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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATTGCAACAGCAATATTTGCTAATTCTCCCTTCAAAGAAGGAAAACCAAATGGGTATCTTAGCTTAAGAAGgtgattgctttattgcttttaaaagtacattgttttgttgtatgaagttgccaacaacatcattcatgatctgcag

Basic information

species Oryza sativa
transcript LOC_Os05g03820.2
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g03820.3 (Oryza sativa), 5'ss of exon 8
lower sequence: GRMZM2G020096_T01 (Zea mays), 5'ss of exon 7
ATTGCAACAGCAATATTTGCTAATTCTCCCTTCAAAGAAGGAAAACCAAATGGGTATCTTAGCTTAAGAAGgtgattgctttattgcttttaa--aagtacattgtt----ttgttgtatgaagttgccaacaacatcattcatgatctgcag
|||||||| ||||||||||| ||||||||||| |||||||||||||||||||| | ||| ||| |||| ||||  || ||| || ||  || |  || |||||  ||    |  ||   || |||| | |||| |||    | | ||||||||
ATTGCAACTGCAATATTTGCCAATTCTCCCTTTAAAGAAGGAAAACCAAATGGATTTCTCAGCCTAAGGAGgtatttacttgatagcccttcaggaaatacataattaatttcattacctgcagttactaaca-catttacccttatctgcag

upper sequence: LOC_Os05g03820.3 (Oryza sativa), 5'ss of exon 8
lower sequence: GRMZM2G111579_T01 (Zea mays), 5'ss of exon 7
ATTGCAACAGCAATATTTGCTAATTCTCCCTTCAAAGAAGGAAAACCAAATGGGTATCTTAGCTTAAGAAGgtgattgctttattgcttttaa------aagtacattgttttgttgtatgaagttgccaacaacatcattcatgatctgcag
|||||||| ||||||||||| |||||||| ||||||||||||||||||||||| | ||| |||||||| |||   |  ||| || ||  ||||      |  ||| |  |||  || | || ||||   ||||   | |  | | ||||||||
ATTGCAACTGCAATATTTGCCAATTCTCCGTTCAAAGAAGGAAAACCAAATGGATTTCTCAGCTTAAGGAGgcattaacttgatagcccttaagtacatagatacttaatttcattttctgcagttattaacacagttaccc-ttatctgcag
















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|33796283|gb|CF324008.1|CF324008
EST:     AATTCTCCCTTCAAAGAAGGAAAACCAAATGGGTATCTTAGCTTAAGAAG                         CCATATTTGGACTGATACTGACAACAACCGCTC
genomic: AATTCTCCCTTCAAAGAAGGAAAACCAAATGGGTATCTTAGCTTAAGAAGgtgattgctt ... tgatctgcagCCATATTTGGACTGATACTGACAACAACCGCTC
EST: gi|55411431|gb|CV723807.1|CV723807
EST:     AATTCTCCCTTCAAAGAAGGAAAACCAAATGGGTATCTTAGCTTAAGAAG                         CCATATTTGGACTGATACTGACAACAACCGCTCAGGGATGCTTCCTTTTGT
genomic: AATTCTCCCTTCAAAGAAGGAAAACCAAATGGGTATCTTAGCTTAAGAAGgtgattgctt ... tgatctgcagCCATATTTGGACTGATACTGACAACAACCGCTCAGGGATGCTTCCTTTTGT
EST: gi|58658531|gb|CK047211.1|CK047211
EST:     AATTCTCCCTTCAAAGAAGGAAAACCAAATGGGTATCTTAGCTTAAGAAG                         CCATATTTGGACTGATACTGACAACAAACGCTCAGGGATGCTTCCTTTTGT
genomic: AATTCTCCCTTCAAAGAAGGAAAACCAAATGGGTATCTTAGCTTAAGAAGgtgattgctt ... tgatctgcagCCATATTTGGACTGATACTGACAACAACCGCTCAGGGATGCTTCCTTTTGT
EST: gi|218498945|gb|FG948066.1|FG948066
EST:     AATTCTCCCTTCAAAGAAGGAAAACCAAATGGGTATCTTAGCTTAAGAAG                         CCATATTTGGACTGATACTGACAACAACCGCTCAGGGATGCTTCCTTTTGT
genomic: AATTCTCCCTTCAAAGAAGGAAAACCAAATGGGTATCTTAGCTTAAGAAGgtgattgctt ... tgatctgcagCCATATTTGGACTGATACTGACAACAACCGCTCAGGGATGCTTCCTTTTGT
EST: gi|58663415|gb|CK052101.1|CK052101
EST:     AATTCTCCCTTCAAAGAAGGAAAACCAAATGGGTATCTTAGCTTAAGAAG                         CCATATTTGGACTGATACTGACAACAACCGCTCAGGGATGCTTCCTTTTGT
genomic: AATTCTCCCTTCAAAGAAGGAAAACCAAATGGGTATCTTAGCTTAAGAAGgtgattgctt ... tgatctgcagCCATATTTGGACTGATACTGACAACAACCGCTCAGGGATGCTTCCTTTTGT
EST: gi|218500233|gb|FG945122.1|FG945122
EST:     AATTCTCCCTTCAAAGAAGGAAAACCAAATGGGTATCTTAGCTTAAGAAG                         CCATATTTGGACTGATACTGACAACAACCGCTCAGGGATGCTTCCTTTTGT
genomic: AATTCTCCCTTCAAAGAAGGAAAACCAAATGGGTATCTTAGCTTAAGAAGgtgattgctt ... tgatctgcagCCATATTTGGACTGATACTGACAACAACCGCTCAGGGATGCTTCCTTTTGT
EST: gi|33676123|gb|CF304362.1|CF304362
EST:     AATTCTCCCTTCAAAGAAGGAAAACCAAATGGGTATCTTAGCTTAAGAAG                         CCATATTTGGACTGATACTGACAACAACCGCTCAGGGATGCTTCCTTTTGT
genomic: AATTCTCCCTTCAAAGAAGGAAAACCAAATGGGTATCTTAGCTTAAGAAGgtgattgctt ... tgatctgcagCCATATTTGGACTGATACTGACAACAACCGCTCAGGGATGCTTCCTTTTGT
EST: gi|29679436|gb|CB675711.1|CB675711
EST:     AATTCTCCCTTCAAAGAAGGAAAACCAAATGGGTATCTTAGCTTAAGAAG                         CCATATTTGGACTGATACTGACAACAACCGCTCAGGGATGCTTCCTTTTGT
genomic: AATTCTCCCTTCAAAGAAGGAAAACCAAATGGGTATCTTAGCTTAAGAAGgtgattgctt ... tgatctgcagCCATATTTGGACTGATACTGACAACAACCGCTCAGGGATGCTTCCTTTTGT
EST: gi|29677970|gb|CB674245.1|CB674245
EST:     AATTCTCCCTTCAAAGAAGGAAAACCAAATGGGTATCTTAGCTTAAGAAG                         CCATATTTGGACTGATACTGACAACAACCGCTCAGGGATGCTTCCTTTTGT
genomic: AATTCTCCCTTCAAAGAAGGAAAACCAAATGGGTATCTTAGCTTAAGAAGgtgattgctt ... tgatctgcagCCATATTTGGACTGATACTGACAACAACCGCTCAGGGATGCTTCCTTTTGT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATTGCAACAGCAATATTTGCTAATTCTCCCTTCAAAGAAGGAAAACCAAATGGGTATCTTAGCTTAAGAAGgtgattgctttattgcttttaaaagtacattgttttgttgtatgaagttgccaacaacatcattcatgatctgcag

- - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - -  AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG