Sequence
atgc intronic sequence ATGC exonic sequencegtgatcatcatctttcttgcatgattcattggattggtgtcttctatttcagaagtcatccaataattaatttccttgtactttacatcttcagCCCTATGCAGCAGCAAAGGCAAGAGAGTATCTTGACAAGCCTGCTATCCATGAGACAATGGTCAAG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv06s0061g01170.t01 (Vitis vinifera), 3'ss of exon 13
lower sequence: LOC_Os03g02150.1 (Oryza sativa), 3'ss of exon 13
gtgatcatcatctttcttgcatgattcattggattggtgtcttctatttcagaagtcatccaataattaatttccttgtactttacatcttcagCCCTATGCAGCAGCAAAGGCAAGAGAGTATCTTGACAAGCCTGCTATCCATGAGACAATGGTCAAG
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------------gttcttgcatatttct---gattgccgatagctatctcaattttgtttgttgaacttgaagtttgacttgtaattttatcagCCATATGCTGCAGCAAAGGCTAGAGAATACCTCGACAAGCCTGCTTTGCATGAAACAATGGTTAAG
upper sequence: Vv06s0061g01170.t01 (Vitis vinifera), 3'ss of exon 13
lower sequence: GRMZM2G137236_T01 (Zea mays), 3'ss of exon 14
gtgatcatcatctttcttgcatgattcattggattggtgtcttctatttcagaagtcatccaataattaatttccttgtactttacatcttcagCCCTATGCAGCAGCAAAGGCAAGAGAGTATCTTGACAAGCCTGCTATCCATGAGACAATGGTCAAG
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------gtttgtgtatatatatagttgagcaaaatcatctctacttttttttttg--aatttatggttcattttttgcaatttta-----tcagTCATACGCTGCAACTAAAGCGAGAGAATATCTTGACAAGCCTGCTTTACATGAGACGATGGTCAAG
upper sequence: Vv06s0061g01170.t01 (Vitis vinifera), 3'ss of exon 13
lower sequence: GLYMA17G05410.1 (Glycine max), 3'ss of exon 13
gtgatcatcatctttcttgcatg-attcattggattggtgtcttctatttcagaagtcatccaataattaatttccttgtactttacatcttcagCCCTATGCAGCAGCAAAGGCAAGAGAGTATCTTGACAAGCCTGCTATCCATGAGACAATGGTCAAG
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-------gtgtgtttgaaacttgtagtgactatgatactgcttcctattttacacatcattcacaaggcattttctgtct--------ttctcagCCTTATGCTGCAGCAAAAGCTCGAGAATATCTTGACAAACCTGCTATACATGAGACAATGGTTAAG
upper sequence: Vv06s0061g01170.t01 (Vitis vinifera), 3'ss of exon 13
lower sequence: GLYMA12G30520.1 (Glycine max), 3'ss of exon 13
gtgatcatcatctttcttgcatg-attcattggattggtgtcttctatttcagaagtcatccaataattaatttccttgtactttacatcttcagCCCTATGCAGCAGCAAAGGCAAGAGAGTATCTTGACAAGCCTGCTATCCATGAGACAATGGTCAAG
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-------gtgtgtttgaaacttgtagtgactatgatactgcttcctaatttacacatcattcacaaggcattttccgt---ctttg-----tcagCCTTATGCTGCGGCAAAAGCTCGAGAATATCTTGACAAACCTGCTATACATGAGACAATGGTTAAGMapped 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|34543150|gb|CF511382.1|CF511382EST: GGTTTCGTGTTGTGCAGTTTGTTACAAACAATGAAGACCTACAG CCCTATGCAGCAGCAAAGGCAAGAGAGTATCTTGACAAGCCTGCTATCCAT
genomic: GGTTTCGTGTTGTGCAGTTTGTTACAAACAATGAAGACCTACAGgtgatcatca ... acatcttcagCCCTATGCAGCAGCAAAGGCAAGAGAGTATCTTGACAAGCCTGCTATCCAT
EST:
gi|71857368|gb|DT006423.1|DT006423EST: ACATATGGTTTCGTGTTGTGCAGTTTGTTACAAACAATGAAGACCTACAG CCCTATGCAGCAGCAAAGGCAAGAGAGTATCTTGACAAGCCTGCTATCCAT
genomic: ACATATGGTTTCGTGTTGTGCAGTTTGTTACAAACAATGAAGACCTACAGgtgatcatca ... acatcttcagCCCTATGCAGCAGCAAAGGCAAGAGAGTATCTTGACAAGCCTGCTATCCAT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcttctatttcagaagtcatccaataattaatttccttgtactttacatcttcagCCCTATGCAGCAGCAAAGGCAAGAGAGTATCTTGACAAGCCTGCTATCCATGAGACAATGGTCAAG
aattaat putative branch site (score: 3)
catcttc putative PPT
atccaataattaattt 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
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gtgatcatcatctttcttgcatgattcattggattggtgtcttctatttcagaagtcatccaataattaatttccttgtactttacatcttcagCCCTATGCAGCAGCAAAGGCAAGAGAGTATCTTGACAAGCCTGCTATCCATGAGACAATGGTCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA