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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCCATCATCGGCGTGATGGGAAAGCAACGGCTGCCTTACCCATCTAGGTCATTTGATATGGCACATTGTTCACGCTGCTTGATTCCTTGGCATGAGTTTGgtgagcacttcaatacatttgaattggtttcaatgtatcttgccccaagttttcaagctatccttaggtccaaatattgttcactaattgagttggatgttctgaattttttgttag

Basic information

species Oryza sativa
transcript LOC_Os10g36690.3
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os10g36690.4 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G114570_T01 (Zea mays), 5'ss of exon 3
GCCATCATCGGCGTGATGGGAAAGCAACGGCTGCCTTACCCATCTAGGTCATTTGATATGGCACATTGTTCACGCTGCTTGATTCCTTGGCATGAGTTTGgtgagcacttcaatacatttgaattggtttcaatgtatcttgccccaagttttcaagctatccttaggtccaaatattgttcactaattgagttggatgttctgaattttttgttag
|||||||| ||||| ||||  ||||| ||| ||||||||||||||||| | || |||||||||||||| || |||||  ||||||||||| ||||    |||||| ||| |||       | |                        | |||||||| | | ||| |||  |||      | ||| | |  || | ||| ||| ||  ||   ||||
GCCATCATTGGCGTCATGGCGAAGCAGCGGTTGCCTTACCCATCTAGGGCGTTCGATATGGCACATTGCTCGCGCTGTCTGATTCCTTGGGATGAACACGgtgagtactccaa-------ggac-----------------------atttttcaagttgttcttgggtagaaaacgaactgactgacttggt-gcatgctctcaaacttcctttag

upper sequence: LOC_Os10g36690.4 (Oryza sativa), 5'ss of exon 3
lower sequence: GLYMA08G03000.1 (Glycine max), 5'ss of exon 2
GCCATCATCGGCGTGATGGGAAAGCAACGGCTGCCTTACCCATCTAGGTCATTTGATATGGCACATTGTTCACGCTGCTTGATTCCTTGGCATGAGTTTGgtgagcac-ttcaatacatttgaattggtttcaatgtatcttgcc---ccaagttttcaagctatccttaggtccaaatattgttcactaattgagttggatgttctgaattttttgttag
|| || || ||| | ||||     ||  || | || |||||| | ||| | ||||||||||| |||||||| ||||||||||| ||||||||  |  |||||   |||  |   ||||||   ||      | || |   ||| |   | || ||   |||  | |  |   || ||  | |  | |||     |  |  || |                 
GCAATGATTGGCATCATGGCTTCACAGAGGATTCCATACCCAGCAAGGGCGTTTGATATGGCTCATTGTTCTCGCTGCTTGATACCTTGGCACAAACTTGgtattcacacttcttacattatgatgaccaactattttcattggctatctaatttaataaggaaacaattaatcaaacaagtagttact----caagtacatat-----------------

upper sequence: LOC_Os10g36690.4 (Oryza sativa), 5'ss of exon 3
lower sequence: GLYMA05G36550.1 (Glycine max), 5'ss of exon 2
GCCATCATCGGCGTGATGGGAAAGCAACGGCTGCCTTACCCATCTAGGTCATTTGATATGGCACATTGTTCACGCTGCTTGATTCCTTGGCATGAGTTTGgtgagcacttcaatacatttgaattggtttcaatgtatcttgccccaagttttcaagctatccttaggtccaaatattgttcactaattgagttggatgtt-ctgaattttttgttag
|| || || ||| | ||||     ||  || | || |||||| | ||| | ||||||||||| |||||||| ||||||||||| ||||||||  | ||||||   |||      || ||| |   | ||   ||| | |   | | |  ||     ||||||     ||  ||  |    | | ||||  |       |||  | || |   | ||  
GCAATGATTGGCATCATGGCTTCACAGAGGATTCCATACCCAGCAAGGGCGTTTGATATGGCTCATTGTTCTCGCTGCTTGATACCTTGGCACAAATTTGgtattcac------acttttta---gattatgatg-acc---cactattttcatgggctatct---agtttaataagaaataattaatcaaacaaatagttatttaagtacatatt--

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|58666287|gb|CK054973.1|CK054973
EST:     ATTTGATATGGCACATTGTTCACGCTGCTTGATTCCTTGGCATGAATTTG                         ATGGAATATACCTAGCTGAAGTCGACAGAATTCTAAGGCCCGGGGGATACT
genomic: ATTTGATATGGCACATTGTTCACGCTGCTTGATTCCTTGGCATGAGTTTGgtgagcactt ... tttttgttagATGGAATATACCTAGCTGAAGTCGACAGAATTCTAAGGCCCGGGGGATACT
EST: gi|4880936|gb|AU065235.1|AU065235
EST:     ATTTGATATGGCACATTGTTCACGCTGCTTGATTCCTTGGCATGAGTTTG                         ATGGAATATACCTAGCTGAAGTCGACAGAATTCTAAGGCCCGGGGGATACT
genomic: ATTTGATATGGCACATTGTTCACGCTGCTTGATTCCTTGGCATGAGTTTGgtgagcactt ... tttttgttagATGGAATATACCTAGCTGAAGTCGACAGAATTCTAAGGCCCGGGGGATACT
EST: gi|58671235|gb|CK059921.1|CK059921
EST:     ATTTGATATGGCACATTGTTCACGCTGCTTGATTCCTTGGCATGAATTTG                         ATGGAATATACCTAGCTGAAGTCGACAGAATTCTAAGGCCCGGGGGATACT
genomic: ATTTGATATGGCACATTGTTCACGCTGCTTGATTCCTTGGCATGAGTTTGgtgagcactt ... tttttgttagATGGAATATACCTAGCTGAAGTCGACAGAATTCTAAGGCCCGGGGGATACT
EST: gi|58658940|gb|CK047620.1|CK047620
EST:     ATTTGATATGGCACATTGTTCACGCTGCTTGATTCCTTGGCATGAATTTG                         ATGGAATATACCTAGCTGAAGTCGACAGAATTCTAAGGCCCGGGGGATACT
genomic: ATTTGATATGGCACATTGTTCACGCTGCTTGATTCCTTGGCATGAGTTTGgtgagcactt ... tttttgttagATGGAATATACCTAGCTGAAGTCGACAGAATTCTAAGGCCCGGGGGATACT
EST: gi|58601521|gb|CK012049.1|CK012049
EST:     GGCACATTGTTCACGCTGCTTGATT-CTTGGCATGAATTTG                         ATGGAATATACCTAGCTGAAGTCGACAGAATTCTAAGG-CCGGGGGATACT
genomic: GGCACATTGTTCACGCTGCTTGATTCCTTGGCATGAGTTTGgtgagcactt ... tttttgttagATGGAATATACCTAGCTGAAGTCGACAGAATTCTAAGGCCCGGGGGATACT
EST: gi|58666828|gb|CK055514.1|CK055514
EST:     ATTTGATATGGCACATTGTTCACGCTGCTTGATTCCTTGGCATGAATTTG                         ATGGAATATACCTAGCTGAAGTCGACAGAATTCTAAGGCCCGGGGGATACT
genomic: ATTTGATATGGCACATTGTTCACGCTGCTTGATTCCTTGGCATGAGTTTGgtgagcactt ... tttttgttagATGGAATATACCTAGCTGAAGTCGACAGAATTCTAAGGCCCGGGGGATACT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCCATCATCGGCGTGATGGGAAAGCAACGGCTGCCTTACCCATCTAGGTCATTTGATATGGCACATTGTTCACGCTGCTTGATTCCTTGGCATGAGTTTGgtgagcacttcaatacatttgaattggtttcaatgtatcttgccccaagttttcaagctatccttaggtccaaatattgttcactaattgagttggatgttctgaattttttgttag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT