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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATGGCGAATCCCATGGAGGGGGTGTTGGTTGCGTTATCAGTGGCTGCCCACCCAGAATTCCTCTCACTGAGGCAGACATGCAAGTAGAACTCGATAGAAGgtgtgtctcttactctcttccacatattagttttaagttattactagtttactaaaatctagcataatacagttcttatatggattttttatatgccact...

Basic information

species Zea mays
transcript GRMZM2G164562_T01
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G164562_T01 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os03g14990.1 (Oryza sativa), 5'ss of exon 2
ATGGCGAATCCCATGGAGGGGGTGTTGGTTGCGTTATCAGTGGCTGCCCACCCAGAATTCCTCTCACTGAGGCAGACATGCAAGTAGAACTCGATAGAAGgtgtgtctctta-------------ctctcttccacatattagttttaagttattactagtttactaaaatctagcataatacagttcttata---tggattttttatatgccact-----------------------------------------
|||| || || |||||||| |||||||||||||| |||||||| |||||||||||||| || || ||||| ||||| |||||||||||||||||  | |||| ||||||||               ||| | |       | | ||      |  ||  | |||   ||||  |         |  ||||  |   |    || |||| |  || |                                         
ATGGAGAGTCTCATGGAGGCGGTGTTGGTTGCGTAATCAGTGGATGCCCACCCAGAATCCCACTTACTGAAGCAGATATGCAAGTAGAACTCGACCGGAGgtttgtctcttgaaaaatccattatttctgtgctgacagctggcttctgtcaaaaacaggattatgcaaatgcaatcctgctaacctcttgcagaatatgattgttatgttacattacaccataatgttaactgacataaaattttgattatcacag
















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|211165638|gb|FL126857.1|FL126857
EST:     CCAGAATTCCTCTCACTGAGGCAGACATGCAAGTAGAACTCGAATAGAAG                         ACGTCCGGGTCAAAGTANAATTACAACCCCAAGAAAGGAGACTGATACAT
genomic: CCAGAATTCCTCTCACTGAGGCAGACATGCAAGTAGAACTCGA-TAGAAGgtgtgtctct ... atttatacagACGTCCGGGTCAAAGTAGAATTACAACCCCAAGAAAGGAGACTGATACAT
EST: gi|211165636|gb|FL126855.1|FL126855
EST:     CCCAGAATTCCTCTCACTGAGGCAGACATGCAAGTAGAACTCGATAGAAG                         ACGTCCGGGTCAAAGTAGAATTACAACCCCAAGAAAGGAGACTGATACATG
genomic: CCCAGAATTCCTCTCACTGAGGCAGACATGCAAGTAGAACTCGATAGAAGgtgtgtctct ... atttatacagACGTCCGGGTCAAAGTAGAATTACAACCCCAAGAAAGGAGACTGATACATG
EST: gi|149088514|gb|EE177624.2|EE177624
EST:     CCCAGAATTCCTCTCACTGAGGCAGACATGCAAGTAGAACTCGATAGAAG                         ACGTCCGGGTCAAAGTAGAATTACAACCCCAAGAAAGGAGACTGATACATG
genomic: CCCAGAATTCCTCTCACTGAGGCAGACATGCAAGTAGAACTCGATAGAAGgtgtgtctct ... atttatacagACGTCCGGGTCAAAGTAGAATTACAACCCCAAGAAAGGAGACTGATACATG
EST: gi|28361588|gb|CB239944.1|CB239944
EST:     CCCAGAATTCCTCTCACTGAGGCAGACATGCAAGTAGAACTCGATAGAAG                         ACGTCCGGGTCAAAGTAGAATTACAACCCCAAGAAAGGAGACTGATACATG
genomic: CCCAGAATTCCTCTCACTGAGGCAGACATGCAAGTAGAACTCGATAGAAGgtgtgtctct ... atttatacagACGTCCGGGTCAAAGTAGAATTACAACCCCAAGAAAGGAGACTGATACATG
EST: gi|211165635|gb|FL126854.1|FL126854
EST:     CCCAGAATTCCTCTCACTGAGGCAGACATGCAAGTAGAACTCGATAGAAG                         ACGTCCGGGTCAAAGTAGAATTACAACCCCAAGAAAGGAGACTGATACATG
genomic: CCCAGAATTCCTCTCACTGAGGCAGACATGCAAGTAGAACTCGATAGAAGgtgtgtctct ... atttatacagACGTCCGGGTCAAAGTAGAATTACAACCCCAAGAAAGGAGACTGATACATG
EST: gi|149070137|gb|EE158538.2|EE158538
EST:     CCCAGAATTCCTCTCACTGAGGCAGACATGCAAGTAGAACTCGATAGAAG                         ACGTCCGGGTCAAAGTAGAATTACAACCCCAAGAAAGGAGACTGATACATG
genomic: CCCAGAATTCCTCTCACTGAGGCAGACATGCAAGTAGAACTCGATAGAAGgtgtgtctct ... atttatacagACGTCCGGGTCAAAGTAGAATTACAACCCCAAGAAAGGAGACTGATACATG
EST: gi|211165641|gb|FL126860.1|FL126860
EST:     CCCAGAATTCCTCTCACTGAGGCAGACATGCAAGTAGAACTCGATAGAAG                         ACGTCCGGGTCAAAGTAGAATTACAACCCCAAGAAAGGAGACTGATACATG
genomic: CCCAGAATTCCTCTCACTGAGGCAGACATGCAAGTAGAACTCGATAGAAGgtgtgtctct ... atttatacagACGTCCGGGTCAAAGTAGAATTACAACCCCAAGAAAGGAGACTGATACATG
EST: gi|211165634|gb|FL126853.1|FL126853
EST:     CCCAGAATTCCTCTCACTGAGGCAGACATGCAAGTAGAACTCGATAGAAG                         ACGTCCGGGTCAAAGTAGAATTACAACCCCAAGAAAGGAGACTGATACATG
genomic: CCCAGAATTCCTCTCACTGAGGCAGACATGCAAGTAGAACTCGATAGAAGgtgtgtctct ... atttatacagACGTCCGGGTCAAAGTAGAATTACAACCCCAAGAAAGGAGACTGATACATG
EST: gi|211062099|gb|FL126842.1|FL126842
EST:     CCCAGAATTCCTCTCACTGAGGCAGACATGCAAGTAGAACTCGATAGAAG                         ACGTCCGGGTCAAAGTAGAATTACAACCCCAAGAAAGGAGACTGATACATG
genomic: CCCAGAATTCCTCTCACTGAGGCAGACATGCAAGTAGAACTCGATAGAAGgtgtgtctct ... atttatacagACGTCCGGGTCAAAGTAGAATTACAACCCCAAGAAAGGAGACTGATACATG
EST: gi|76020355|gb|DT947525.1|DT947525
EST:     CCCAGAATTCCTCTCACTGAGGCAGACATGCAAGTAGAACTCGATAGAAG                         ACGTCCGGGTCAAAGTAGAATTACAACCCCAAGAAAGGAGACTGATACATG
genomic: CCCAGAATTCCTCTCACTGAGGCAGACATGCAAGTAGAACTCGATAGAAGgtgtgtctct ... atttatacagACGTCCGGGTCAAAGTAGAATTACAACCCCAAGAAAGGAGACTGATACATG
EST: gi|211165637|gb|FL126856.1|FL126856
EST:     CCCAGAATTCCTCTCACTGAGGCAGACATGCAAGTAGAACTCGATAGAAG                         ACGTCCGGGTCAAAGTAGAATTACAACCCCAAGAAAGGAGACTGATACATG
genomic: CCCAGAATTCCTCTCACTGAGGCAGACATGCAAGTAGAACTCGATAGAAGgtgtgtctct ... atttatacagACGTCCGGGTCAAAGTAGAATTACAACCCCAAGAAAGGAGACTGATACATG
EST: gi|211062105|gb|FL126848.1|FL126848
EST:     CCCAGAATTCCTCTCACTGAGGCAGACATGCAAGTAGAACTCGATAGAAG                         ACGTCCGGGTCAAAGTAGAATTACAACCCCAAGAAAGGAGACTGATACATG
genomic: CCCAGAATTCCTCTCACTGAGGCAGACATGCAAGTAGAACTCGATAGAAGgtgtgtctct ... atttatacagACGTCCGGGTCAAAGTAGAATTACAACCCCAAGAAAGGAGACTGATACATG
EST: gi|149015775|gb|EE045474.2|EE045474
EST:     CCCAGAATTCCTCTCACTGAGGCAGACATGCAAGTAGAACTCGATAGAAG                         ACGTCCGGGTCAAAGTAGAATTACAACCCCAAGAAAGGAGACTGATACATG
genomic: CCCAGAATTCCTCTCACTGAGGCAGACATGCAAGTAGAACTCGATAGAAGgtgtgtctct ... atttatacagACGTCCGGGTCAAAGTAGAATTACAACCCCAAGAAAGGAGACTGATACATG
EST: gi|71442663|gb|DR823713.1|DR823713
EST:     CCCAGAATTCCTCTCACTGAGGCAGACATGCAAGTAGAACTCGATAGAAG                         ACGTCCGGGTCAAAGTAGAATTACAACCCCAAGAAAGGAGACTGATACATG
genomic: CCCAGAATTCCTCTCACTGAGGCAGACATGCAAGTAGAACTCGATAGAAGgtgtgtctct ... atttatacagACGTCCGGGTCAAAGTAGAATTACAACCCCAAGAAAGGAGACTGATACATG
EST: gi|37424877|gb|CF650172.1|CF650172
EST:     CCCAGAATTCCTCTCACTGAGGCAGACATGCAAGTAGAACTCGATAGAAG                         ACGTCCGGGTCAAAGTAGAATTACAACCCCAAGAAAGGAGACTGATACATG
genomic: CCCAGAATTCCTCTCACTGAGGCAGACATGCAAGTAGAACTCGATAGAAGgtgtgtctct ... atttatacagACGTCCGGGTCAAAGTAGAATTACAACCCCAAGAAAGGAGACTGATACATG
EST: gi|211062107|gb|FL126850.1|FL126850
EST:     CCCAGAATTCCTCTCACTGAGGCAGACATGCAAGTAGAACTCGATAGAAG                         ACGTCCGGGTCAAAGTAGAATTACAACCCCAAGAAAGGAGACTGATACATG
genomic: CCCAGAATTCCTCTCACTGAGGCAGACATGCAAGTAGAACTCGATAGAAGgtgtgtctct ... atttatacagACGTCCGGGTCAAAGTAGAATTACAACCCCAAGAAAGGAGACTGATACATG
EST: gi|148963945|gb|EE015067.2|EE015067
EST:     CCCAGAATTCCTCTCACTGAGGCAGACATGCAAGTAGAACTCGATAGAAG                         ACGTCCGGGTCAAAGTAGAATTACAACCCCAAGAAAGGAGACTGATACATG
genomic: CCCAGAATTCCTCTCACTGAGGCAGACATGCAAGTAGAACTCGATAGAAGgtgtgtctct ... atttatacagACGTCCGGGTCAAAGTAGAATTACAACCCCAAGAAAGGAGACTGATACATG
EST: gi|211062101|gb|FL126844.1|FL126844
EST:     CCCAGAATTCCTCTCACTGAGGCAGACATGCAAGTAGAACTCGATAGAAG                         ACGTCCGGGTCAAAGTAGAATTACAACCCCAAGAAAGGAGACTGATACATG
genomic: CCCAGAATTCCTCTCACTGAGGCAGACATGCAAGTAGAACTCGATAGAAGgtgtgtctct ... atttatacagACGTCCGGGTCAAAGTAGAATTACAACCCCAAGAAAGGAGACTGATACATG
EST: gi|28390366|gb|CB250180.1|CB250180
EST:     CCCAGAATTCCTCTCACTGAGGCAGACATGCAAGTAGAACTCGATAGAAG                         A
genomic: CCCAGAATTCCTCTCACTGAGGCAGACATGCAAGTAGAACTCGATAGAAGgtgtgtctct ... atttatacag-
EST: gi|28390366|gb|CB250180.1|CB250180
EST:     CCCAGAATTCCTCTCACTGAGGCAGACATGCAAGTAGAACTCGATAGAAG                         A
genomic: CCCAGAATTCCTCTCACTGAGGCAGACATGCAAGTAGAACTCGATAGAAGgtgtgtctct ... atttatacag-
EST: gi|78089034|gb|DV517427.1|DV517427
EST:     CCCAGAATTCCTCTCACTGAGGCAGACATGCAAGTAGAACTCGATAGAAG                         ACGTCCGGGTCAAAGTAGAATTACAACCCCAAGAAAGGAGACTGATACATG
genomic: CCCAGAATTCCTCTCACTGAGGCAGACATGCAAGTAGAACTCGATAGAAGgtgtgtctct ... atttatacagACGTCCGGGTCAAAGTAGAATTACAACCCCAAGAAAGGAGACTGATACATG
EST: gi|211165640|gb|FL126859.1|FL126859
EST:     CCCAGAATTCCTCTCACTGAGGCAGACATGCAAGTAGAACTCGATAGAAG                         ACGTCCGGGTCAAAGTAGAATTACAACCCCAAGAWAGGAGACTGATACATG
genomic: CCCAGAATTCCTCTCACTGAGGCAGACATGCAAGTAGAACTCGATAGAAGgtgtgtctct ... atttatacagACGTCCGGGTCAAAGTAGAATTACAACCCCAAGAAAGGAGACTGATACATG
EST: gi|149100015|gb|EE186068.2|EE186068
EST:     CCCAGAATTCCTCTCACTGAGGCAGACATGCAAGTAGAACTCGATAGAAG                         ACGTCCGGGTCAAAGTAGAATTACAACCCCAAGAAAGGAGACTGATACATG
genomic: CCCAGAATTCCTCTCACTGAGGCAGACATGCAAGTAGAACTCGATAGAAGgtgtgtctct ... atttatacagACGTCCGGGTCAAAGTAGAATTACAACCCCAAGAAAGGAGACTGATACATG
EST: gi|148966882|gb|EE018003.2|EE018003
EST:     CCCAGAATTCCTCTCACTGAGGCAGACATGCAAGTAGAACTCGATAGAAG                         ACGTCCGGGTCAAAGTAGAATTACAACCCCAAGAAAGGAGACTGATACATG
genomic: CCCAGAATTCCTCTCACTGAGGCAGACATGCAAGTAGAACTCGATAGAAGgtgtgtctct ... atttatacagACGTCCGGGTCAAAGTAGAATTACAACCCCAAGAAAGGAGACTGATACATG
EST: gi|211165639|gb|FL126858.1|FL126858
EST:     CCCAGAATTCCTCTCACTGAGGCAGACATGCAAGTAGAACTCGATAGAAG                         ACGTCCGGGTCAAAGTAGAATTACAACCCCAAGAAAGGAGACTGATACATG
genomic: CCCAGAATTCCTCTCACTGAGGCAGACATGCAAGTAGAACTCGATAGAAGgtgtgtctct ... atttatacagACGTCCGGGTCAAAGTAGAATTACAACCCCAAGAAAGGAGACTGATACATG

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 4 RNA-Seq libraries.


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 238

ATGGCGAATCCCATGGAGGGGGTGTTGGTTGCGTTATCAGTGGCTGCCCACCCAGAATTCCTCTCACTGAGGCAGACATGCAAGTAGAACTCGATAGAAGgtgtgtctct ... atttatacagACGTCCGGGTCAAAGTAGAATTACAACCCCAAGAAAGGAGACTGATACATGCAAAATTCTATCAGGGACACATGATG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 580

ATGGCGAATCCCATGGAGGGGGTGTTGGTTGCGTTATCAGTGGCTGCCCACCCAGAATTCCTCTCACTGAGGCAGACATGCAAGTAGAACTCGATAGAAGgtgtgtctct ... atttatacagACGTCCGGGTCAAAGTAGAATTACAACCCCAAGAAAGGAGACTGATACATGCAAAATTCTATCAGGGACACATGATG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 578

ATGGCGAATCCCATGGAGGGGGTGTTGGTTGCGTTATCAGTGGCTGCCCACCCAGAATTCCTCTCACTGAGGCAGACATGCAAGTAGAACTCGATAGAAGgtgtgtctct ... atttatacagACGTCCGGGTCAAAGTAGAATTACAACCCCAAGAAAGGAGACTGATACATGCAAAATTCTATCAGGGACACATGATG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 656

ATGGCGAATCCCATGGAGGGGGTGTTGGTTGCGTTATCAGTGGCTGCCCACCCAGAATTCCTCTCACTGAGGCAGACATGCAAGTAGAACTCGATAGAAGgtgtgtctct ... atttatacagACGTCCGGGTCAAAGTAGAATTACAACCCCAAGAAAGGAGACTGATACATGCAAAATTCTATCAGGGACACATGATG