Sequence
atgc intronic sequence ATGC exonic sequenceTCTTCCTCTTATAGTAGCCATCGATTTGCAGCCTATGGCTCCAATTGAAGGTGTCATCCAGGTTCAAGGGGACATAACTAATGCTCGGACTGCTGAAGTGgtaaaatttctcgactcctatctcataaatttttctacatctctttcttcctctttaattatgcttcaagtttgtgtttgtttccatggcttaccttttccggtgttttttttcaag
Basic information
species | Arabidopsis thaliana |
transcript | AT5G01230.1 |
intron # | 6 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G01230.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: LOC_Os06g49140.1 (Oryza sativa), 5'ss of exon 5
TCTTCCTCTTATAGTAGCCATCGATTTGCAGCCTATGGCTCCAATTGAAGGTGTCATCCAGGTTCAAGGGGACATAACTAATGCTCGGACTGCTGAAGTGgtaaaatttctcgactcctatctcataaatttttctacatctctttcttcctct--ttaattatgcttcaagtt-tgtgtttgtttccatggcttaccttttccggtgttttttttcaag
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CCTTCCTCTTATTGTTGCCATTGATTTGCAACCAATGGCTCCGATAGAAGGCGTTATACAAGTTCAAGGGGACATCACTAATGCTCGAACAGCAGAAGTGgta-----------cttttctcatatggatttggcttgctgtattttctcccatggtttgtcttgctgcaactgatataattttgttactag----------------------------
upper sequence: AT5G01230.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: GLYMA13G31380.1 (Glycine max), 5'ss of exon 6
TCTTCCTCTTATAGTAGCCATCGATTTGCAGCCTATGGCTCCAATTGAAGGTGTCATCCAGGTTCAAGGGGACATAACTAATGCTCGGACTGCTGAAGTGgtaaaatttctcgactcctatctcataaatttttctacatctctttcttcctctttaattatgcttcaagtttgtgtttgtttccatggcttaccttttccggtgttttttttcaag
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TCTTCCTCTTATTGTAGCTATTGATTTGCAACCAATGGCTCCAATTGAAGGTGTCATCCAGGTGCAGGGTGATATAACTAATGCTCGGACAGCTGAAGTGgtatatattata------tatagcataa------tcaccttagttttttcatagattattttatttggaagatgtgttga-----acaagctgcatgtctaggtagaaatagaaaat
upper sequence: AT5G01230.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: GLYMA13G31350.1 (Glycine max), 5'ss of exon 1
TCTTCCTCTTATAGTAGCCATCGATTTGCAGCCTATGGCTCCAATTGAAGGTGTCATCCAGGTTCAAGGGGACATAACTAATGCTCGGACTGCTGAAGTGgtaaaatttctcgactcctatctcataaatttttctacatctctttcttcctctttaattatgcttcaagtttgtgtttgtttccatggcttaccttttccggtgttttttttcaag
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TCTTCCTCTTATTGTAGCTATTGATTTGCAACCAATGGCTCCAATTGAAGGTGTCATCCAGGTGCAGGGTGATATAACTAATGCTCGGACAGCTGAAGTGgtatatattata------tatagcataa------ttaccttagttttttcatagattattttatttggaaaatgtgttga-----acaagctgcatgtctaggtagaaatagaaaat
upper sequence: AT5G01230.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: GLYMA15G07970.2 (Glycine max), 5'ss of exon 6
TCTTCCTCTTATAGTAGCCATCGATTTGCAGCCTATGGCTCCAATTGAAGGTGTCATCCAGGTTCAAGGGGACATAACTAATGCTCGGACTGCTGAAGTGgtaaaatttctcgactcctatctcataaatttttctacatctctttcttc------ctctttaattatgcttcaagtttgtgtttgtttccatggcttaccttttccggtgttttttttcaag
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TCTTCCTCTTATTGTAGCTATTGATTTGCAACCAATGGCTCCAATTGAAGGTGTCATCCAGGTGCAGGGTGATATAACTAACGCTCGGACAGCTGAAGTGgtatatacagcagaat--taccttcagttttttcatggattattttatttggaagatgtgttgagtaagctgcatgtcttggtagaaatagaaaatacatct---------------------
upper sequence: AT5G01230.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: Vv08s0007g01960.t01 (Vitis vinifera), 5'ss of exon 5
TCTTCCTCTTATAGTAGCCATCGATTTGCAGCCTATGGCTCCAATTGAAGGTGTCATCCAGGTTCAAGGGGACATAACTAATGCTCGGACTGCTGAAGTGgtaa---aatttctcgactcctatctcataaatttttctacatctctttcttcctctttaattatgcttcaagtttgtgtttgtttccatggcttaccttttccggtgttttttttcaag
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TCTTCCTCTTATTGTGGCGATTGATTTGCAGCCCATGGCTCCAATTGAAGGGGTGATTCAAGTCCAGGGTGATATAACAAATGCTCGTACAGCTGAACTGgttagtcaatttctc--cccccaagtcattg-ttatccattatttgtttgacagtgtaaagatataaatggcgcttctttaaaattatgtaactgatttaata-----------------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|164218939|gb|ES095525.1|ES095525EST: ACATAACTAATGCTCGGACTGCTGAAGTG GTCATTAGACACTTTGACGGCTGCAAAGCGGACCTGGTTGTCTGTGATGGT
genomic: ACATAACTAATGCTCGGACTGCTGAAGTGgtaaaatttc ... ttttttcaagGTCATTAGACACTTTGACGGCTGCAAAGCGGACCTGGTTGTCTGTGATGGT
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
TCTTCCTCTTATAGTAGCCATCGATTTGCAGCCTATGGCTCCAATTGAAGGTGTCATCCAGGTTCAAGGGGACATAACTAATGCTCGGACTGCTGAAGTGgtaaaatttctcgactcctatctcataaatttttctacatctctttcttcctctttaattatgcttcaagtttgtgtttgtttccatggcttaccttttccggtgttttttttcaag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG