Sequence
atgc intronic sequence ATGC exonic sequenceCTGTGCCGGCACTGGTGGTTCGATGCTTGTCATTGGTTCTGCTGCTGGTGTAGCCTTCATGGGGATGGAGAAAGTCGATTTCTTTTGGTATTTCCGAAAGgtaagatacattcttccggcttgtctaacgatcaacaacacaacattgcattaaccagactgaaactcaatactcttgtggctctgcgcaagaaactcagttttttttttttttctccatgcag
Basic information
| species | Arabidopsis thaliana |
| transcript | AT3G19490.1 |
| intron # | 9 |
| splice site | 5' |
| intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G19490.1 (Arabidopsis thaliana), 5'ss of exon 9
lower sequence: LOC_Os09g02214.1 (Oryza sativa), 5'ss of exon 9
CTGTGCCGGCACTGGTGGTTCGATGCTTGTCATTGGTTCTGCTGCTGGTGTAGCCTTCATGGGGATGGAGAAAGTCGATTTCTTTTGGTATTTCCGAAAGgtaagatacattcttccggcttgtctaacgatcaacaacacaacattgcattaaccagactgaaactcaatactcttgtggctctgcgcaagaaactcagttttttttttttttctccatgcag
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CTGTGCTGGTACGGGTGGTTCTATGCTTATCATTGGCTCTGCAGCAGGTGTGGCTTTCATGGGAATGGAAAAGGTGGATTTCTTTTGGTATTTCCGCAAGgtaaattgaacttttac------tctaataataagtgg---agctgtggaacaacttacacaatacagaat---cgtatgttacagaacaagaaacttattcggtgtggttg------------
upper sequence: AT3G19490.1 (Arabidopsis thaliana), 5'ss of exon 9
lower sequence: GRMZM2G053927_T02 (Zea mays), 5'ss of exon 9
CTGTGCCGGCACTGGTGGTTCGATGCTTGTCATTGGTTCTGCTGCTGGTGTAGCCTTCATGGGGATGGAGAAAGTCGATTTCTTTTGGTATTTCCGAAAGgtaagatacattcttccggcttgtctaacgatcaacaacacaacat--tgcatta-accagactgaaactcaatactcttgtggctctgcgcaagaaactcagttttttttttttttctccatgcag
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CTGTGCGGGTACTGGTGGTTCAATGCTTATCATTGGCTCCGCAGCAGGAGTTGCTTTTATGGGAGTGGAGAAGGTGGATTTCTTTTGGTATTTTCGCAAGgtaaacggc--tcctttgtcaaatatgaagagaaactatctaaaaagatatattacagcgatatgaagttctttattatggtagccatgtg----aaatttaactg---------------------
upper sequence: AT3G19490.1 (Arabidopsis thaliana), 5'ss of exon 9
lower sequence: GLYMA10G40920.1 (Glycine max), 5'ss of exon 9
CTGTGCCGGCACTGGTGGTTCGATGCTTGTCATTGGTTCTGCTGCTGGTGTAGCCTTCATGGGGATGGAGAAAGTCGATTTCTTTTGGTATTTCCGAAAGgtaagatacattcttccggcttgtctaacgatcaacaacacaacattgcattaaccagactgaaactcaatactcttgtggctctgcgcaagaaactcagttttttttttttttctccatgcag
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TTGTGCTGGTACTGGTGGATCCATGTTAATTATTGGCTCAGCTGCTGGAGTTGCGTTCATGGGGATGGAAAAGGTGGACTTCTTTTGGTACTTACGAAAGgtatttcctactctac------acataa-gacttatatgatgtttgtaagtaatttatgacagaagtcatttgtctc----ctttttgcag---------------------------------
upper sequence: AT3G19490.1 (Arabidopsis thaliana), 5'ss of exon 9
lower sequence: Vv03s0180g00120.t01 (Vitis vinifera), 5'ss of exon 9
CTGTGCCGGCACTGGTGGTTCGATGCTTGTCATTGGTTCTGCTGCTGGTGTAGCCTTCATGGGGATGGAGAAAGTCGATTTCTTTTGGTATTTCCGAAAGgtaagatacattcttccggcttgtctaacgatcaacaacacaacattgcattaaccagactgaaactcaatactcttgtggctctgcgcaagaaactcagttttttttttttttctccatgcag
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TTGTGCTGGTACGGGTGGATCCATGCTAGTTATTGGCTCTGCTGCTGGAGTTGCATTTATGGGGATGGAAAAAGTGGACTTCTTTTGGTACTTAAGGAAGgtatg------tgctgcggtgctgctatttgatgataattcggtttta----------attaaaattggaaactttc----cttagtgaaagaaatt--gtttccttttatgcag---------
upper sequence: AT3G19490.1 (Arabidopsis thaliana), 5'ss of exon 9
lower sequence: PP1S298_28V6.1 (Physcomitrella patens), 5'ss of exon 9
CTGTGCCGGCACTGGTGGTTCGATGCTTGTCATTGGTTCTGCTGCTGGTGTAGCCTTCATGGGGATGGAGAAAGTCGATTTCTTTTGGTATTTCCGAAAGgtaaga---tacattcttccggcttgtctaacgatcaaca--acacaacattgcattaacc-agactgaaactcaatactcttgtggctctgcgcaagaaactcagtt-----ttttttttttttctccatgcag------------------------------------
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TTGTGCTGGAACTGGTGGTTCTATTCTTGTCATTGGCTCTGCTGCGGGTGTGGCCTACATGGGCATGGAAAAAGCTGACTTCTTATGGTATCTAAAAAAGgtatgaatctgcatttatcttgctttttcatttatctgtattgtataaaaaatccttgttcgaggtcgatgatttgaaaacaggtcacaacacagtagagattttgaccgtgattttgttttattgctcttgcatgcttggtatcaaatagtgattctttttatatggcagMapped 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|86084545|gb|DR380304.1|DR380304EST: TAGCCTTCATGGGGATGGAGAAAGTCGATTTCTTTTGGTATTTCCGAAAG GTTAGTGGTTTTGCTTTTGCTGGCTATGCTGCTGGTATCGCAGCTTATCTG
genomic: TAGCCTTCATGGGGATGGAGAAAGTCGATTTCTTTTGGTATTTCCGAAAGgtaagataca ... ctccatgcagGTTAGTGGTTTTGCTTTTGCTGGCTATGCTGCTGGTATCGCAGCTTATCTG
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
CTGTGCCGGCACTGGTGGTTCGATGCTTGTCATTGGTTCTGCTGCTGGTGTAGCCTTCATGGGGATGGAGAAAGTCGATTTCTTTTGGTATTTCCGAAAGgtaagatacattcttccggcttgtctaacgatcaacaacacaacattgcattaaccagactgaaactcaatactcttgtggctctgcgcaagaaactcagttttttttttttttctccatgcag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
