Sequence
atgc intronic sequence ATGC exonic sequencegttggcgtaaaagattacctctatttagttttattatttgtctgtccaatgcattcatacctgacttttggtttggcgatattttcagGGCTCTTGGATAGTTAAGCAAAGTGTGGGAAAGAAAGCATGCCTTATTGGTCAAGCCCTGGAGATCAACTACTTCAGGGGAAAGAACTATATTGAG
Basic information
species | Arabidopsis thaliana |
transcript | AT2G28320.1 |
intron # | 18 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT2G28320.1 (Arabidopsis thaliana), 3'ss of exon 18
lower sequence: LOC_Os10g33930.1 (Oryza sativa), 3'ss of exon 7
gttggcgtaaaagattacctctatttagttttatta---tttgtctgtccaatgcattcatacctgacttttggtttggcgatattttcagGGCTCTTGGATAGTTAAGCAAAGTGTGGGAAAGAAAGCATGCCTTATTGGTCAAGCCCTGGAGATCAACTACTTCAGGGGAAAGAACTATATTGAG
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gtacctattctgcactaccagccttcattcttgtcaagctttacttagtaaatgc--tgatggtttatcttcggtatatgtgccgcttcagGGGTCTTGGATAGTAAAGCAAAGTGTGGGAAAGAAAGCCTGTTTGGTTGGTCAAGCACTAGAGATCAATTATTTCCGTGGAAGCAATTATTTGGAG
upper sequence: AT2G28320.1 (Arabidopsis thaliana), 3'ss of exon 18
lower sequence: GLYMA12G29750.1 (Glycine max), 3'ss of exon 18
------------gttggcgtaaaagattacctctatttagt-tttattatttgtctgtccaatgcattcatacctgacttttggtttggcgatat--tttcagGGCTCTTGGATAGTTAAGCAAAGTGTGGGAAAGAAAGCATGCCTTATTGGTCAAGCCCTGGAGATCAACTACTTCAGGGGAAAGAACTATATTGAG
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actatatgtatagtccatgttaagaaggcaaaatgtctattgttcatcatttgtttagcacgt-tgtttacaaattacaa--gacttgacattcctgtttcagGGTTCATGGATAGTAAAGCAGAGTGTGGGAAAGAAGGCATGCCTAGTTGGTCAAGCACTGGAAATCAATTATTTCCAGGGAAGTAACTATTTGGAG
upper sequence: AT2G28320.1 (Arabidopsis thaliana), 3'ss of exon 18
lower sequence: GLYMA13G40010.1 (Glycine max), 3'ss of exon 18
------------gttggcgtaaaagattacctctatttagt-tttattatttgtctgtccaatgcattcatacctgacttttggtttggcgatat--tttcagGGCTCTTGGATAGTTAAGCAAAGTGTGGGAAAGAAAGCATGCCTTATTGGTCAAGCCCTGGAGATCAACTACTTCAGGGGAAAGAACTATATTGAG
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aatatatgtatagtccatgttaagaaggcaaaatgtctattattcgccatttgtttagcccgt-catttacaaattacaa--gactcgacattcctgtttcagGGTTCATGGATAGTAAAGCAGAGTGTGGGAAAGAAGGCATGCCTAGTTGGTCAAGCACTGGAAATCAATTATTTCCAGGGAAGTAACTATTTGGAG
upper sequence: AT2G28320.1 (Arabidopsis thaliana), 3'ss of exon 18
lower sequence: Vv06s0004g02720.t01 (Vitis vinifera), 3'ss of exon 18
----------gttggcgtaaaagattacctctatttagttttatt-atttgtctgtccaatgcattcatacctgacttttggtttggcgata--ttttcagGGCTCTTGGATAGTTAAGCAAAGTGTGGGAAAGAAAGCATGCCTTATTGGTCAAGCCCTGGAGATCAACTACTTCAGGGGAAAGAACTATATTGAG
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aagacttattatttctttaaacaatattttgcttttaggtctttagaattgact-tcaaatttggcgtaatataatgaggactgtaagcttaatttctcagGGGTCCTGGATAGTTAAGCAGAGCGTTGGAAAGAAAGCATGCCTAGTGGGTCAAGCGCTTGAAATTAATTATTTCCATGGGAAGAACTACTTGGAGMapped 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|164010439|gb|ES058505.1|ES058505EST: ATGACGCATATAGGAATTCAAGGTTCAAGCTCATTCCCTACATATCCAAG GGCTCTTGGATAGTTAAGCAAAGTGTGGGAAAGAAAGCA
genomic: ATGACGCATATAGGAATTCAAGGTTCAAGCTCATTCCCTACATATCCAAGgttggcgtaa ... atattttcagGGCTCTTGGATAGTTAAGCAAAGTGTGGGAAAGAAAGCA
EST:
gi|86059973|gb|DR355730.1|DR355730EST: ATGACGCATATAGGAATTCAAGGTTCAAGCTCATTCCCTACATATCCAAG GGCTCTTGGATAGTTAAGCAAAGTGTGGGAAAGAAAGCATGCCTTATTGGT
genomic: ATGACGCATATAGGAATTCAAGGTTCAAGCTCATTCCCTACATATCCAAGgttggcgtaa ... atattttcagGGCTCTTGGATAGTTAAGCAAAGTGTGGGAAAGAAAGCATGCCTTATTGGT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttatttgtctgtccaatgcattcatacctgacttttggtttggcgatattttcagGGCTCTTGGATAGTTAAGCAAAGTGTGGGAAAGAAAGCATGCCTTATTGGTCAAGCCCTGGAGATCAACTACTTCAGGGGAAAGAACTATATTGAG
acctgac putative branch site (score: 3)
tattttc putative PPT
atattttca 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttggcgtaaaagattacctctatttagttttattatttgtctgtccaatgcattcatacctgacttttggtttggcgatattttcagGGCTCTTGGATAGTTAAGCAAAGTGTGGGAAAGAAAGCATGCCTTATTGGTCAAGCCCTGGAGATCAACTACTTCAGGGGAAAGAACTATATTGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
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- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC