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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatggaccagttcaccattttttggttatttatatgccacatcatatgcattttcacactcttcttttttgcacgaattgaaatagGTATCTGAAAGAAAGGAAACAGTTTGGAGTTCCTCTAGTAGCTTTTCAGCTGAACCAAGAAAAACTTGTGCGAATGCTTGGTAACATCCAAGCGATGCTT

Basic information

species Oryza sativa
transcript LOC_Os01g06600.1
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g06600.2 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM5G862219_T02 (Zea mays), 3'ss of exon 10
gtatggaccagttcaccattttttggttatttatatgccacatcatatgcattt-tcacactcttcttttttgc------------------------acgaattgaaatagGTATCTGAAAGAAAGGAAACAGTTTGGAGTTCCTCTAGTAGCTTTTCAGCTGAACCAAGAAAAACTTGTGCGAATGCTTGGTAACATCCAAGCGATGCTT
||| |     |  |   |  || ||    ||  |    ||||    || | ||   | | | ||| | |||||                         ||  || |||| |||||||||||||||||||| ||||| ||||| ||||| |  || ||||||||||||||||| || || |  || ||||| |||||| ||||  ||||| | 
gtacg---tggcgccatacgttctgacacttctttcatcacaggcaatcctttcaccccccccttttcttttgtcatgtaaaaaacaaaaaaacaaaaaccgatcgaaacagGTATCTGAAAGAAAGGAAGCAGTTCGGAGTCCCTCTGGCGGCGTTTCAGCTGAACCAAGAGAAGCTCGCCCGGATGCTCGGTAACGTCCAGTCGATGGTC

upper sequence: LOC_Os01g06600.2 (Oryza sativa), 3'ss of exon 9
lower sequence: PP1S95_81V6.1 (Physcomitrella patens), 3'ss of exon 11
--------------------------------------------------------------------------------------------------gtatggaccagtt----caccattttttggttatttatatgccacatcatatgcattttcacactcttcttttttgcacgaattgaa-atagGTATCTGAAAGAAAGGAAACAGTTTGGAGTTCCTCTAGTAGCTTTTCAGCTGAACCAAGAAAAACTTGTGCGAATGCTTGGTAACATCCAAGCGATGCTT
                                                                                                  || || ||  |      ||||||      || |    ||||    ||  | |   |||     |    || |    |     ||||  | || ||  || |||||||||||||||| ||||  ||  ||| |||  ||||  | |||||||||||||||||||| |||||||| ||||| || || ||| ||
gtatgatgaaatcagattctgcgcgttttggatcaaattttgcttgtcatgtgttctgtaaaaatgtttgatgtatcgaaaatttctttatgttggccgtgtgaactcgcaggaacaccatcaacaagtcacaagtatgtggtat-gtgtttgtttcgcttcctgactataagactttggttgagtacagATACTTGCAAGAAAGGAAACAGTTCGGAGCCCCGTTAGCAGCCCTTCAAATCAACCAAGAAAAACTTGTGCGGATGCTTGGGAACATTCAGGCAATGTTT
















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|29658082|gb|CB654357.1|CB654357
EST:     CGATTGGTATATCAATGGGGGTGTTTGATGTCTGCCATCG                         GTATC-GAAAGAAAGGAAACAGTTTGGAGTTCCTCTAGTAGCTTTTCAGCT
genomic: CGATTGGTATATCAATGGGGGTGTTTGATGTCTGCCATCGgtatggacca ... attgaaatagGTATCTGAAAGAAAGGAAACAGTTTGGAGTTCCTCTAGTAGCTTTTCAGCT
EST: gi|88344179|gb|CI654609.1|CI654609
EST:     GCATGGCAACCGATTGGTATATCAATGGGGGTGTTTGATGTCTGCCATCG                         GTATCTGAAAGAAAGGAAACAGTTTGGAGTTCCTCTAGTAGCTTTTCAGCT
genomic: GCATGGCAACCGATTGGTATATCAATGGGGGTGTTTGATGTCTGCCATCGgtatggacca ... attgaaatagGTATCTGAAAGAAAGGAAACAGTTTGGAGTTCCTCTAGTAGCTTTTCAGCT
EST: gi|56157778|gb|C26441.2|C26441
EST:     CATGGCAACCGATTGGTATATCAATGGGGGGTGTTTGATGTCTGCCATCG                         -TATCTGAAAGAAAGG
genomic: CATGGCAACCGATTGGTATATCAATGGGGG-TGTTTGATGTCTGCCATCGgtatggacca ... attgaaatagGTATCTGAAAGAAAGG
EST: gi|29668419|gb|CB664694.1|CB664694
EST:     GATTGGTATATCAATGGGGGTGTTTGATGTCTGCCATCG                         GTATCTGAAAGAAAGGAAACAGTTTGGAGTTCCTCTAGTAGCTTTTCAGCT
genomic: GATTGGTATATCAATGGGGGTGTTTGATGTCTGCCATCGgtatggacca ... attgaaatagGTATCTGAAAGAAAGGAAACAGTTTGGAGTTCCTCTAGTAGCTTTTCAGCT
EST: gi|29660291|gb|CB656566.1|CB656566
EST:     GCATGGCAACCGATTGGTATATCAATGGGGGTGTTTGATGTCTGCCATCG                         GTATCTGAAAGAAAGGAAACAGTTTGGAGTTCCTCTAGTAGCTTTTCAGCT
genomic: GCATGGCAACCGATTGGTATATCAATGGGGGTGTTTGATGTCTGCCATCGgtatggacca ... attgaaatagGTATCTGAAAGAAAGGAAACAGTTTGGAGTTCCTCTAGTAGCTTTTCAGCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atatgccacatcatatgcattttcacactcttcttttttgcacgaattgaaatagGTATCTGAAAGAAAGGAAACAGTTTGGAGTTCCTCTAGTAGCTTTTCAGCTGAACCAAGAAAAACTTGTGCGAATGCTTGGTAACATCCAAGCGATGCTT
                                            aattgaaata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatggaccagttcaccattttttggttatttatatgccacatcatatgcattttcacactcttcttttttgcacgaattgaaatagGTATCTGAAAGAAAGGAAACAGTTTGGAGTTCCTCTAGTAGCTTTTCAGCTGAACCAAGAAAAACTTGTGCGAATGCTTGGTAACATCCAAGCGATGCTT

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