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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGATCAAAGGCTACTGGTGCCTTCATTTTAACAGCTAGTCACAACCCTGGTGGTCCTACTGAGgtatcacagttatgatgtatctctgctgctaatcaagtggcacgattttctgtgtttatcagcaacttttcatttgatcttggcag

Basic information

species Oryza sativa
transcript LOC_Os03g50480.1
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g50480.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM2G109383_T01 (Zea mays), 5'ss of exon 5
GGATCAAAGGCTACTGGTGCCTTCATTTTAACAGCTAGTCACAACCCTGGTGGTCCTACTGAGgtatcacagttatgat--gtatctctgctgctaatcaagtggca-cgattttctgtgtttatcagcaacttttcatttgatcttggcag
|||||||||||||||||||||||||| || ||||| || || ||||| ||||||||||  |||||| |    |||      ||||||||| ||| |||||||||      ||  ||| |||| ||     || | ||||  || |||  |||
GGATCAAAGGCTACTGGTGCCTTCATCTTGACAGCGAGCCATAACCCAGGTGGTCCTAAGGAGgtacctattttactgctagtatctctgatgcaaatcaagtgctggtcatgctctatgtt-attgaatacatctcatc-gaactttccag

upper sequence: LOC_Os03g50480.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM2G023289_T03 (Zea mays), 5'ss of exon 5
GGATCAAAGGCTACTGGTGCCTTCATTTTAACAGCTAGTCACAACCCTGGTGGTCCTACTGAGgtatcacagttatgat--gtatctctgctgctaatcaagtggcacg-attttctgtgtttatcagcaacttttcatttgatcttggcag
|||||||||||||||||||||||||| || ||||| || || ||||| ||||||||||| |||||| ||   |||      || ||| || ||| ||||||||| |||  ||  ||| |||| ||     ||   ||| | || |||  |||
GGATCAAAGGCTACTGGTGCCTTCATCTTGACAGCGAGCCATAACCCAGGTGGTCCTACGGAGgtaccaagtttactgctagtgtctttgttgcaaatcaagtgccacacatgctctatgtt-attgaatacgcctcact-gaactttccag
















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|33675938|gb|CF304177.1|CF304177
EST:     CTGGTGCCTTCATTTTAACAGCTAGTCACAACCCTGGTGGTCCTACTGAG                         GACTTCGGAATCAAATATAACATGGAAAATGGTGGACCTGCCCCTGAATCG
genomic: CTGGTGCCTTCATTTTAACAGCTAGTCACAACCCTGGTGGTCCTACTGAGgtatcacagt ... atcttggcagGACTTCGGAATCAAATATAACATGGAAAATGGTGGACCTGCCCCTGAATCG
EST: gi|58688355|gb|CK077042.1|CK077042
EST:     CTGGTGCCTTCATTTTAACAGCTAGTCACAACCCTGGTGGTCCTACTGAG                         GACTTCGGAATCAAATATAACATGGAAAATGGTGGACCTGCCCCTGAATCG
genomic: CTGGTGCCTTCATTTTAACAGCTAGTCACAACCCTGGTGGTCCTACTGAGgtatcacagt ... atcttggcagGACTTCGGAATCAAATATAACATGGAAAATGGTGGACCTGCCCCTGAATCG
EST: gi|58675297|gb|CK063984.1|CK063984
EST:     CTGGTGCCTTCATTTTAACAGCTAGTCACAACCCTGGTGGTCCTACTGAG                         GACTTCGGAATCAAATATAACATGGAAAATGGTGGACCTGCCCCTGAATCG
genomic: CTGGTGCCTTCATTTTAACAGCTAGTCACAACCCTGGTGGTCCTACTGAGgtatcacagt ... atcttggcagGACTTCGGAATCAAATATAACATGGAAAATGGTGGACCTGCCCCTGAATCG
EST: gi|29612833|gb|CB617846.1|CB617846
EST:     CTGGTGCCTTCATTTTAACAGCTAGTCACAACCCTGGTGGTCCTACTGAG                         GACTTCGGAATCAAATATAACATGGAAAATGGTGGACCTGCCCCTGAATCG
genomic: CTGGTGCCTTCATTTTAACAGCTAGTCACAACCCTGGTGGTCCTACTGAGgtatcacagt ... atcttggcagGACTTCGGAATCAAATATAACATGGAAAATGGTGGACCTGCCCCTGAATCG
EST: gi|29689598|gb|CB685873.1|CB685873
EST:     CTGGTGCCTTCATTTTAACAGCTAGTCACAACCCTGGTGGTCCTACTGAG                         GACTTCGGAATCAAATATAACATGGAAAATGGTGGACCTGCCCCTGAATCG
genomic: CTGGTGCCTTCATTTTAACAGCTAGTCACAACCCTGGTGGTCCTACTGAGgtatcacagt ... atcttggcagGACTTCGGAATCAAATATAACATGGAAAATGGTGGACCTGCCCCTGAATCG
EST: gi|29671540|gb|CB667815.1|CB667815
EST:     CTGGTGCCTTCATTTTAACAGCTAGTCACAACCCTGGTGGTCCTACTGAG                         GACTTCGGAATCAAATATAACATGGAAAATGGTGGACCTGCCCCTGAATCG
genomic: CTGGTGCCTTCATTTTAACAGCTAGTCACAACCCTGGTGGTCCTACTGAGgtatcacagt ... atcttggcagGACTTCGGAATCAAATATAACATGGAAAATGGTGGACCTGCCCCTGAATCG
EST: gi|29664693|gb|CB660968.1|CB660968
EST:     CTGGTGCCTTCATTTTAACAGCTAGTCACAACCCTGGTGGTCCTACTGAG                         GACTTCGGAATCAAATATAACATGGAAAATGGTGGACCTGCCCCTGAATCG
genomic: CTGGTGCCTTCATTTTAACAGCTAGTCACAACCCTGGTGGTCCTACTGAGgtatcacagt ... atcttggcagGACTTCGGAATCAAATATAACATGGAAAATGGTGGACCTGCCCCTGAATCG
EST: gi|58654844|gb|CK043524.1|CK043524
EST:     CTGGTGCCTTCATTTTAACAGCTAGTCGGAACCCTGGTGGTCCTACTGAG                         GACTTCGGAATCAAATATAACATGGAAAATGGTGGACCTGCCCCTGAATCG
genomic: CTGGTGCCTTCATTTTAACAGCTAGTCACAACCCTGGTGGTCCTACTGAGgtatcacagt ... atcttggcagGACTTCGGAATCAAATATAACATGGAAAATGGTGGACCTGCCCCTGAATCG
EST: gi|58682481|gb|CK071168.1|CK071168
EST:     CTGGTGCCTTCATTTTAACAGCTAGTCACAACCCTGGTGGTCCTACTGAG                         GACTTCGGAATCAAATATAACATGGAAAATGGTGGACCTGCCCCTGAATCG
genomic: CTGGTGCCTTCATTTTAACAGCTAGTCACAACCCTGGTGGTCCTACTGAGgtatcacagt ... atcttggcagGACTTCGGAATCAAATATAACATGGAAAATGGTGGACCTGCCCCTGAATCG
EST: gi|58670502|gb|CK059188.1|CK059188
EST:     CTGGTGCCTTCATTTTAACAGCTAGTCACAACCCTGGTGGTCCTACTGAG                         GACTTCGGAATCAAATATAACATGGAAAATGGTGGACCTGCCCCTGAATCG
genomic: CTGGTGCCTTCATTTTAACAGCTAGTCACAACCCTGGTGGTCCTACTGAGgtatcacagt ... atcttggcagGACTTCGGAATCAAATATAACATGGAAAATGGTGGACCTGCCCCTGAATCG
EST: gi|58666397|gb|CK055083.1|CK055083
EST:     CTGGTGCCTTCATTTTAACAGCTAGTCACAACCCTGGTGGTCCTACTGAG                         GACTTCGGAATCAAATATAACATGGAAAATGGTGGACCTGCCCCTGAATCG
genomic: CTGGTGCCTTCATTTTAACAGCTAGTCACAACCCTGGTGGTCCTACTGAGgtatcacagt ... atcttggcagGACTTCGGAATCAAATATAACATGGAAAATGGTGGACCTGCCCCTGAATCG
EST: gi|29682384|gb|CB678659.1|CB678659
EST:     CTGGTGCCTTCATTTTAACAGCTAGTCACAACCCTGGTGGTCCTACTGAG                         GACTTCGGAATCAAATATAACATGGAAAATGGTGGACCTGCCCCTGAATCG
genomic: CTGGTGCCTTCATTTTAACAGCTAGTCACAACCCTGGTGGTCCTACTGAGgtatcacagt ... atcttggcagGACTTCGGAATCAAATATAACATGGAAAATGGTGGACCTGCCCCTGAATCG
EST: gi|33676013|gb|CF304252.1|CF304252
EST:     CTGGTGCCTTCATTTTAACAGCTAGTCACAACCCTGGTGGTCCTACTGAG                         GACTTCGGAATCAAATATAACATGGAAAATGGTGGACCTGCCCCTGAATCG
genomic: CTGGTGCCTTCATTTTAACAGCTAGTCACAACCCTGGTGGTCCTACTGAGgtatcacagt ... atcttggcagGACTTCGGAATCAAATATAACATGGAAAATGGTGGACCTGCCCCTGAATCG
EST: gi|87015499|gb|CI303105.1|CI303105
EST:     CTGGTGCCTTCATTTTAACAGCTAGTCACAACCCTGGTGGTCCTACTGAG                         GACTTCGGAAT
genomic: CTGGTGCCTTCATTTTAACAGCTAGTCACAACCCTGGTGGTCCTACTGAGgtatcacagt ... atcttggcagGACTTCGGAAT
EST: gi|58667231|gb|CK055917.1|CK055917
EST:     CTGGTGCCTTCATTTTAACAGCTAGTCACAACCCTGGTGGTCCTACTGAG                         GACTTCGGAATCAAATA
genomic: CTGGTGCCTTCATTTTAACAGCTAGTCACAACCCTGGTGGTCCTACTGAGgtatcacagt ... atcttggcagGACTTCGGAATCAAATA
EST: gi|58667790|gb|CK056476.1|CK056476
EST:     CTGGTGCCTTCATTTTAACAGCTAGTCACAACCCTGGTGGTCCTACTGAG                         GACTTCGGAATCAAATATAACATGGAAAATGGTGGACCTGCCCCTGAATCG
genomic: CTGGTGCCTTCATTTTAACAGCTAGTCACAACCCTGGTGGTCCTACTGAGgtatcacagt ... atcttggcagGACTTCGGAATCAAATATAACATGGAAAATGGTGGACCTGCCCCTGAATCG
EST: gi|58666319|gb|CK055005.1|CK055005
EST:     CTGGTGCCTTCATTTTAACAGCTAGTCACAACCCTGGTGGTCCTACTGAG                         GACTTCGGAATCAAATATAACATGGAAAATGGTGGACCTGCCCCTGAATCG
genomic: CTGGTGCCTTCATTTTAACAGCTAGTCACAACCCTGGTGGTCCTACTGAGgtatcacagt ... atcttggcagGACTTCGGAATCAAATATAACATGGAAAATGGTGGACCTGCCCCTGAATCG
EST: gi|29614791|gb|CB619804.1|CB619804
EST:     CTGGTGCCTTCATTTTAACAGCTAGTCACAACCCTGGTGGTCCTACTGAG                         GACTTCGGAATCAAATATAACATGGAAAATGGTGGACCTGCCCCTGAATCG
genomic: CTGGTGCCTTCATTTTAACAGCTAGTCACAACCCTGGTGGTCCTACTGAGgtatcacagt ... atcttggcagGACTTCGGAATCAAATATAACATGGAAAATGGTGGACCTGCCCCTGAATCG
EST: gi|29671584|gb|CB667859.1|CB667859
EST:     CTGGTGCCTTCATTTTAACAGCTAGTCACAACCCTGGTGGTCCTACTGAG                         GACTTCGGAATCAAATATAACATGGAAAATGGTGGACCTGCCCCTGAATCG
genomic: CTGGTGCCTTCATTTTAACAGCTAGTCACAACCCTGGTGGTCCTACTGAGgtatcacagt ... atcttggcagGACTTCGGAATCAAATATAACATGGAAAATGGTGGACCTGCCCCTGAATCG
EST: gi|58668595|gb|CK057281.1|CK057281
EST:     CTGGTGCCTTCATTTTAACAGCTAGTCACAACCCTGGTGGTCCTACTGAG                         GACTTCGGAATCAAATA
genomic: CTGGTGCCTTCATTTTAACAGCTAGTCACAACCCTGGTGGTCCTACTGAGgtatcacagt ... atcttggcagGACTTCGGAATCAAATA
EST: gi|33675599|gb|CF303838.1|CF303838
EST:     CTGGTGCCTTCATTTTAACAGCTAGTCACAACCCTGGTGGTCCTACTGAG                         GACTTCGGAATCAAATATAACATGGAAAATGGTGGACCTGCCCCTGAATCG
genomic: CTGGTGCCTTCATTTTAACAGCTAGTCACAACCCTGGTGGTCCTACTGAGgtatcacagt ... atcttggcagGACTTCGGAATCAAATATAACATGGAAAATGGTGGACCTGCCCCTGAATCG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGATCAAAGGCTACTGGTGCCTTCATTTTAACAGCTAGTCACAACCCTGGTGGTCCTACTGAGgtatcacagttatgatgtatctctgctgctaatcaagtggcacgattttctgtgtttatcagcaacttttcatttgatcttggcag

- - - - - - - - - - - - - - - - - - - - - - -  TGGTGG