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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATGGTGAAGCTTATAAAGGATCTAAAGAAGGATAATGAATTCATGAAGAGTAAATGTGAGAATTCAGATGTTGCTCTAGTGAAGTTGATTGAGGAGgtaaatgtctaaccttccatgtaccttcacatgcataatggaagctcttgtgcaggtctttctttcttgcatgatgattaattgaacccttgtttgctttctccgcag

Basic information

species Oryza sativa
transcript LOC_Os03g17930.3
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g17930.3 (Oryza sativa), 5'ss of exon 10
lower sequence: GRMZM2G015730_T03 (Zea mays), 5'ss of exon 12
ATGGTGAAGCTTATAAAGGATCTAAAGAAGGATAATGAATTCATGAAGAGTAAATGTGAGAATTCAGATGTTGCTCTAGTGAAGTTGATTGAGGAGgtaa-atgtctaaccttcca-tgtaccttcacatgcataatggaagctcttgtgcaggtctttctttcttgcatgatgattaattgaacccttgtttgctttctccgcag
||| |   | | |||||  |||| |||||||| ||||||||  ||||| | ||||||||||| |||||| ||||||| |||||| | ||||| ||||||| | ||  | |     |   || | ||  |    || |  |||   |||    | | | |    |  ||||||    |           | || |            
ATGATTTTGGTGATAAAAAATCTTAAGAAGGACAATGAATTTCTGAAGGGAAAATGTGAGAACTCAGATATTGCTCTTGTGAAGCTCATTGAAGAGgtaatacgtgcatcgcaaaagcctagcctc-tagctgtactaaaagtggttgctatgttttctggaacgcgcatgagagctgcacatctttatattagaga---------

upper sequence: LOC_Os03g17930.3 (Oryza sativa), 5'ss of exon 10
lower sequence: GRMZM2G107731_T02 (Zea mays), 5'ss of exon 12
ATGGTGAAGCTTATAAAGGATCTAAAGAAGGATAATGAATTCATGAAGAGTAAATGTGAGAATTCAGATGTTGCTCTAGTGAAGTTGATTGAGGAGgtaaatgtcta-accttccatgtaccttcacatgcataatggaagctcttgtgcaggtctttctttcttgcatgatgattaattgaacccttgtttgctttctccgcag
||| |     | |||||| |||| |||||||| || |||||  ||||| | ||||||||||| |||||| ||||| | |||||| | ||||| ||||||| ||| |  | |    | |    |||  |    || |  |||  ||||| | | |  |      |||||    || |  ||    |         ||| |      
ATGATTTCAGTGATAAAGAATCTTAAGAAGGAGAACGAATTTCTGAAGGGAAAATGTGAGAACTCAGATATTGCTATTGTGAAGCTCATTGAAGAGgtaa-tgtgtgcatcgcaaaagctagttcctagttgtact--aaggccttgttc-gtttgtgtcggattgcacctggaatcgttccggctaatcaaagtttata-----

upper sequence: LOC_Os03g17930.3 (Oryza sativa), 5'ss of exon 10
lower sequence: GLYMA20G31830.1 (Glycine max), 5'ss of exon 12
ATGGTGAAGCTTATAAAGGATCTAAAGAAGGATAATGAATTCATGAAGAGTAAATGTGAGAATTCAGATGTTGCTCTAGTGAAGTTGATTGAGGAGgtaaatg---tctaaccttccatgtaccttcacatgcataatggaagctcttgtgcaggtctttctttcttgcatgatgattaattgaacccttgtttgctttctccgcag
||||  ||    || ||||| || |||||||| ||| ||||| |||||||||||| |||||| || |||||| | ||  |  ||||  |||| |||||| ||    | |  | ||   | |   | |     | | |    |    ||  | | |     | |   |  | |  |||||||||   |||   |||  ||        
ATGGCAAAATCAATCAAGGAACTCAAGAAGGAGAATCAATTCTTGAAGAGTAAATCTGAGAAGTCTGATGTTACACTCATAGAGTTAGTTGATGAGgtatataacttttttctttttctttttttccctggtcttgaccataagaattaagaaagagaaacatagataaagg--gattaattgg--cctcaattgtgtta-------

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|86432851|gb|CI086462.1|CI086462
EST:     AGAGTAAATGTGAGAATTCAGATGTTGCTCTAGTGAAGTTGATTGAGGAG                         CGTGAGTTAATGAAGAAGCAAGTTGATAAGTTCAAGAATCAAAAAGAGAAG
genomic: AGAGTAAATGTGAGAATTCAGATGTTGCTCTAGTGAAGTTGATTGAGGAGgtaaatgtct ... ttctccgcagCGTGAGTTAATGAAGAAGCAAGTTGATAAGTTCAAGAATCAAAAAGAGAAG
EST: gi|33809158|gb|CF330463.1|CF330463
EST:     AGAGTAAATGTGAGAATTCAGATGTTGCTCTAGTGAAGTTGATTGAGGAG                         CGTGAGTTAATGAAGAAGCAAGTTGATAAGTTCAAGAATCAAAAAGAGAAG
genomic: AGAGTAAATGTGAGAATTCAGATGTTGCTCTAGTGAAGTTGATTGAGGAGgtaaatgtct ... ttctccgcagCGTGAGTTAATGAAGAAGCAAGTTGATAAGTTCAAGAATCAAAAAGAGAAG
EST: gi|55412014|gb|CV724390.1|CV724390
EST:     AGAGTAAATGTGAGAATTCAGATGTTGCTCTAGTGAAGTTGATTGAGGAG                         CGTGAGTTAATGAAGAAGCAAGTTGATAAGTTCAAGAATCAAAAAGAGAAG
genomic: AGAGTAAATGTGAGAATTCAGATGTTGCTCTAGTGAAGTTGATTGAGGAGgtaaatgtct ... ttctccgcagCGTGAGTTAATGAAGAAGCAAGTTGATAAGTTCAAGAATCAAAAAGAGAAG
EST: gi|89166181|gb|CI103271.1|CI103271
EST:     AGAGTAAATGTGAGAATTCAGATGTTGCTCTAGTGAAGTTGATTGAGGAG                         CGTGAGTTAATGAAGAAGCAAGTTGATAAGTTCAAGAATCAAAAAGAGAAG
genomic: AGAGTAAATGTGAGAATTCAGATGTTGCTCTAGTGAAGTTGATTGAGGAGgtaaatgtct ... ttctccgcagCGTGAGTTAATGAAGAAGCAAGTTGATAAGTTCAAGAATCAAAAAGAGAAG
EST: gi|88955373|gb|CI091465.1|CI091465
EST:     AGAGTAAATGTGAGAATTCAGATGTTGCTCTAGTGAAGTTGATTGAGGAG                         CGTGAGTTAATGAAGAAGCAAGTTGATAAGTTCAAGAATCAAAAAGAGAAG
genomic: AGAGTAAATGTGAGAATTCAGATGTTGCTCTAGTGAAGTTGATTGAGGAGgtaaatgtct ... ttctccgcagCGTGAGTTAATGAAGAAGCAAGTTGATAAGTTCAAGAATCAAAAAGAGAAG
EST: gi|38479504|gb|CF963613.1|CF963613
EST:     AGAGTAAATGTGAGAATTCAGATGTTGCTCTAGTGAAGTTGATTGAGGAG                         CGTGAGTTAATGAAGAAGCAAGTTGATAAGTTCAAGAATCAAAAAGAGAAG
genomic: AGAGTAAATGTGAGAATTCAGATGTTGCTCTAGTGAAGTTGATTGAGGAGgtaaatgtct ... ttctccgcagCGTGAGTTAATGAAGAAGCAAGTTGATAAGTTCAAGAATCAAAAAGAGAAG
EST: gi|86436064|gb|CI107297.1|CI107297
EST:     AGAGTAAATGTGAGAATTCAGATGTTGCTCTAGTGAAGTTGATTGAGGGG                         CGTGAGTTAATGAAGAAGCAAGTTGATAAGTTCAAGAATCAAAAAGAGAAG
genomic: AGAGTAAATGTGAGAATTCAGATGTTGCTCTAGTGAAGTTGATTGAGGAGgtaaatgtct ... ttctccgcagCGTGAGTTAATGAAGAAGCAAGTTGATAAGTTCAAGAATCAAAAAGAGAAG
EST: gi|88219408|gb|CI218968.1|CI218968
EST:     AGAGTAAATGTGAGAATTCAGATGTTGCTCTAGTGAAGTTGATTGAGGAG                         CGTGAGTTAATGAAGAAGCAAGTTGATAAGTTCAAGAATCAAAAAGAGAAG
genomic: AGAGTAAATGTGAGAATTCAGATGTTGCTCTAGTGAAGTTGATTGAGGAGgtaaatgtct ... ttctccgcagCGTGAGTTAATGAAGAAGCAAGTTGATAAGTTCAAGAATCAAAAAGAGAAG
EST: gi|29639434|gb|CB644443.1|CB644443
EST:     AGAGTAAATGTGAGAATTCAGATGTTGCTCTAGTGAAGTTGATTGAGGAG                         CGTGAGTTAATGAAGAAGCAAGTTGATAAGTTCAAGAATCAAAAAGAGAAG
genomic: AGAGTAAATGTGAGAATTCAGATGTTGCTCTAGTGAAGTTGATTGAGGAGgtaaatgtct ... ttctccgcagCGTGAGTTAATGAAGAAGCAAGTTGATAAGTTCAAGAATCAAAAAGAGAAG
EST: gi|86499080|gb|CI141713.1|CI141713
EST:     AGAGTAAATGTGAGAATTCAGATGTTGCTCTAGTGAAGTTGATTGAGGAG                         CGTGAGTTAATGAAGAAGCAAGTTGATAAGTTCAAGAATCAAAAAGAGAAG
genomic: AGAGTAAATGTGAGAATTCAGATGTTGCTCTAGTGAAGTTGATTGAGGAGgtaaatgtct ... ttctccgcagCGTGAGTTAATGAAGAAGCAAGTTGATAAGTTCAAGAATCAAAAAGAGAAG
EST: gi|58675688|gb|CK064375.1|CK064375
EST:     AGAGTAAATGTGAGAATTCAGATGTTGCTCTAGTGAAGTTGATTGAGGAG                         CGTGAGTTAATGAAGAAGCAAGTTGATAAGTTCAAGAATCAAAAAGAGAAG
genomic: AGAGTAAATGTGAGAATTCAGATGTTGCTCTAGTGAAGTTGATTGAGGAGgtaaatgtct ... ttctccgcagCGTGAGTTAATGAAGAAGCAAGTTGATAAGTTCAAGAATCAAAAAGAGAAG
EST: gi|88263669|gb|CI366570.1|CI366570
EST:     AGAGTAAATGTGAGAATTCAGATGTTCCTCTAGTGAAGTTGATTGAGGAG                         CGTGAGTTAATGAAGAAGCAAGTTGATAAGTTCAAGAATCAAAAAGAGAAG
genomic: AGAGTAAATGTGAGAATTCAGATGTTGCTCTAGTGAAGTTGATTGAGGAGgtaaatgtct ... ttctccgcagCGTGAGTTAATGAAGAAGCAAGTTGATAAGTTCAAGAATCAAAAAGAGAAG
EST: gi|86425721|gb|CI070818.1|CI070818
EST:     AGAGTAAATGTGAGAATTCAGATGTTGCTCTAGTGAAGTTGATTGAAGAG                         CGTGAGTTAATGAAGAAGCAAGTTGATAAGTTCAAGAATCAAAAAGAGAAG
genomic: AGAGTAAATGTGAGAATTCAGATGTTGCTCTAGTGAAGTTGATTGAGGAGgtaaatgtct ... ttctccgcagCGTGAGTTAATGAAGAAGCAAGTTGATAAGTTCAAGAATCAAAAAGAGAAG
EST: gi|86498241|gb|CI140874.1|CI140874
EST:     AAGTTGATTGAGGAG                         CGTGAGTTAATGAAGAAGCAAGTTGATAAGTTCAAGAATCAAAAAGAGAAG
genomic: AAGTTGATTGAGGAGgtaaatgtct ... ttctccgcagCGTGAGTTAATGAAGAAGCAAGTTGATAAGTTCAAGAATCAAAAAGAGAAG
EST: gi|3767268|gb|AU031378.1|AU031378
EST:     GCTCTAGTGAAGTTGATTGAGGAG                         CGTGAGTTAATGAAGAAGCAAGTTGATAAGTTCAAGAATCAAAAAGAGAAG
genomic: GCTCTAGTGAAGTTGATTGAGGAGgtaaatgtct ... ttctccgcagCGTGAGTTAATGAAGAAGCAAGTTGATAAGTTCAAGAATCAAAAAGAGAAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATGGTGAAGCTTATAAAGGATCTAAAGAAGGATAATGAATTCATGAAGAGTAAATGTGAGAATTCAGATGTTGCTCTAGTGAAGTTGATTGAGGAGgtaaatgtctaaccttccatgtaccttcacatgcataatggaagctcttgtgcaggtctttctttcttgcatgatgattaattgaacccttgtttgctttctccgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG