Sequence
atgc intronic sequence ATGC exonic sequence...gatacatggaaagtccatggtttgatgtttaggtcatgcatctggctcattgttccccaattatatattggatcttttgattgattcaagtatttcttagGTTTGGTCCTGTGAACTTGTTTTGGAGCACACGCTATGACAAAGCAATGACGTTATTCTTGACATGCCTTAAGGACTTTGCTGATTTTGCCAATTCCAAG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv15s0046g00950.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: LOC_Os01g48920.1 (Oryza sativa), 3'ss of exon 8
----gatacatggaaagtcca-tggtttgatgtttaggtcatgcatctggctcattgttccccaattatatattggatcttttgattgattcaagtatttcttagGTTTGGTCCTGTGAACTTGTTTTGGAGCACACGCTATGACAAAGCAATGACGTTATTCTTGACATGCCTTAAGGACTTTGCTGATTTTGCCAATTCCAAG
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tttctatatttgccctatttactgacagtttgctctgggtgtgcatttttcatatttgttgtccctt---tgttgagcactgcagttatatca--tgctaaccagGTTTGGTCCCGTGAATTTATTCTGGAGCACACGTTTTGACAAAGCCATGACATGGTTTCTAACCTGCCTGCAAGATTTTGCTGAGTTCGCTATTAGCTTG
upper sequence: Vv15s0046g00950.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GRMZM2G092112_T01 (Zea mays), 3'ss of exon 8
---------------------------------------------------------------------------------------gatacatggaaagtccatggtttgatgtttaggtcatgcatctggctcattgttccccaattatatattggatcttt-tgattgattcaagtatttcttagGTTTGGTCCTGTGAACTTGTTTTGGAGCACACGCTATGACAAAGCAATGACGTTATTCTTGACATGCCTTAAGGACTTTGCTGATTTTGCCAATTCCAAG
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gtaagctttctgcaagcaaatgtacttctatttctctctgagatgatggtctatagtttagtagtcctcactttcttaggttgagtctataattttcatttgcaaacttttttgccttagcactgtaccaggc--agtgcaacttaatcatgcttgggatgttaataagacacactgttgatgttcagGTTTGGTCCCGTGAATTTGTTCTGGAGCACCCGATTTGACAAAGCCATGACATGGTTTCTTACTTGCCTGCAAGAGTTTGCTGAGTTTGCCATAAGTTTG
upper sequence: Vv15s0046g00950.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GRMZM2G027857_T02 (Zea mays), 3'ss of exon 1
gatac-atggaaagtccatggtttgatgtttaggtcatgcatctggctcattgttccccaattatatattggatcttt-tgattgattcaagtatttcttagGTTTGGTCCTGTGAACTTGTTTTGGAGCACACGCTATGACAAAGCAATGACGTTATTCTTGACATGCCTTAAGGACTTTGCTGATTTTGCC--AATTCCAAG
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aatcctatttagtttaaaaaccttcttgtcttagcactatatcaggc--agtgcaaattagtcatgcttgggatgttaataagacgtgttgttgatgttcagGTTTGGTCCCGTGAATTTGTTCTGGAGCACCCGATTTGACAAAGCCATGACATGGTTTCTGACTTGCCTGCAAGAGTTCGCTGAGTTTGCCATAAGTCTG--
upper sequence: Vv15s0046g00950.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GLYMA11G21490.1 (Glycine max), 3'ss of exon 8
-gatacat-ggaaagtccatggtttgatgtttaggtcatgcatctggctcattgttccccaa-ttatatattggatc--ttttgattgattcaagtatttcttagGTTTGGTCCTGTGAACTTGTTTTGGAGCACACGCTATGACAAAGCAATGACGTTATTCTTGACATGCCTTAAGGACTTTGCTGATTTTGCCAATTCCAAG
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tactaagttgtaaacaaaataatataataa--acttcctgcttttagat--ttgttcttaaacttgtctactgagtcactattaatggatgtta-tggttttcagGTTTGGTCCAGTCAACTTGTTCTGGAGTACTCGCTATGACAAAGCAATGACATTGTTTTTAGCATGCCTCAAGGATTTTGCAGACTTTGCCAAATCCAAG
upper sequence: Vv15s0046g00950.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GLYMA04G26840.1 (Glycine max), 3'ss of exon 8
gatacatggaaagtccatggtttgatgtttaggt-catgcatctggctcattgttccccaa-ttatatattggatc--ttttgattgattcaagtatttcttagGTTTGGTCCTGTGAACTTGTTTTGGAGCACACGCTATGACAAAGCAATGACGTTATTCTTGACATGCCTTAAGGACTTTGCTGATTTTGCCAATTCCAAG
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-ggactaaaaacttaattaaccctataataaacttcctgcttttagat--ttgttcttaaacttgtctactgagtcactattaatggatgtta-tggttttcagGTTTGGTCCTGTCAACTTGTTCTGGAGTACTCGCTATGACAAAGCAATGACTTTGTTTTTAGCATGCCTCAAGGATTTCGCAGACTTTGCCAAATCTAAG
upper sequence: Vv15s0046g00950.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: AT3G61710.1 (Arabidopsis thaliana), 3'ss of exon 8
--------gatacatggaaagtccatggtttgatgtttaggtc-------------atgcatctggctcattgttccccaattatatattggatcttttga--------ttgattcaagtatttcttagGTTTGGTCCTGTGAACTTGTTTTGGAGCACACGCTATGACAAAGCAATGACGTTATTCTTGACATGCCTTAAGGACTTTGCTGATTTTGCCAATTCCAAG
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gtaagtaaattgcatattcttgtcctggtttgttattggggttgaactgaaaacagatgtcctgtgctgagttttgtctttgtttttcttgaccctttttaactaaaagctgttgataatcttcggcagGTTTGGTCCTGTTAACTTGTTTTGGAGCACTCGGTACGATAAAGCCATGACACTGTATTTGATGTGTCTTAAAGACTTTGCTGATTTTGCAAATTCAAAGMapped 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|110724261|gb|EE099932.1|EE099932EST: ATGGGAAGTTACCCTCGGATTACGGACAGCAACAACAGTACTTATGAACT GTTTGGTCCTGTGAACTTGTTTTGGAGCACACGCTATGACAAAGCAATGAC
genomic: ATGGGAAGTTACCCTCGGATTACGGACAGCAACAACAGTACTTATGAACTgtaagtatag ... tatttcttagGTTTGGTCCTGTGAACTTGTTTTGGAGCACACGCTATGACAAAGCAATGAC
EST:
gi|34548484|gb|CF516716.1|CF516716EST: ATGGGAAGTTACCCTCGGATTACGGACAGCAACAACAGTACTTATGAACT GTTTGGTCCTGTGAACTTGTTTTGGAGCACACGCTATGACAAAGCAATGAC
genomic: ATGGGAAGTTACCCTCGGATTACGGACAGCAACAACAGTACTTATGAACTgtaagtatag ... tatttcttagGTTTGGTCCTGTGAACTTGTTTTGGAGCACACGCTATGACAAAGCAATGAC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctcattgttccccaattatatattggatcttttgattgattcaagtatttcttagGTTTGGTCCTGTGAACTTGTTTTGGAGCACACGCTATGACAAAGCAATGACGTTATTCTTGACATGCCTTAAGGACTTTGCTGATTTTGCCAATTCCAAG
gattgat putative branch site (score: 4)
tatttctt putative PPT
aattatatattggat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gatacatggaaagtccatggtttgatgtttaggtcatgcatctggctcattgttccccaattatatattggatcttttgattgattcaagtatttcttagGTTTGGTCCTGTGAACTTGTTTTGGAGCACACGCTATGACAAAGCAATGACGTTATTCTTGACATGCCTTAAGGACTTTGCTGATTTTGCCAATTCCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- tacatgg
- - - - - - - ccatggt
- - - - - - - - - - - - - - - - -tcatgca