Sequence
atgc intronic sequence ATGC exonic sequenceGTAACTGTTGGAGCCTCGTTCTTGTCCCAAACTATAGCATTGCAAGACTCTACCACAGTGAAGTTTGAAATATGGGATACAGCAGGACAGGAGAGgtattaaacccttcatgcagatttgtattgcttattttattagataaacgctttgcaaacttactaggatttaacctgcattcactttatttttag
Basic information
| species | Arabidopsis thaliana |
| transcript | AT3G54840.2 |
| intron # | 4 |
| splice site | 5' |
| intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G54840.2 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: LOC_Os10g30520.1 (Oryza sativa), 5'ss of exon 4
GTAACTGTTGGAGCCTCGTTCTTGTCCCAAACTATAGCATTGCAAGACTCTACCACAGTGAAGTTTGAAATATGGGATACAGCAGGACAGGAGAGgtattaaacccttcatgcagatttgtattgcttattttattagataaacgctt-tgcaaacttactaggatttaa--cctgcattcactttatttttag--------------------------------------------------------------------------------------------
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GTGACTGTTGGTGCATCATTTTTGTCACAAACATTGGCGTTGGAGGATTCCACAACAGTAAAGTTTGAAATATGGGATACTGCTGGTCAGGAGAGgtgcataaatatta--gaagctttg-attaactattttcccaagtgcatccttgcattaactctgtactatggaatttctgtaccatcttttgcttcacatatgtcttcttcacccttgatttacattgtttgcaagcatatgtgttgctattcgttaccaaagaagtcacgagaactggttaattttcag
upper sequence: AT3G54840.2 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: LOC_Os03g05740.1 (Oryza sativa), 5'ss of exon 4
GTAACTGTTGGAGCCTCGTTCTTGTCCCAAACTATAGCATTGCAAGACTCTACCACAGTGAAGTTTGAAATATGGGATACAGCAGGACAGGAGAGgtattaaacccttcatgcagatttgtattgcttattttattagataa----acgct-ttgcaaacttactaggatttaacctgcattca--ctttatttttag---------------------------------------------------------------------------------------------
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GTAACTGTCGGTGCATCATTTTTATCACAAACATTGGCTTTGGAGGACTCAACAATAGTGAAATTTGAAATATGGGATACCGCTGGACAAGAGAGgtacacatacagcactatggttttagcttcttccaatcttgggataatggcatgctgttggtgcattagaagcattggttttgtgagaaagttctagtagtatgtgttactgatttttacaattgatccatcttacgtgccacacatgcatatggtttttctcaatcaagaactcattggtaccagccaattttag
upper sequence: AT3G54840.2 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GLYMA10G35230.3 (Glycine max), 5'ss of exon 4
GTAACTGTTGGAGCCTCGTTCTTGTCCCAAACTATAGCATTGCAAGACTCTACCACAGTGAAGTTTGAAATATGGGATACAGCAGGACAGGAGAGgtat---taaacccttcatgcagatt-tgtattgcttattttattagataaacgctttgcaa--------acttactaggatttaacctgcattcactttat---ttttag
|||||||||||||| || || ||||| ||||| ||||| ||||||||||||| ||||| |||||||||||||||||||| || || || ||||||| | | | | |||||| || || | |||| || | | | || ||| || | || || || | | |||| ||| ||
GTAACTGTTGGAGCTTCTTTTTTGTCGCAAACAATAGCTCTGCAAGACTCTACAACAGTCAAGTTTGAAATATGGGATACTGCTGGTCAAGAGAGgtgactgtcatttatctttccagattatgcataacctattgtacaaaccattcttatttcaacaacaaatgttttttgaaatgaaatttgtttgctaattatctgtttcag
upper sequence: AT3G54840.2 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GLYMA20G32320.1 (Glycine max), 5'ss of exon 4
GTAACTGTTGGAGCCTCGTTCTTGTCCCAAACTATAGCATTGCAAGACTCTACCACAGTGAAGTTTGAAATATGGGATACAGCAGGACAGGAGAGgta---ttaaacccttcatgcagatttgt-attgcttattttattagataaacgctttgcaa--------acttactaggatttaacctgc--attcactttat-ttttag
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GTAACTGTTGGAGCTTCTTTTTTGTCACAAACAATAGCTCTGCAAGACTCTACAACAGTCAAGTTTGAAATATGGGATACTGCTGGTCAAGAGAGgtgactctcatttatctttccagattaatcataatctattgtacaaaccattcttttttcaacaaaaaatgatttttgaaataaaatttgtttgctaattctctatttcag
upper sequence: AT3G54840.2 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: Vv13s0019g04680.t01 (Vitis vinifera), 5'ss of exon 4
GTAACTGTTGGAGCCTCGTTCTTGTCCCAAACTATAGCATTGCAAGACTCTACCACAGTGAAGTTTGAAATATGGGATACAGCAGGACAGGAGAGgtatta---aacccttcatgcagatttgtatt-gcttattttattagataaacgctttgcaaacttactaggatttaacctgcattcactttatttttag----------------------------------------------------------------------
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GTGACTGTAGGAGCTTCATTCTTGTCACAAACAATTGCCTTGCAAGATTCTACGACAGTTAAGTTTGAAATATGGGACACTGCTGGTCAAGAGAGgtatcattggccaacccattttttttcctgttcacctatctgactttctaaattcaatagaaataactcaacttatagtcttc-ttgagtctattgaaatggatctagagctctctctcttccatgaaaacccatttgagaaaattacagaggataacttcattcctcagMapped 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|19875441|gb|AU236272.1|AU236272EST: GACTCTACCACAGTGAAGTTTGAAATATGGGATACAGCAGGACAGGAGAG GTATTCTGCTCTTGCACCACTATACTACCGNGGAGCTGGAGTTGCTGTTAT
genomic: GACTCTACCACAGTGAAGTTTGAAATATGGGATACAGCAGGACAGGAGAGgtattaaacc ... ttatttttagGTATTCTGCTCTTGCACCACTATACTACCGTGGAGCTGGAGTTGCTGTTAT
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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GTAACTGTTGGAGCCTCGTTCTTGTCCCAAACTATAGCATTGCAAGACTCTACCACAGTGAAGTTTGAAATATGGGATACAGCAGGACAGGAGAGgtattaaacccttcatgcagatttgtattgcttattttattagataaacgctttgcaaacttactaggatttaacctgcattcactttatttttag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
