Sequence
atgc intronic sequence ATGC exonic sequence...tttttatgtaagatcattctaaggcatgatcctctgcttcttcactgcttatgtttattgattactaagtacctttaatatttatctggtattccataagGATTGATGTGTGAACTGCTGTGGAGTGATCCCCAACCTTACCCTGGAAGAGGCCCTAGCAAGCGGGGTGTAGGTCTTTCCTTTGGTGTAGATGTGACAAA
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv12s0142g00720.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: LOC_Os05g11550.1 (Oryza sativa), 3'ss of exon 9
tttttatgtaagatcattctaaggcatgatcctctgctt-cttcactgcttatgtttattgattactaagtacctttaatatttatctggtattccataagGATTGATGTGTGAACTGCTGTGGAGTGATCCCCAACCTTACCCTGGAAGAGGCCCTAGCAAGCGGGGTGTAGGTCTTTCCTTTGGTGTAGATGTGACAAA
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-aaccattaatttgcattataagtgttggcatattatttaccttgatgccttttttcccatgttagttatctgccaacatgactcctgtttctgctgacagGTCTAATGTGTGAAGTATTATGGAGTGATCCTCAGCCTCAACTTGGTAGAGGTCCAAGCAAACGCGGTGTTGGTCTTTCGTTTGGTGCAGATGTGACTAA
upper sequence: Vv12s0142g00720.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA18G12440.1 (Glycine max), 3'ss of exon 9
--------------------------------------------tttttatgta---agatcattctaaggcat--gatcctctgcttc-----ttcactgcttatgtttattgattactaagtacctt--taatatttatctg-gtattccata---agGATTGATGTGTGAACTGCTGTGGAGTGATCCCCAACCTTACCCTGGAAGAGGCCCTAGCAAGCGGGGTGTAGGTCTTTCCTTTGGTGTAGATGTGACAAA-
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ttagataaatccttttttgttgtctctaattgatctcccagttatctgcacatatctaaatccctctaaaccttccattcttgcacttcatagactaaacccctctggctttttcacccttagtattttagttttatttacctatgtttggtatgtgtaggGTTGATGTGTGAATTGCTCTGGAGTGATCCACAACCTCTCCCTGGAAGGGGCCCAAGCAAGCGTGGTGTAGGCCTTTCTTTTGGTGCAGATGTTACAAAA
upper sequence: Vv12s0142g00720.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA08G42380.1 (Glycine max), 3'ss of exon 9
-------------------------------------------------tttttatgtaagatcattctaaggcatgatcct----ctgcttcttcactgcttatgtttattgattactaa----gtaccttta-atatttatctggtattccataagGATTGATGTGTGAACTGCTGTGGAGTGATCCCCAACCTTACCCTGGAAGAGGCCCTAGCAAGCGGGGTGTAGGTCTTTCCTTTGGTGTAGATGTGACAAA
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gttagatacatccttttttgttgtctctaattgatctcccagttaaccacacatacctaaatccctctaaactttccattcttgcactacatagactcacctttggctttttcaccctcagtattgtagttttatgtacctatgtttggtatgtgtagGGTTGATGTGTGAATTGCTATGGAGCGATCCACAACCTCTCCCTGGAAGGGGCCCAAGTAAGCGTGGTGTAGGCCTTTCTTTTGGTGCAGATGTTACAAA
upper sequence: Vv12s0142g00720.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: AT2G42810.1 (Arabidopsis thaliana), 3'ss of exon 9
tttttatgtaagatcattctaaggcatg-atcctctgcttcttcactgcttatgtttattgattactaagtacctttaatatttatctggtattccata-agGATTGATGTGTGAACTGCTGTGGAGTGATCCCCAACCTTACCCTGGAAGAGGCCCTAGCAAGCGGGGTGTAGGTCTTTCCTTTGGTGTAGATGTGACAAA
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-----------gtatgtttcatcatatacatcttctgtaagattacttctcatgta-attgtgttctgtttaatcatcttatcttgctaatggtttatgcagGACTAATGTGTGAACTATTGTGGAGTGATCCTCAACCTCTCCCTGGAAGAGGCCCAAGCAAGCGAGGAGTTGGTCTATCATTTGGTGGAGATGTGACAAA
upper sequence: Vv12s0142g00720.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: PP1S80_144V6.1 (Physcomitrella patens), 3'ss of exon 8
tttttatgtaagatcattctaaggcatgatcct--ctgcttcttcactgcttatgtttattgattactaagtacctttaatatttatctggtattccataagGATTGATGTGTGAACTGCTGTGGAGTGATCCCCAACCTTACCCTGGAAGAGGCCCTAGCAAGCGGGGTGTAGGTCTTTCCTTTGGTGTAGATGTGACAAA
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-atctcttggattttactgtaggctgcaattgtgacgggatttatgtgaatttggtgatcttacttcacagtaactgtcctcgttaatttgtattctgca-gGGTTAATGTGTGAGCTGCTGTGGAGTGATCCCCACCCTGGCACGGGGCGTGCACCTAGCAAACGCGGTGTCGGTGTTGCATTTGGATCTGATGTCACCCAMapped 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|110380672|gb|EC945956.1|EC945956EST: GCTCTCTGACATTAGAGCAATTGACCGGTTTTGTGAGCCTCCTGAGGAAG GATTGATGTGTGAACTGCTGTGGAGTGATCCCCAACCTTACCCTGGAAGAG
genomic: GCTCTCTGACATTAGAGCAATTGACCGGTTTTGTGAGCCTCCTGAGGAAGgtaagctaga ... attccataagGATTGATGTGTGAACTGCTGTGGAGTGATCCCCAACCTTACCCTGGAAGAG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgcttatgtttattgattactaagtacctttaatatttatctggtattccataagGATTGATGTGTGAACTGCTGTGGAGTGATCCCCAACCTTACCCTGGAAGAGGCCCTAGCAAGCGGGGTGTAGGTCTTTCCTTTGGTGTAGATGTGACAAA
tacctttaatatttat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tttttatgtaagatcattctaaggcatgatcctctgcttcttcactgcttatgtttattgattactaagtacctttaatatttatctggtattccataagGATTGATGTGTGAACTGCTGTGGAGTGATCCCCAACCTTACCCTGGAAGAGGCCCTAGCAAGCGGGGTGTAGGTCTTTCCTTTGGTGTAGATGTGACAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - catgatc
- - - - - - - - - - - - - - - - -ctgcttc
- - - - - - - - - - - - - - - - - - - - -tcactgc