LOC_Os10g05690.1 (Oryza sativa), 3'ss of exon 1
gtacgtgttctttcttttagaaatcatgaaatttgaggtgcttcagccatttttgttaaaacgagaagaaagaagaggggaaaggggacatatgggcttgattcataagtgattcatgcatgcagTGGTTTGAAGTCCTTGATGGGCTTTTGGGGAAGCACTGGAGGAATGTAGGCCTACTTTTCAACTGCACTTTCCTTCTCTTTGGCTCCGTGATACAGCTGA
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---tttatggctggctttatatagcctactattatacctgctctaa----tatcgttaacgatatataaatcagtacgtga---------tatgg---tgatacatg-----tttttgtac-cagTGGTTTGAGGTGCTGGATGGGCTACTGGGGAGGCACTGGAGGAATGTGGGACTGGCCTTCAACTGCACGTTTTTGCTGTTCGGGTCGGTGATCCAACTGA
upper sequence: Vv18s0001g03540.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G045057_T02 (Zea mays), 3'ss of exon 2
-------------------gtacgtgtt-ctttcttttagaaatcatgaaatttgaggtgcttcagccatttttgttaaaacgagaagaaagaagaggggaaaggggacatatgggcttgattcataagtgattcatgca---tgcagTGGTTTGAAGTCCTTGATGGGCTTTTGGGGAAGCACTGGAGGAATGTAGGCCTACTTTTCAACTGCACTTTCCTTCTCTTTGGCTCCGTGATACAGCTGA
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gtgcgtgtgtcatgtgtatatatatatgactatttgctagctatacttgtattttgtttgttccaa--attttggtttgaattaacaccatcagaagtttgtggaaattctacaccaataattgtcttttttttctggggagccgcagTGGTTTGAGGTTCTGGATGGGCTACTGGGGAAGCACTGGAGGAACGTCGGCCTCTTCTTCAACTGCACTTTCCTCCTCTTCGGCTCCGTCATCCAGCTCA
upper sequence: Vv18s0001g03540.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA06G11540.1 (Glycine max), 3'ss of exon 3
------gtacgtgttctttcttttagaaat---catgaaatttgag---gtgcttcagccatttttgttaaaacgagaagaaagaagaggggaaaggggacatatgggcttgattcataagtgattcatgcatgcagTGGTTTGAAGTCCTTGATGGGCTTTTGGGGAAGCACTGGAGGAATGTAGGCCTACTTTTCAACTGCACTTTCCTTCTCTTTGGCTCCGTGATACAGCTGA
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gtaataata-gttttcattttattattcttttcccttgaatatgaatctatgtgtaaggctgatatatagccttgtgagttactttaataactttagattcttctaatcttggtttctta-tgacc---gtttgcagTGGTTTGAAGTGCTTGATGGACTTTTGGGCAAACACTGGAGGAATCTTGGTCTTTTTTTCAACTGTACTTTCCTTCTGTTTGGATCAGTAATTCAACTAA
upper sequence: Vv18s0001g03540.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA04G43150.2 (Glycine max), 3'ss of exon 3
------gtacgtgttctttcttttagaaatcatgaaatttgag-gtgcttcagccatttttgttaaaacgagaagaaagaagaggggaaaggggaca--tatgggcttgattcataagtgattca-------tgcatgcagTGGTTTGAAGTCCTTGATGGGCTTTTGGGGAAGCACTGGAGGAATGTAGGCCTACTTTTCAACTGCACTTTCCTTCTCTTTGGCTCCGTGATACAGCTGA
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gtaataatatatattttgcattttattattcttttcccttgaatatgaaccaatgtgtaaggctgatatatatatagcctggtgagttactttaataactttagattcttctaatctttggtttcgtttgaccgtttgcagTGGTTTGAAGTGCTTGATGGACTTTTGGGCAAACACTGGAGAAATCTTGGTCTTTTTTTCAACTGTACTTTCCTTCTGTTTGGATCAGTAATTCAACTAAMapped 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|294965879|gb|GW837362.1|GW837362EST: GAACTAGAAAGGAGAGAGAAAAGGTTGATTTTAGAAATCATGTAATTCAG TGGTTTGAAGTCCTTGATGGGCTTTTGGGGAAGCACTGGAGGAATGTAGGC
genomic: GAACTAGAAAGGAGAGAGAAAAGGTTGATTTTAGAAATCATGTAATTCAGgtacgtgttc ... atgcatgcagTGGTTTGAAGTCCTTGATGGGCTTTTGGGGAAGCACTGGAGGAATGTAGGC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.agaagaggggaaaggggacatatgggcttgattcataagtgattcatgcatgcagTGGTTTGAAGTCCTTGATGGGCTTTTGGGGAAGCACTGGAGGAATGTAGGCCTACTTTTCAACTGCACTTTCCTTCTCTTTGGCTCCGTGATACAGCTGA
gcttgat putative branch site (score: 5)
attcataa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtacgtgttctttcttttagaaatcatgaaatttgaggtgcttcagccatttttgttaaaacgagaagaaagaagaggggaaaggggacatatgggcttgattcataagtgattcatgcatgcagTGGTTTGAAGTCCTTGATGGGCTTTTGGGGAAGCACTGGAGGAATGTAGGCCTACTTTTCAACTGCACTTTCCTTCTCTTTGGCTCCGTGATACAGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA