Sequence
atgc intronic sequence ATGC exonic sequenceTGCAACTTTGATTTTCGAGGTGGAATTGGTTGCTTGTAGACCGAGGAAAGGTGCTAGTGTTGGAAGTGTTTCTGAAGAGAGAGCCAGGCTAGAgtaagtattataaataccatttggacctaacttttgacttgttatcatgtgtgtaaatatgaaaacttttttgcttcatggttgcag
Basic information
species | Arabidopsis thaliana |
transcript | AT3G55520.1 |
intron # | 5 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G55520.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: LOC_Os05g38370.1 (Oryza sativa), 5'ss of exon 5
TGCAACTTTGATTTTCGAGGTGGAATTGGTTGCTTGTAGACCGAGGAAAGGTGCTAGTGTTGGAAGTGTTTCTGAAGAGAGAGCCAGGCTAGAgtaag-tattat-aaataccatttggacctaact----tttga-----cttgttatcatgtgtgtaaatatgaaaacttttttgcttcatggttgcag-----
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TGCAACACTCATTTTTGAGGTGGAGTTAGTGGCTTGTAGGCCTAGGAAAGGTTCAAGCCTGGGCAGTGTTTCTGATGAGAAAGCCAGGCTAGAgtaagatgttttcaaatgtcttcttgttatgattacaatatgaagttcccagttattatgt---taaatagcacagctgtacaagatacagaaaactggttaa
upper sequence: AT3G55520.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: LOC_Os05g38370.3 (Oryza sativa), 5'ss of exon 4
-------TGCAACTTTGATTTTCGAGGTGGAATTGGTTGCTTGTAGACCGAGGAAAGGTGCTAGTGTTGGAAGTGTTTCTGAAGAGAGAGCCAGGCTAGAgtaag-tattat-aaataccatttggacctaact----tttga-----cttgttatcatgtgtgtaaatatgaaaacttttttgcttcatggttgcag-----
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TTTGCAGTGCAACACTCATTTTTGAGGTGGAGTTAGTGGCTTGTAGGCCTAGGAAAGGTTCAAGCCTGGGCAGTGTTTCTGATGAGAAAGCCAGGCTAGAgtaagatgttttcaaatgtcttcttgttatgattacaatatgaagttcccagttattatgt---taaatagcacagctgtacaagatacagaaaactggttaa
upper sequence: AT3G55520.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: LOC_Os01g62610.1 (Oryza sativa), 5'ss of exon 7
TGCAACTTTGATTTTCGAGGTGGAATTGGTTGCTTGTAGACCGAGGAAAGGTGCTAGTGTTGGAAGTGTTTCTGAAGAGAGAGCCAGGCTAGAgtaagtattataaataccattt--ggacctaact-tttgacttgttatcatgtgtgtaaatatgaaaactttttt------gcttcatggttgcag----
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TGCAACTCTCACTTTTGAGGTTGAGTTAATCGCATGCAGGCCGAGGAAAGGTTCTAGTGTGGAAAGTGTATCTGAAGAGAAAGCTAGGCTTGAgtaagatatctgaacaatgttttcgtgcttcacaatttaagttcaagtaaagcattctattgacagcactacacgtgcaagactctgagtttgtgatgcaMapped 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|86027815|gb|DR323568.1|DR323568EST: AGGAAAGGTGCTAGTGTTGGAAGTGTTTCTGAAGAGAGAGC-ACGCTAGA AGATCTGAAGAA-CAGAGAGAGATTGCTGCAGCTGCGACAGAGGATGATAA
genomic: AGGAAAGGTGCTAGTGTTGGAAGTGTTTCTGAAGAGAGAGCCAGGCTAGAgtaagtatta ... atggttgcagAGATCTGAAGAAGCAGAGAGAGATTGCTGCAGCTGCGAAAGAGGATGATAA
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
TGCAACTTTGATTTTCGAGGTGGAATTGGTTGCTTGTAGACCGAGGAAAGGTGCTAGTGTTGGAAGTGTTTCTGAAGAGAGAGCCAGGCTAGAgtaagtattataaataccatttggacctaacttttgacttgttatcatgtgtgtaaatatgaaaacttttttgcttcatggttgcag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA