Sequence
atgc intronic sequence ATGC exonic sequenceGGAGTTGACTCTTGACGATTTTCAGAAAGTTAGCGATGCGGTTCCATTTCTAGCAGATCTTAAACCCAGTGGGAAGTATGTTATGGAGGATATACATAAGgtaaggctttggcgaaatcgttttgcttattacttatctgtttttttattggtcagtttgtaagttttgttgtttaatctacag
Basic information
species | Arabidopsis thaliana |
transcript | AT3G23940.2 |
intron # | 6 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G23940.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: GLYMA13G27810.1 (Glycine max), 5'ss of exon 6
GGAGTTGACTCTTGACGATTTTCAGAAAGTTAGCGATGCGGTTCCATTTCTAGCAGATCTTAAACCCAGTGGGAAGTATGTTATGGAGGATATACATAAGgtaaggctttggcgaaatcgttttgcttattacttatctgtttttttattggtcagtttgtaagttttgttgttta--atctacag---------------------------------------------------
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TGATTTGACTCTTGATGATTTTCAGAAGGTTAGCGATGAGGTTCCTTTTATTGCAGATCTTAAGCCTAGTGGGAAATATGTCATGGAAGATGTTCACAAGgtatgcatttaatgcttttgtta-actaattgaacactgcttcacttatcaataactccaaatcatataatgtttatactcttctgtcattattattcttgcttaaatttcctattcttttcccctttctttggtag
upper sequence: AT3G23940.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: Vv05s0051g00830.t01 (Vitis vinifera), 5'ss of exon 6
GGAGTTGACTCTTGACGATTTTCAGAAAGTTAGCGATGCGGTTCCATTTCTAGCAGATCTTAAACCCAGTGGGAAGTATGTTATGGAGGATATACATAAGgt---aaggctttggcgaaatcgttttgcttattacttatctgtttttttattggtcagtttgtaagttttgttgttt-aatctacag----------------
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GCAGTTAACTCTTGATGATTTTCAGAAAGTAAGTGATGAGGTTCCATTCCTTGCTGATCTTAAGCCCAGTGGCAAATACGTCATGGAGGACATACACAAGgtttcaatgatttctt----ttgtttccctttttgtttctctttgttttccttctttcttaaattaaatatgttgtcccagcctgtttctgagttctatataac
upper sequence: AT3G23940.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: EFJ18571 (Selaginella moellendorffii), 5'ss of exon 7
GGAGTTGACTCTTGACGATTTTCAGAAAGTTAGCGATGCGGTTCCATTTCTAGCAGATCTTAAACCCAGTGGGAAGTATGTTATGGAGGATATACATAAGgtaaggctttggcgaaatcgttttg-cttattacttatctgtttttttattggtcagtttgtaagttttgttgtttaatctacag
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GCCACTGACCTTGGACGACTTTCAGAAAGTTAGTGACAAAGTTCCGTTTATCGCTGATCTTAAACCCAGCGGGAAGTATGTAATGGAGGACTTGCATAAGgtctgtaattcccagttttgtggtgactcacaatatat-tgcgatgtcacag---------------------------------
upper sequence: AT3G23940.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: EFJ18570 (Selaginella moellendorffii), 5'ss of exon 6
GGAGTTGACTCTTGACGATTTTCAGAAAGTTAGCGATGCGGTTCCATTTCTAGCAGATCTTAAACCCAGTGGGAAGTATGTTATGGAGGATATACATAAGgtaaggctttggcgaaatcgttttg-cttattacttatctgtttttttattggtcagtttgtaagttttgttgtttaatctacag
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ACCACTGACCTTGGACGACTTTCAGAAAGTTAGTGACAAAGTTCCGTTTATCGCTGATCTTAAACCCAGCGGGAAGTATGTAATGGAGGACTTGCATAAGgtctgtaattcccagttttgtggtgactcacaatatat-tgcgatgtcacag---------------------------------
upper sequence: AT3G23940.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: EFJ36479 (Selaginella moellendorffii), 5'ss of exon 6
GGAGTTGACTCTTGACGATTTTCAGAAAGTTAGCGATGCGGTTCCATTTCTAGCAGATCTTAAACCCAGTGGGAAGTATGTTATGGAGGATATACATAAGgtaaggctttggcgaaatcgttttg-cttattacttatctgtttttttattggtcagtttgtaagttttgttgtttaatctacag
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ACCACTGACCTTGGACGACTTTCAGAAAGTTAGTGACGAAGTTCCGTTTATCGCTGATCTTAAACCCAGCGGGAAGTATGTAATGGAGGACTTGCATAAGgtctgtaattcccagttttgtggtgactcacaatatat-tgcgatgtcacag---------------------------------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|124967287|gb|EL041331.1|EL041331EST: TAGCAGATCTTAAACCCAGTGGGAAGTATGTTATGGAGGATATACATAAG ATAGGTGGTAC
genomic: TAGCAGATCTTAAACCCAGTGGGAAGTATGTTATGGAGGATATACATAAGgtaaggcttt ... taatctacagATAGGTGGTAC
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
GGAGTTGACTCTTGACGATTTTCAGAAAGTTAGCGATGCGGTTCCATTTCTAGCAGATCTTAAACCCAGTGGGAAGTATGTTATGGAGGATATACATAAGgtaaggctttggcgaaatcgttttgcttattacttatctgtttttttattggtcagtttgtaagttttgttgtttaatctacag
- - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT