Sequence
atgc intronic sequence ATGC exonic sequencegtaagaacaaatgttttagaaaaatggaaactttttttgttatgtttcatttcgattggtctgaaaacgtattgtttgctttgtcctatgtttctagATTTTTGCATCTGATAGTTTCTTGGAGCTCACGGAATATAGCCGTGAAGAAATTCTTGGAAGAAATTGCAG
Basic information
species | Arabidopsis thaliana |
transcript | AT3G45780.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G45780.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA12G07890.2 (Glycine max), 3'ss of exon 7
------------------gtaagaacaaatgttttag------aaaaatggaaactttttttgttatgtt--tcatttcgattggtctgaaaacgtattgtttgctttgtcctatg--tttctagATTTTTGCATCTGATAGTTTCTTGGAGCTCACGGAATATAGCCGTGAAGAAATTCTTGGAAGAAATTGCAG
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gtaagatgatcctttttgataccatttaatactccaatgcaacaaaaatggtgaatttctctatgggattaattcgtgtactagagatgagcttaagacgattacgtttttatttggttttccagATTTTTGCATCTGATAGCTTCCTGGAGCTTACAGAGTATAGTCGTGAAGAAATCTTGGGAAGAAATTGCAG
upper sequence: AT3G45780.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA15G04850.1 (Glycine max), 3'ss of exon 5
-----------------gtaagaacaaatgttttagaaaaatgg------aaactttttttgttatgtttcatttcgattggtctgaaaacgta---ttgtttgctttgtcct--------atgtttctagATTTTTGCATCTGATAGTTTCTTGGAGCTCACGGAATATAGCCGTGAAGAAATTCTTGGAAGAAATTGCAG
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gtaagactctctgaatcatttgtaccgcagtactgaaaaagtgtttctctaattctgttctgtgttggattcttgtactggaggtgaacatgtaacactgtaaagtttgtacttgctttttactttttcagATCTTTGCATCGGATAGCTTCTTAGAGCTTACAGAATATAGCCGTGAAGAAATCTTGGGAAGGAACTGCAG
upper sequence: AT3G45780.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA13G40550.1 (Glycine max), 3'ss of exon 5
----------gtaagaacaaatgttttagaaaaatggaaactttttttgttatgtttcatttcgattggtctgaaaacgtattgtttgctttgtcctatgtttctagATTTTTGCATCTGATAGTTTCTTGGAGCTCACGGAATATAGCCGTGAAGAAATTCTTGGAAGAAATTGCAG
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gtaaagattctctgaatcatttgtactactgtacttaaaaattgtttccctaggaggtgaacatgtaacactgtaaactttgtacttggtttttact---ttttcagATCTTTGCATCGGATAGCTTCTTAGAGCTTACAGAATATAGTCGTGAAGAAATCTTGGGAAGGAATTGCAG
upper sequence: AT3G45780.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: Vv06s0004g03700.t01 (Vitis vinifera), 3'ss of exon 6
gtaagaacaaatgttttagaaaaatggaaactt--------tttttgttatgtttcatttcgattg-----gtctgaaaacgtat------tgtttgctttgt-----------cctatgtttctagATTTTTGCATCTGATAGTTTCTTGGAGCTCACGGAATATAGCCGTGAAGAAATTCTTGGAAGAAATTGCAG
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gtgagaataa-tacttcaaattattggttactgcaatcatgttctttttaaattatgatttgagcatgcacataagaagaaatatgggatttgtttgtttgatagttctaactttttgaattttcagATATTCGCATCTGATAGCTTCTTGGAACTAACAGAATACAGTCGTGAAGAAATTTTGGGAAGAAATTGCAGMapped 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|124812262|gb|EH897128.1|EH897128EST: TCGAGAAGAATTTCGTCATCACTGATCCTAGGCTTCCCGATAATCCCATT ATTTTTGCATCTGATA
genomic: TCGAGAAGAATTTCGTCATCACTGATCCTAGGCTTCCCGATAATCCCATTgtaagaacaa ... atgtttctagATTTTTGCATCTGATA
EST:
gi|86087858|gb|DR383617.1|DR383617EST: TCGAGAAGAATTTCGTCATCACTGATCCTAGGCTTCCCGATAATCCCATT ATTTTTGCATCTGATAGTTTCTTGGAGCTCACGGAATATAGCCGTGAAGAA
genomic: TCGAGAAGAATTTCGTCATCACTGATCCTAGGCTTCCCGATAATCCCATTgtaagaacaa ... atgtttctagATTTTTGCATCTGATAGTTTCTTGGAGCTCACGGAATATAGCCGTGAAGAA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgtttcatttcgattggtctgaaaacgtattgtttgctttgtcctatgtttctagATTTTTGCATCTGATAGTTTCTTGGAGCTCACGGAATATAGCCGTGAAGAAATTCTTGGAAGAAATTGCAG
tgtttct CT-rich tract
tattgttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagaacaaatgttttagaaaaatggaaactttttttgttatgtttcatttcgattggtctgaaaacgtattgtttgctttgtcctatgtttctagATTTTTGCATCTGATAGTTTCTTGGAGCTCACGGAATATAGCCGTGAAGAAATTCTTGGAAGAAATTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA