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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtctattgttttgttcaagtttacaatacactattcacagtaatactgtttacaatatgctattttggactgcgctgaataatttgtgcttgcattacagGCAGAGTAATTCCGGAGAGTGTGATCTATAGCTATGGAACTGTCCTGTTGGATCTTTTGAGCGGAAAACACATTCCTCCTAGTCAT

Basic information

species Zea mays
transcript GRMZM2G054634_T01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G054634_T02 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os10g42110.1 (Oryza sativa), 3'ss of exon 5
-----------------------------------------------gtctattgttttgttcaagtttacaatacactattcacagtaatact-gtttacaatatgct-----------------att-ttggactgcgctgaataatttgtg-------cttgcattacagGCAGAGTAATTCCGGAGAGTGTGATCTATAGCTATGGAACTGTCCTGTTGGATCTTTTGAGCGGAAAACACATTCCTCCTAGTCAT
                                                ||||||| | | ||| ||   | |  | ||   |||   || | |  | || | ||||  |                 ||| || |||||| | ||| ||||||||       |||| || ||||||||||| ||  | ||||||||||| |||||||||||||| || || |||||||||||||| || || ||||| |||||||| |||
gtaggaatttacacatgatccttattaccgcactcatgggcaccttactctattgatgttttccagcaaaaatgaaacatgtcaacttatttcaagcttgctatatatttactcccaagtactaacattgtttgactgcaccgaacaatttgtgcatgacacttgtatgacagGCAGAGTCATCGCCGAGAGTGTGATATATAGCTATGGAACAGTTCTTTTGGATCTTTTGAGTGGGAAGCACATACCTCCTAGCCAT

upper sequence: GRMZM2G054634_T02 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA17G16420.1 (Glycine max), 3'ss of exon 5
gtctattgttttgttcaagtttacaatacactattcacagtaatactgtttacaatat-gctattttggactgc--gctgaataatttgtgcttgcat-tacagGCAGAGTAATTCCGGAGAGTGTGATCTATAGCTATGGAACTGTCCTGTTGGATCTTTTGAGCGGAAAACACATTCCTCCTAGTCAT
    ||||||||     |  || || |      |||| |    |  | ||   | | | ||||  |   | |     |   || ||   |     ||  | |||||||  |||| || |||||||||||||| || ||||||||||| ||  |||||||||| || || || ||||||||||| || |||
----attgttttacctgatgttccattgattgtttcagaactgtcttattagaagtcttgctaactataattaatgacaatatgatacttaacaacacctgcagGCAGGATAATCCCAGAGAGTGTGATCTACAGTTATGGAACTGTTCTTCTGGATCTTTTAAGTGGCAAGCACATTCCTCCAAGCCAT

upper sequence: GRMZM2G054634_T02 (Zea mays), 3'ss of exon 5
lower sequence: AT5G46570.1 (Arabidopsis thaliana), 3'ss of exon 4
gtctattgttttgttcaagtttacaatacactattcacagtaatactgtttacaatatgctattttggactgcgctgaataatttgtgcttgcattacagGCAGAGTAATTCCGGAGAGTGTGATCTATAGCTATGGAACTGTCCTGTTGGATCTTTTGAGCGGAAAACACATTCCTCCTAGTCAT
            ||  || | |  |       | ||  |||   |       ||||    ||||   || |    |   |   | ||  ||   || |||| ||||| ||||| || |||||||| |  || ||||||||| | || || |||||||| ||||| ||||||||||| ||||| |||
------------gtaaaattcttgatcttgtgaatcgtagtcgaagacaaaccaattcattattgaagattaaagt---tctctggtttttcttttgcagGTAGAGTCATTCCTGAAAGTGTGATATTCAGTTATGGAACTATTCTTTTAGATCTTTTAAGCGGCAAACACATTCCACCTAGCCAT

upper sequence: GRMZM2G054634_T02 (Zea mays), 3'ss of exon 5
lower sequence: EFJ20301 (Selaginella moellendorffii), 3'ss of exon 4
gtctattgttttgttcaagtttacaatacactattcacagtaatactgtttacaatatgctattttggactgcgctgaataatttgtgcttgcattacagGCAGAGTAATTCCGGAGAGTGTGATCTATAGCTATGGAACTGTCCTGTTGGATCTTTTGAGCGGAAAACACATTCCTCCTAGTCAT
                                       ||||  || |      | ||  |  |||    |   | ||   |||||  |    || |||| |||||||  || |||||||| || ||||| ||||| ||||| || ||||||||| | ||||| || ||||||||||| || || 
---------------------------------------gtaaagctctcgtgcctttgtcaccttg---cgtattcaaagctttgttttctgtttgcagGTAGAGTAACACCCGAGAGTGTTATTTATAGTTATGGTACTGTTCTCTTGGATCTTCTTAGCGGGAAGCACATTCCTCCAAGCCAC

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|89248037|gb|DY619823.1|DY619823
EST:     AAGTTATAGCACTAACCTGGCTTACACTCCACCAGAGTTTCTACGAACTG                         GCAGAGTAATTCCGGAGAGTGTGATCTATAGCTATGGAACTGTCCTGTTGG
genomic: AAGTTATAGCACTAACCTGGCTTACACTCCACCAGAGTTTCTACGAACTGgtaagacccc ... tgcattacagGCAGAGTAATTCCGGAGAGTGTGATCTATAGCTATGGAACTGTCCTGTTGG
EST: gi|211485328|gb|FL295172.1|FL295172
EST:     AAGTTATAGCACTAACCTGGCTTACACTCCACCAGAGTTTCTACGAACTG                         GCAGAGTAATTCCGGAGAGTGTGATCTATAGCTATGGAACTGTCCTGTTGG
genomic: AAGTTATAGCACTAACCTGGCTTACACTCCACCAGAGTTTCTACGAACTGgtaagacccc ... tgcattacagGCAGAGTAATTCCGGAGAGTGTGATCTATAGCTATGGAACTGTCCTGTTGG
EST: gi|71760095|gb|DR958032.1|DR958032
EST:     AAGTTATAGCACTAACCTGGCTTACACTCCACCAGAGTTTCTACGAACTG                         GCAGAGTAATTCCGGAGAGTGTGATCTATAGCTATGGAACTGTCCTGTTGG
genomic: AAGTTATAGCACTAACCTGGCTTACACTCCACCAGAGTTTCTACGAACTGgtaagacccc ... tgcattacagGCAGAGTAATTCCGGAGAGTGTGATCTATAGCTATGGAACTGTCCTGTTGG
EST: gi|211485330|gb|FL295174.1|FL295174
EST:     AAGTTATAGCACTAACCTGGCTTACACTCCACCAGAGTTTCTACGAACTG                         GCAGAGTAATTCCGGAGAGTGTGATCTATAGCTATGGAACTGTCCTGTTGG
genomic: AAGTTATAGCACTAACCTGGCTTACACTCCACCAGAGTTTCTACGAACTGgtaagacccc ... tgcattacagGCAGAGTAATTCCGGAGAGTGTGATCTATAGCTATGGAACTGTCCTGTTGG
EST: gi|211485329|gb|FL295173.1|FL295173
EST:     AAGTTATAGCACTAACCTGGCTTACACTCCACCAGAGTTTCTACGAACTG                         GCAGAGTAATTCCGGAGAGTGTGATCTATAGCTATGGAACTGTCCTGTTGG
genomic: AAGTTATAGCACTAACCTGGCTTACACTCCACCAGAGTTTCTACGAACTGgtaagacccc ... tgcattacagGCAGAGTAATTCCGGAGAGTGTGATCTATAGCTATGGAACTGTCCTGTTGG
EST: gi|78122641|gb|DV541025.1|DV541025
EST:     AAGTTATAGCACTAACCTGGCTTACACTCCACCAGAGTTTCTACGAACTG                         GCAGAGAGAAATTCCGGAGAGTGTGATCTATAGCTATGGAACTGTCCTGTT
genomic: AAGTTATAGCACTAACCTGGCTTACACTCCACCAGAGTTTCTACGAACTGgtaagacccc ... tgcattacagGCAGAGT-AA-TTCCGGAGAGTGTGATCTATAGCTATGGAACTGTCCTGTT
EST: gi|32930139|gb|CF034951.1|CF034951
EST:     AAGTTATAGCACTAACCTGGCTTACACTCCACCAGAGTTTCTACGAACTG                         GCAGAGTAATTCCGGAGAGTGTGATCTATAGCTATGGAACTGTCCTGTTGG
genomic: AAGTTATAGCACTAACCTGGCTTACACTCCACCAGAGTTTCTACGAACTGgtaagacccc ... tgcattacagGCAGAGTAATTCCGGAGAGTGTGATCTATAGCTATGGAACTGTCCTGTTGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctgtttacaatatgctattttggactgcgctgaataatttgtgcttgcattacagGCAGAGTAATTCCGGAGAGTGTGATCTATAGCTATGGAACTGTCCTGTTGGATCTTTTGAGCGGAAAACACATTCCTCCTAGTCAT
                              tgaataattt  TA-rich tract