Sequence
atgc intronic sequence ATGC exonic sequence...atttcccttggatatgatttgcataattatttaggatctcttactttaacgatgtaggaataattgtgagttcattctgatttattaaatttactcatagGTCCTTTGGGAAGCCGAGCTGCCAAGGCAATTGGATTCATTGAGAAGATGATAGAATACTCTTATGTTAATGCACCGTTGCAGAAAGAACTGTTGGCAG
Basic information
species | Oryza sativa |
transcript | LOC_Os08g23810.2 |
intron # | 11 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os08g23810.2 (Oryza sativa), 3'ss of exon 11
lower sequence: GRMZM2G070422_T03 (Zea mays), 3'ss of exon 10
----atttcccttg-gatatgatttgcataat-----tatttaggatctcttactttaacgatgtaggaataat-tgtgagttcattctgatttattaaatttactcatagGTCCTTTGGGAAGCCGAGCTGCCAAGGCAATTGGATTCATTGAGAAGATGATAGAATACTCTTATGTTAATGCACCGTTGCAGAAAGAACTGTTGGCAG
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gtacttttatcacgtaatactgttgaagtaaaaggaatattagcagtatattttttt--tggtgagctattcctctatgccttgacaattaacctacacctgtacctatagGCCCTCTTGGGAGCCGAGCTGCTAAGGCAATTGGATTTATTGAGAAGATGATAGAGTACTCATATGTTAATGCACCATTGCAGAAGGAGCTGTTGGCTG
upper sequence: LOC_Os08g23810.2 (Oryza sativa), 3'ss of exon 11
lower sequence: GRMZM2G125052_T01 (Zea mays), 3'ss of exon 9
--atttcccttggatatgatttgcataattatttaggatctct-tactttaacgatgtaggaa--taattgtgagttcattctgattta--ttaaatttactcat--agGTCCTTTGGGAAGCCGAGCTGCCAAGGCAATTGGATTCATTGAGAAGATGATAGAATACTCTTATGTTAATGCACCGTTGCAGAAAGAACTGTTGGCAG
| || | || | | || || || || || | | || | | | | | || | | | | || | ||| ||| | || || ||| ||| | || ||||||||||| |||||||||||||| || |||||||||||| | ||||| |||||||||||||| |||||||| ||||||||||| |
gtagttttgtcaagtaatactgatg-aagtaaaaagaatatcagcagtataccttttttgttagctattcttttatgctttgacaattaacttacacttgtatatgtagGCCCTCTTGGGAGCCGAGCTGCTAAGGCAATTGGATTTATCGAGAAGATGATATAGTACTCATATGTTAATGCACCATTGCAGAAGGAACTGTTGGCTG
upper sequence: LOC_Os08g23810.2 (Oryza sativa), 3'ss of exon 11
lower sequence: EFJ25882 (Selaginella moellendorffii), 3'ss of exon 9
atttcccttggatatgatttgcataattatttaggatctcttactttaacgatgtaggaataattgtgagttcattctgatttattaaatttactcatagGTCCTTTGGGAAGCCGAGCTGCCAAGGCAATTGGATTCATTGAGAAGATGATAGAATACTCTTATGTTAATGCACCGTTGCAGAAAGAACTGTTGGCAG
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---------------------------------------------gtaaaatcttacaaatctatcaaagctgtggctcatgcatgacatgctttttcagGTCCCTTGAAAAGCAGAGCTGCCAAGGCAATCGGATTCATTGAGAAGATGATCGATTACTCCAAGGCAAATTCTCCCCTGCAAAGAGATCTCGAAGCTG
upper sequence: LOC_Os08g23810.2 (Oryza sativa), 3'ss of exon 11
lower sequence: EFJ10940 (Selaginella moellendorffii), 3'ss of exon 9
atttcccttggatatgatttgcataattatttaggatctcttactttaacgatgtaggaataattgtgagttcattctgatttattaaatttactcatagGTCCTTTGGGAAGCCGAGCTGCCAAGGCAATTGGATTCATTGAGAAGATGATAGAATACTCTTATGTTAATGCACCGTTGCAGAAAGAACTGTTGGCAG
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---------------------------------------------gtaaaatcttacaaatctattaaagctgtggctcatgcatgacatgc-ttttcagGTCCCTTGAAAAGCAGAGCTGCCAAGGCAATCGGATTCATTGAGAAGATGATCGATTACTCCAAGGCAAACTCTCCCCTGCAAAGAGATCTCGAAGCTGMapped 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|88672973|gb|CI727088.1|CI727088EST: TTTTGAAGCTGGAAGGAAAGGGAAAATCAGAGTTAACACCATATCTGCAG GTCCTTTGGGAAGCCGAGCTGCCAAGGCAATTGGATTCATTGAGAAGATGA
genomic: TTTTGAAGCTGGAAGGAAAGGGAAAATCAGAGTTAACACCATATCTGCAGgtattttctt ... ttactcatagGTCCTTTGGGAAGCCGAGCTGCCAAGGCAATTGGATTCATTGAGAAGATGA
EST:
gi|29613729|gb|CB618742.1|CB618742EST: TTTTGAAGCTGGAAGGAAAGGGAAAATCAGAGTTAACACCATATCTGCAG GTCCTTTGGGAAGCCGAGCTGCCAAGGCAATTGGATTCATTGAGAAGATGA
genomic: TTTTGAAGCTGGAAGGAAAGGGAAAATCAGAGTTAACACCATATCTGCAGgtattttctt ... ttactcatagGTCCTTTGGGAAGCCGAGCTGCCAAGGCAATTGGATTCATTGAGAAGATGA
EST:
gi|3767353|gb|AU031463.1|AU031463EST: CACCATATCTGCAG GTCCTTTGGGAAGCCGAGCTGCCAAGGCAATTGGATTCATTGAGAAGATGA
genomic: CACCATATCTGCAGgtattttctt ... ttactcatagGTCCTTTGGGAAGCCGAGCTGCCAAGGCAATTGGATTCATTGAGAAGATGA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttaacgatgtaggaataattgtgagttcattctgatttattaaatttactcatagGTCCTTTGGGAAGCCGAGCTGCCAAGGCAATTGGATTCATTGAGAAGATGATAGAATACTCTTATGTTAATGCACCGTTGCAGAAAGAACTGTTGGCAG
ttctgat putative branch site (score: 3)
tttactc putative PPT
ttcattctgatttatt TA-rich tract
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
atttcccttggatatgatttgcataattatttaggatctcttactttaacgatgtaggaataattgtgagttcattctgatttattaaatttactcatagGTCCTTTGGGAAGCCGAGCTGCCAAGGCAATTGGATTCATTGAGAAGATGATAGAATACTCTTATGTTAATGCACCGTTGCAGAAAGAACTGTTGGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC
- - - - - - - - - ttgcata
- - - - - - - - - - - - - - - - - - - - - - - - - - - -aggaataa