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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGCTTCAGCAGAAACAGAAAATAGGCCATTGCCTCTGTCGCACACTAGCAATGATGTCCGTGCATTAAGAATAAGTGATTTCATACATGCGCATGAACAGgtatgatcttatataagtattaacttcggattcatttattttgacactagtttgtccttctgccagttgaaattctttattatgatattaacgattacat...

Basic information

species Zea mays
transcript GRMZM2G042074_T02
intron # 22
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G042074_T02 (Zea mays), 5'ss of exon 22
lower sequence: LOC_Os03g22420.1 (Oryza sativa), 5'ss of exon 27
AGCTTCAGCAGAAACAGAAAATAGGCCATTGCCTCTGTCGCACACTAGCAATGATGTCCGTGCATTAAGAATAAGTGATTTCATACATGCGCATGAACAGgtatgatcttatataagtattaacttcggattcatttattttgacactagtttgtccttctgccagt-tgaaattctttattatgatattaacgattacat
||||| ||||||  |||||||||||||  |||| |  ||     | || || ||||||||||| ||| || |||||||||||| |||||| |||||||||||||||||    |||| ||  ||||| |  ||||  || |    |  |  | |       | | |   |||  ||  || |||      | |       ||
AGCTTTAGCAGAGGCAGAAAATAGGCCGCTGCCCCAATCATTTTCAAGTAACGATGTCCGTGCCTTACGACTAAGTGATTTCAAACATGCTCATGAACAGgtatgatccataataaataagaactt-gctttcaagtactcgtgctgtgatgtacatacatactaccatgatttttcttgttaaatgcctgaatcaagaat
















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|60672183|gb|DN474952.1|DN474952
EST:     ATGATGTCCGTGCATTAAGAATAAGTGATTTCATACATGCGCATGAACAG                         GTGTGTGCAAGTGTTTCCTCAGATTCCAGTAACATGAACGAGCTTGTGCAA
genomic: ATGATGTCCGTGCATTAAGAATAAGTGATTTCATACATGCGCATGAACAGgtatgatctt ... tttcttgtagGTGTGTGCAAGTGTTTCCTCAGATTCCAGTAACATGAACGAGCTTGTGCAA
EST: gi|32936435|gb|CF041254.1|CF041254
EST:     ATGATGTCCGTGCATTAAGAATAAGTGATTTCATACATGCGCATGAACAG                         GTGTGTGCAAGTGTTTCCTCAGATTCCAGTAACATGAACGAGCTTGTGCAA
genomic: ATGATGTCCGTGCATTAAGAATAAGTGATTTCATACATGCGCATGAACAGgtatgatctt ... tttcttgtagGTGTGTGCAAGTGTTTCCTCAGATTCCAGTAACATGAACGAGCTTGTGCAA
EST: gi|211424429|gb|FK972466.1|FK972466
EST:     ATGATGTCCGTGCATTAAGAATAAGTGATTTCATACATGCGCATGAACAG                         GTGTGTGCAAGTGTTTCCTCAGATTCCAGTAACATGAACGAGCTTGTGCAA
genomic: ATGATGTCCGTGCATTAAGAATAAGTGATTTCATACATGCGCATGAACAGgtatgatctt ... tttcttgtagGTGTGTGCAAGTGTTTCCTCAGATTCCAGTAACATGAACGAGCTTGTGCAA
EST: gi|6828013|gb|AW331656.1|AW331656
EST:     ATGATGTCCGTGCATTAAGAATAAGTGATTTCATACATGCACATGAACAG                         GTGTGTGCAAGTGTTTCCTCAGATTCCAGTAACATGAACGAGCTTGTGCAA
genomic: ATGATGTCCGTGCATTAAGAATAAGTGATTTCATACATGCGCATGAACAGgtatgatctt ... tttcttgtagGTGTGTGCAAGTGTTTCCTCAGATTCCAGTAACATGAACGAGCTTGTGCAA
EST: gi|7238135|gb|AW573357.1|AW573357
EST:     ATGATGTCCGTGCATTAAGAATAAGTGATTTCATACATGCGCATGAACAG                         GTGTGTGCAAGTGTTTCCTCAGATTCCAGTAACATGAACGAGCTTGTGCAA
genomic: ATGATGTCCGTGCATTAAGAATAAGTGATTTCATACATGCGCATGAACAGgtatgatctt ... tttcttgtagGTGTGTGCAAGTGTTTCCTCAGATTCCAGTAACATGAACGAGCTTGTGCAA
EST: gi|19770017|gb|BQ034738.1|BQ034738
EST:     ATGATGTCCGTGCATTAAGAATAAGTGATTTCATACATGCGCATGAACAG                         GTGTGTGCAAGTGTTTCCTCAGATTCCAGTAACATGAGCGAGCTTGTGCAA
genomic: ATGATGTCCGTGCATTAAGAATAAGTGATTTCATACATGCGCATGAACAGgtatgatctt ... tttcttgtagGTGTGTGCAAGTGTTTCCTCAGATTCCAGTAACATGAACGAGCTTGTGCAA
EST: gi|7227796|gb|AW566437.1|AW566437
EST:     ATGATGTCCGTGCATTAAGAATAAGTGATTTCATACATGCGCATGAACAG                         GTGTGTGCAAGTGTTTCCTCAGATTCCAGTAACATGAACGAGCTTGTGCAA
genomic: ATGATGTCCGTGCATTAAGAATAAGTGATTTCATACATGCGCATGAACAGgtatgatctt ... tttcttgtagGTGTGTGCAAGTGTTTCCTCAGATTCCAGTAACATGAACGAGCTTGTGCAA
EST: gi|6536570|gb|AW224883.1|AW224883
EST:     ATGATGTCCGTGCATTAAGAATAAGTGATTTCATACATGCACATGAACAG                         GTGTGTGCAAGTGTTTCCTCAGATTCCAGTAACATGAACGAGCTTGTGCAA
genomic: ATGATGTCCGTGCATTAAGAATAAGTGATTTCATACATGCGCATGAACAGgtatgatctt ... tttcttgtagGTGTGTGCAAGTGTTTCCTCAGATTCCAGTAACATGAACGAGCTTGTGCAA
EST: gi|20506891|gb|BQ279387.1|BQ279387
EST:     ATGATGTCCGTGCATTAAGAATAAGTGATTTCATACATGCGCATGAACAG                         GTGTGTGCAAGTGTTTCCTCAGATTCCAGTAACATGAACGAGCTTGTGCAA
genomic: ATGATGTCCGTGCATTAAGAATAAGTGATTTCATACATGCGCATGAACAGgtatgatctt ... tttcttgtagGTGTGTGCAAGTGTTTCCTCAGATTCCAGTAACATGAACGAGCTTGTGCAA
EST: gi|33096896|gb|CF056856.1|CF056856
EST:     ATGATGTCCGTGCATTAAGAATAAGTGATTTCATACATGCGCATGAACAG                         GTGTGTGCAAGTGTTTCCTCAGATTCCAGTAACATGAACGAGCTTGTGCAA
genomic: ATGATGTCCGTGCATTAAGAATAAGTGATTTCATACATGCGCATGAACAGgtatgatctt ... tttcttgtagGTGTGTGCAAGTGTTTCCTCAGATTCCAGTAACATGAACGAGCTTGTGCAA
EST: gi|26456741|gb|CA828324.1|CA828324
EST:     ATGATGTCCGTGCATTAAGAATAAGTGATTTCATACATGCGCATGAACAG                         GTGTGTGCAAGTGTTTCCTCAGATTCCAGTAACATGAACGAGCTTGTGCAA
genomic: ATGATGTCCGTGCATTAAGAATAAGTGATTTCATACATGCGCATGAACAGgtatgatctt ... tttcttgtagGTGTGTGCAAGTGTTTCCTCAGATTCCAGTAACATGAACGAGCTTGTGCAA
EST: gi|22819410|gb|BU499500.1|BU499500
EST:     ATGATGTCCGTGCATTAAGAATAAGTGATTTCATACATGCGCATGAACAG                         GTGTGTGCAAGTGTTTCCTCAGATTCCAGTAACATGAACGAGCTTGTGCAA
genomic: ATGATGTCCGTGCATTAAGAATAAGTGATTTCATACATGCGCATGAACAGgtatgatctt ... tttcttgtagGTGTGTGCAAGTGTTTCCTCAGATTCCAGTAACATGAACGAGCTTGTGCAA

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: 45 (upstream exon), 49 (downstream exon)
Score: 93

AGCTTCAGCAGAAACAGAAAATAGGCCATTGCCTCTGTCGCACACTAGCAATGATGTCCGTGCATTAAGAATAAGTGATTTCATACATGCGCATGAACAGgtatgatctt ... tttcttgtagGTGTGTGCAAGTGTTTCCTCAGATTCCAGTAACATGAACGAGCTTGTGCAATGGAATGATCTCTATGGAGAAGGCGGGTCAAGGAAAAAGACAACGCTAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 147

AGCTTCAGCAGAAACAGAAAATAGGCCATTGCCTCTGTCGCACACTAGCAATGATGTCCGTGCATTAAGAATAAGTGATTTCATACATGCGCATGAACAGgtatgatctt ... tttcttgtagGTGTGTGCAAGTGTTTCCTCAGATTCCAGTAACATGAACGAGCTTGTGCAATGGAATGATCTCTATGGAGAAGGCGGGTCAAGGAAAAAGACAACGCTAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 108

AGCTTCAGCAGAAACAGAAAATAGGCCATTGCCTCTGTCGCACACTAGCAATGATGTCCGTGCATTAAGAATAAGTGATTTCATACATGCGCATGAACAGgtatgatctt ... tttcttgtagGTGTGTGCAAGTGTTTCCTCAGATTCCAGTAACATGAACGAGCTTGTGCAATGGAATGATCTCTATGGAGAAGGCGGGTCAAGGAAAAAGACAACGCTAA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 198

AGCTTCAGCAGAAACAGAAAATAGGCCATTGCCTCTGTCGCACACTAGCAATGATGTCCGTGCATTAAGAATAAGTGATTTCATACATGCGCATGAACAGgtatgatctt ... tttcttgtagGTGTGTGCAAGTGTTTCCTCAGATTCCAGTAACATGAACGAGCTTGTGCAATGGAATGATCTCTATGGAGAAGGCGGGTCAAGGAAAAAGACAACGCTAA