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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagggcatacatgtctccccccatatgtttaataattagtttccactaatgtctgagctaatggaagttccttttcactttgatttcttgaagtggctatctttcacctgagtacgccatgagaggtcacatgactgagaaagttgatatttttgcttttggtgtggtcatgttggagATTATTGCTGGAAGGCCGAACTATGATGGTAAGCTTGACCAAGACATGGCTTATCTTTTAGAATGG

Basic information

species Zea mays
transcript GRMZM2G126858_T01
intron # 20
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G126858_T01 (Zea mays), 3'ss of exon 20
lower sequence: LOC_Os04g52640.1 (Oryza sativa), 3'ss of exon 22
----gtaagggcatacat---gtctccccccata---tgtttaataattagtttccactaatgtctgagctaatggaagttccttttcactttgatttcttgaagtggctatctttcacctgagtacgccatgagaggtcacatgactgagaaagttgatatttttgcttttggtgtggtcatgttggagATTATTGCTGGAAGGCCGAACTATGATGGTAAGCTTGACCAAGACATGGCTTATCTTTTAGAATGG
      ||   | |||||   |||      ||||    |||||   |||| |||    ||||   ||   | | || | |    |||   ||||  |  ||  ||||| |||||| |||||||||||||||||||||| || |||||||||||||||||| | ||||| ||||| |||||| | ||||||| | | |||||  ||                                                   
catacaaaccccttacataatgtcaaattacataagcagtttacatattatttttttttaatacatg---tgaaggtaatgatgtttt--tttggctctttccagTGGTTATCTTGCACCTGAGTACGCCATGAGAGGACATATGACTGAGAAAGTTGATGTGTTTGCATTTGGCGTGGTCTTATTGGAGACTTTAGCTGGCCGG---------------------------------------------------

upper sequence: GRMZM2G126858_T01 (Zea mays), 3'ss of exon 20
lower sequence: LOC_Os04g52600.1 (Oryza sativa), 3'ss of exon 22
gtaagggcatacatgtctccccccatatgtttaataatta-gtttccactaatgtctgagctaatggaagttccttttcactttgatttcttgaagtggctatctttcacctgagtacgccatgagaggtcacatgactgagaaagttgatatttttgcttttggtgtggtcatgttggagATTATTGCTGGAAGGCCGAACTATGATGGTAAGCTTGACCAAGACATGGCTTATCTTTTAGAATGG
            | ||  |   |||| ||||  |   ||| |||| || | || | |  | |||||| | ||     |  | ||  |       || || |||||| |||||||||| |||||||||||||| |||||||||||||||||| | ||||| ||||| |||||| | ||||||| | | |||||| ||                                                   
----------gtaagta-cattccatctgttccacctttatgtttacaatcatatttatgttaatggtatttttgggtatcctttgtcc-----agCGGTTATCTTGCACCTGAGTATGCCATGAGAGGTCATATGACTGAGAAAGTTGATGTCTTTGCATTTGGCGTGGTCTTATTGGAGACTTTAGCTGGACGG---------------------------------------------------

upper sequence: GRMZM2G126858_T01 (Zea mays), 3'ss of exon 20
lower sequence: LOC_Os04g52630.1 (Oryza sativa), 3'ss of exon 20
gtaagggcatac-atgtctccc-cccatatgtttaataattagtttccactaatgtctgagctaatggaagttccttttcactttgatttcttgaagtggctatctttcacctgagtacgccatgagaggtcacatgactgagaaagttgatatttttgcttttggtgtggtcatgttggagATTATTGCTGGAAGGCCGAACTATGATGGTAAGCTTGACCAAGACATGGCTTATCTTTTAGAATGG
|||||  ||| | || | || | ||  | | ||||  || ||      |||||      ||||||||  | ||     || | ||  |       ||||| |||||| |||||||||| ||||||||||| |  |||||||||||||||||| | || || ||||| |||||| | ||||||||| | |||||  |                                                    
gtaagttcattccatctttctcacctttgtctttacaaactacggagtactaa------agctaatgagatttttggctctcctttgtcc-----agTGGTTATCTTGCACCTGAGTATGCCATGAGAGGCCGTATGACTGAGAAAGTTGATGTCTTCGCATTTGGCGTGGTCTTATTGGAGATTTTAGCTGGCCGA---------------------------------------------------

upper sequence: GRMZM2G126858_T01 (Zea mays), 3'ss of exon 20
lower sequence: LOC_Os04g52614.1 (Oryza sativa), 3'ss of exon 18
gtaagggcatacatgtctccccccatatgt-ttaataattagtttccactaatgtctgagctaatggaagttccttttcactttgatttcttgaagtggctatctttcacctgagtacgccatgagaggtcacatgactgagaaagttgatatttttgcttttggtgtggtcatgttggagATTATTGCTGGAAGGCCGAACTATGATGGTAAGCTTGACCAAGACATGGCTTATCTTTTAGAATGG
|||||  ||| | |   | ||| | | | | || | ||||  ||||     ||   |  | |   ||  | |  ||||  || |  ||| |  | | || |||||| |||||||||||||||||||||| || ||||| |||||||||||  | ||||| ||||| |||                                                                              
gtaagtacattccttctttcccacctttatgtttacaatt--tttc-----atacttatgttggcggtggctt-ttttggctctcctttgtcca-gCGGTTATCTTGCACCTGAGTACGCCATGAGAGGCCATATGACCGAGAAAGTTGACGTCTTTGCATTTGGCGTG------------------------------------------------------------------------------

upper sequence: GRMZM2G126858_T01 (Zea mays), 3'ss of exon 20
lower sequence: LOC_Os04g52606.2 (Oryza sativa), 3'ss of exon 19
gtaagggcatac-atgtctc-cccccatatgtttaataattagtttccactaatgtctgagctaatggaagttccttttcactttgatttcttgaagtggctatctttcacctgagtacgccatgagaggtcacatgactgagaaagttgatatttttgcttttggtgtggtcatgttggagATTATTGCTGGAAGGCCGAACTATGATGGTAAGCTTGACCAAGACATGGCTTATCTTTTAGAATGG
|||||  ||| | || | || | ||   |||||||  ||||| ||||      |  ||| ||||| || |     || |  ||||  |||  |  ||||| |||||| |||||||||| || ||||||||||   |||| |||||||||||| | ||||| ||||| |||||| | ||||||| | | |||||  |                                                    
gtaagttcattccatctttcgcaccttcatgtttacaaattattttc-----gtacctgtgctaacggga----tttatggcttttcttttatctagTGGTTATCTTGCACCTGAGTATGCTATGAGAGGTCGTTTGACCGAGAAAGTTGATGTCTTTGCATTTGGCGTGGTCTTATTGGAGACTTTAGCTGGCCGA---------------------------------------------------

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|74246488|gb|DT654402.1|DT654402
EST:     CTTTATGACGATAAAAAGACACATGTTAGCACAAAAGTTGCTGGTACATT                         ATTATTGCTGGAAGGCCGAACTATGATGGTAAGCTTGACCAAGACATGGCT
genomic: CTTTATGACGATAAAAAGACACATGTTAGCACAAAAGTTGCTGGTACATTgtaagggcat ... catgttggagATTATTGCTGGAAGGCCGAACTATGATGGTAAGCTTGACCAAGACATGGCT






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aggtcacatgactgagaaagttgatatttttgcttttggtgtggtcatgttggagATTATTGCTGGAAGGCCGAACTATGATGGTAAGCTTGACCAAGACATGGCTTATCTTTTAGAATGG
                  agttgat  putative branch site (score: 5)
                aaagttgatattttt  TA-rich tract