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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ccccaatggtactgcacaagttttacttgaactgtgtggagagcaactgttgagttctccttttaggtatatgcatgatgttctcttatccgttatacagGTAATTACCTCAAGTTTTATAATGCTATAAGGGAGGCCTATCCGGACATTCAAATGATTTCAAATTGTGATGCTTCATCAAGACCACTTGACCATCCTGC

Basic information

species Oryza sativa
transcript LOC_Os12g03470.5
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os12g03470.5 (Oryza sativa), 3'ss of exon 11
lower sequence: GRMZM2G077299_T03 (Zea mays), 3'ss of exon 10
----ccccaatggtactgcacaagttttacttgaactgtgtggagagcaact-gttgagttctccttttaggtatatg-catgatgttctct-tatccgttatacagGTAATTACCTCAAGTTTTATAATGCTATAAGGGAGGCCTATCCGGACATTCAAATGATTTCAAATTGTGATGCTTCATCAAGACCACTTGACCATCCTGC
     |||| ||||| |  ||| ||       ||| |   |      ||| | ||||    || ||||||  |  ||| |||||| |||||| | ||  ||  |||||||| ||||||||||| || |||||||||||  |||||||||| |||||||||||||||||||| || |||| |||||| | ||||||||| ||||||||
tatctcccagtggtagtcgacatgt-------gaaatacttcagccacaatttgttgtaacctacttttaatttcatggcatgatattctctatttctattgaacagGTAACTACCTCAAGTTCTACAATGCTATAAGACAGGCCTATCCAGACATTCAAATGATTTCAAACTGCGATGGTTCATCTACACCACTTGATCATCCTGC

upper sequence: LOC_Os12g03470.5 (Oryza sativa), 3'ss of exon 11
lower sequence: GRMZM2G006130_T04 (Zea mays), 3'ss of exon 11
ccccaatggtactgcacaa--gttttacttgaactgtgtggaga--gcaactgttgagttctccttttaggtatatgca-tgatgttctct-tatccgttatacagGTAATTACCTCAAGTTTTATAATGCTATAAGGGAGGCCTATCCGGACATTCAAATGATTTCAAATTGTGATGCTTCATCAAGACCACTTGACCATCCTGC
      ||| | |  ||||  |   ||||| | ||   |       | |  | || ||  || ||||||| |  ||| | ||||  ||| | | || |||| ||||||||||||||||| || || ||||||||||| ||||||||||| |||||||| ||||||||||| ||||||| |||||| ||||||||||||||||||||
-----gtggaagtcgacaaaggaaatacttcacctacattttttttgtacatattaagc-ctgcttttagttgcatggaatgatagtctttatgtctgttaaacagGTAATTACCTCAAATTCTACAATGCTATAAGAGAGGCCTATCCAGACATTCAGATGATTTCAAACTGTGATGGTTCATCTAGACCACTTGACCATCCTGC

upper sequence: LOC_Os12g03470.5 (Oryza sativa), 3'ss of exon 11
lower sequence: GRMZM2G006130_T05 (Zea mays), 3'ss of exon 10
ccccaatggtactgcacaa--gttttacttgaactgtgtggaga-gcaactgttgagttctccttttaggtatatgca-tgatgttctct-tatccgttatacagGTAATTACCTCAAGTTTTATAATGCTATAAGGGAGGCCTATCCGGACATTCAAATGATTTCAAATTGTGATGCTTCATCAAGACCACTTGACCATCCTGC
    | ||| | |  ||||  |   ||||| | ||   |      | |  | || ||  ||  |||||| |  ||| | ||||  ||| | | || |||| ||||||||||||||||| || || ||||||||||| ||||||||||| |||||||| ||||||||||| ||||||| |||||| ||||||||||||||||||||
----agtggaagtcgacaaaggaaatacttcacctacatttttttgtacatattaagc-ctgtttttagttgcatggaatgatagtctttatgtctgttaaacagGTAATTACCTCAAATTCTACAATGCTATAAGAGAGGCCTATCCAGACATTCAGATGATTTCAAACTGTGATGGTTCATCTAGACCACTTGACCATCCTGC

upper sequence: LOC_Os12g03470.5 (Oryza sativa), 3'ss of exon 11
lower sequence: GRMZM2G393002_T01 (Zea mays), 3'ss of exon 20
--------------------------------------ccccaatggtactgcacaagttttacttgaactgtgtggagagc--aactgttgagttctccttttaggtatatgcatgatgttctcttat-ccgttatacagGTAATTACCTCAAGTTTTATAATGCTATAAGGGAGGCCTATCCGGACATTCAAATGATTTCAAATTGTGATGCTTCATCAAGACCACTTGACCATCCTGC
                                       ||||||| |  |||| ||  || |     ||| ||| |   |   | | |  || |  | ||||||| ||    || ||||||||||  | |  ||  ||||||||||||||||||||||| || |||||||| |||| |||||| ||||||||| ||||||| || |||||||  || ||  |||||||||| ||||||||
gtaagatgacgggtacttttctatcgcatctgttttactcccaatgtttgtgcagaaaattcaa--agactatgtagtttgtttagcagaggaatcgtacttttagtta----caagatgttctctactgctattggacagGTAATTACCTCAAGTTTTACAACGCTATAAGAGAGGTCTATCCAGACATTCAACTGATTTCGAACTGTGATGGCTCGTCCGGACCACTTGATCATCCTGC

upper sequence: LOC_Os12g03470.5 (Oryza sativa), 3'ss of exon 11
lower sequence: GLYMA03G27490.1 (Glycine max), 3'ss of exon 10
ccccaatggtactgcacaagttttacttgaactgtgtggagagcaactgttgagttctccttttaggtatatgcatgatgttctcttatccgttatacagGTAATTACCTCAAGTTTTATAATGCTATAAGGGAGGCCTATCCGGACATTCAAATGATTTCAAATTGTGATGCTTCATCAAGACCACTTGACCATCCTGC------------
    | |  || |       ||||| || ||   | | |  |   |    | | |      || | |  | ||  | || || | | |  | ||    ||| || |||||    || ||  | || ||| |  | || |||||||| ||||||||||||||||||||||||||||| || | |||  | || || || ||            
---tagtt-tattctctttattttatttcaaaattttcgttactgagaaataaatg-----ttaaagggtttgtctaatcttttttaaaacatt---taggaaactacctagCTTTCTACGAGGCAATACGACATGCTTATCCGGATATTCAAATGATTTCAAATTGTGATGCTTCGTCTAAACCGTTAGATCACCCAGCTGATATGTATGA

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|29667817|gb|CB664092.1|CB664092
EST:     CAAATACGTTGCAATTGGAAATGAAGATTGTGGGAAAAAATTTTACCGCG                         GTAATTACCTCAAGTTTTATAATGCTATAAGGGAGGCCTATCCGGACATTC
genomic: CAAATACGTTGCAATTGGAAATGAAGATTGTGGGAAAAAATTTTACCGCGgtatattcct ... cgttatacagGTAATTACCTCAAGTTTTATAATGCTATAAGGGAGGCCTATCCGGACATTC
EST: gi|33381874|gb|CF197217.1|CF197217
EST:     CAAATACGTTGCAATTGGAAATGAAGATTGTGGGAAAAAATTTTACCGCG                         GTAATTACCTCAAGTTTTATAATGCTATAAGGGAGGCCTATCCGGACATTC
genomic: CAAATACGTTGCAATTGGAAATGAAGATTGTGGGAAAAAATTTTACCGCGgtatattcct ... cgttatacagGTAATTACCTCAAGTTTTATAATGCTATAAGGGAGGCCTATCCGGACATTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

actgttgagttctccttttaggtatatgcatgatgttctcttatccgttatacagGTAATTACCTCAAGTTTTATAATGCTATAAGGGAGGCCTATCCGGACATTCAAATGATTTCAAATTGTGATGCTTCATCAAGACCACTTGACCATCCTGC
                                   ttctcttatccgtt  CT-rich tract
                                               ttataca  TA-rich tract