Sequence
atgc intronic sequence ATGC exonic sequencegttagagaaattcatttatttatttatgatcgttatttgtgtcacattagatagtttgatcgtgtgttttctaacctttataccctctatttagACTCGAAAAGGGATCCTGAAGAGCGGATTATTCCTCGCAGTGTAGATGCTGATGATTCTGATGTTGATATCAAAAGTGACGATGATAG
Basic information
species | Arabidopsis thaliana |
transcript | AT3G13200.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G13200.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA17G15050.3 (Glycine max), 3'ss of exon 1
gttagagaaattcatttatttatttatgatcgttatttgtgtcacattagatagt-ttgatcgtgtgttttctaacctttataccctctatttagACTCGAAAAGGGATCCTGAAGAGCGGATTATTCCTCGCAGTGTAGATGCTGATGATTCTGATGTTGATATCAAAAGTGACGATGATAG
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gtgaaaaaataagataaggaaagaaaccataattgttttc--tatattcagtattgttgattgataggtcctttatcttgaca-----------gGATCGAAGAGAGAAATGGAAGATCACATTGTTCCACGTAGTGTTGATGCAGATGATTCTGATGTTGAAGTCAAAAGTGATGATGACAG
upper sequence: AT3G13200.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA17G15050.2 (Glycine max), 3'ss of exon 2
------------------------gttagagaaattcatttatttatttatgatcgttatttgtgtcacattag------atagtttgatcgtgtgttttctaacctttat------accctctatttagAC----TCGAAAAGGGATCCTGAAGAGCGGATTATTCCTCGCAGTGTAGATGCTGATGATTCTGATGTTGATATCAAAAGTGACGATGATAG
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gtattctatctcctaactaaaatactttgcaatggccttccatctaaaagaggtgaaaaaataagataaggaaagaaaccataattgttttctatattcagtattgttgattgataggtcctttatcttgacagGATCGAAGAGAGAAATGGAAGATCACATTGTTCCACGTAGTGTTGATGCAGATGATTCTGATGTTGAAGTCAAAAGTGATGATGACAG
upper sequence: AT3G13200.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA05G04620.1 (Glycine max), 3'ss of exon 3
-------------------------------------gttagagaaattcatttatttattt----atgatcgttatttgtgtcacattagatagtttgatcgtgtgt-----------tttctaacctttataccctctatttagAC----TCGAAAAGGGATCCTGAAGAGCGGATTATTCCTCGCAGTGTAGATGCTGATGATTCTGATGTTGATATCAAAAGTGACGATGATAG
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gtattctatctataattagtatacatttactaaaatactttgaaatggccttctatctaaaagaggaggaagaaaaagaagataaggaaagaaaccataattgtattttatattcagtattgttgactgatgggtcctttatcttgacagGTTCCAAGAGAGACATTGAAGATCGCATTGTTGCTCGTAGTGTTGATGCAGATGATTCTGACGTTGAAGTCAAAAGTGATGATGACAG
upper sequence: AT3G13200.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv19s0015g00980.t01 (Vitis vinifera), 3'ss of exon 3
gttagagaaattcatttatttatttatgatcgttatttgtgtcacattagatagtttgatcgtgtgttttctaacctttataccctctatttagACTCGAAAAGGGATCCTGAAGAGCGGATTATTCCTCGCAGTGTAGATGCTGATGATTCTGATGTTGATATCAAAAGTGACGATGATAG
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gtaaatgccatctggtctcttgtgtatg-tgcttattaaactca---taaatatttacct----tgccaactgatcacatagccattta--tagGGGTAAAGAGGGATGCTGACGATCGAATCGTTCCGCGGAGTGTAGATGCTGATGATTCTGATATTGAAGTCAAAAGTGATGAGAG---Mapped 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|164031182|gb|ES079669.1|ES079669EST: GCAGAAGAGGAAGTCAGCTTTTACTGGAAG GCTCGAAAAGGGATCCTGAAGAGCGGATTATTCCTCGCAGTGTAGATGCTG
genomic: GCAGAAGAGGAAGTCAGCTTTTACTGGAAGgttagagaaa ... ctctatttagACTCGAAAAGGGATCCTGAAGAGCGGATTATTCCTCGCAGTGTAGATGCTG
EST:
gi|124880445|gb|EH959347.1|EH959347EST: ATGATAGAGATCGCAGAAGAGGAAGTCAGCTTTTACNGGAAG ACTCGAAAAGGG
genomic: ATGATAGAGATCGCAGAAGAGGAAGTCAGCTTTTACTGGAAGgttagagaaa ... ctctatttagACTCGAAAAGGG
EST:
gi|124715067|gb|EH806469.1|EH806469EST: ATGATAGAGATCGCAGAAGAGGAAGTCAGC-TTTACTGGAAG ACTCGAAAAGGGATCCTGAAGAGCGGATTATTCCTCGCAGTG
genomic: ATGATAGAGATCGCAGAAGAGGAAGTCAGCTTTTACTGGAAGgttagagaaa ... ctctatttagACTCGAAAAGGGATCCTGAAGAGCGGATTATTCCTCGCAGTG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgtcacattagatagtttgatcgtgtgttttctaacctttataccctctatttagACTCGAAAAGGGATCCTGAAGAGCGGATTATTCCTCGCAGTGTAGATGCTGATGATTCTGATGTTGATATCAAAAGTGACGATGATAG
ttctaac putative branch site (score: 1)
cctttataccctct CT-rich tract
attagata 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 |
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---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttagagaaattcatttatttatttatgatcgttatttgtgtcacattagatagtttgatcgtgtgttttctaacctttataccctctatttagACTCGAAAAGGGATCCTGAAGAGCGGATTATTCCTCGCAGTGTAGATGCTGATGATTCTGATGTTGATATCAAAAGTGACGATGATAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT