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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGATCCTGGTGCTGAACAAAAGTTCAAGGATATCAGTAATGCTTATGAGgttgggcccactgttcatactcaactccaaaatccaaattccattttcggtagtaggattacacatttatttatgcttacgtagaaaggatgtctgtag

Basic information

species Zea mays
transcript GRMZM5G856084_T01
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G856084_T01 (Zea mays), 5'ss of exon 6
lower sequence: LOC_Os05g26914.1 (Oryza sativa), 5'ss of exon 6
AGATCCTGGTGCTGAACAAAAGTTCAAGGATATCAGTAATGCTTATGAGgttgggcccactgttcatactcaactccaaaatccaaattccatt-ttcggtagtaggattacacatttatttatgcttacgtagaaaggatgtctgtag
||||||||||||||||||||||||||||||||| || ||||||||||||||| | ||  ||   ||||  ||| ||| |        |   | | |   || ||||| |||||  |   |    ||| || || | |||||  | |   
AGATCCTGGTGCTGAACAAAAGTTCAAGGATATTAGCAATGCTTATGAGgttagtccagctaaccataaccaaatcccattgtttcttatgactatgttgttgtagggttacaggtgcttgccagctaacataaataggattgcag---
















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|61119026|gb|DN559987.1|DN559987
EST:     AGATCCTGGTGCTGAACAAAAGTTCAAGGATATCAGTAATGCTTATGAG                         GTTCTGTCTGATGATGAGAAGCGATCGATCTATGATAAATATGGAGAAGCA
genomic: AGATCCTGGTGCTGAACAAAAGTTCAAGGATATCAGTAATGCTTATGAGgttgggccca ... atgtctgtagGTTCTGTCTGATGATGAGAAGCGATCGATCTATGATAAATATGGAGAAGCA
EST: gi|148950667|gb|EC896255.2|EC896255
EST:     AGATCCTGGTGCTGAACAAAAGTTCAAGGATATCAGTAATGCTTATGAG                         GTTCTGTCTGATGATGAGAAGCGATCGATCTATGATAAATATGGAGAAGCA
genomic: AGATCCTGGTGCTGAACAAAAGTTCAAGGATATCAGTAATGCTTATGAGgttgggccca ... atgtctgtagGTTCTGTCTGATGATGAGAAGCGATCGATCTATGATAAATATGGAGAAGCA
EST: gi|148955679|gb|EC901358.2|EC901358
EST:     AGATCCTGGTGCTGAACAAAAGTTCAAGGATATCAGTAATGCTTATGAG                         GTTCTGTCTGATGATGAGAAGCGATCGATCTATGATAAATATGGAGAAGCA
genomic: AGATCCTGGTGCTGAACAAAAGTTCAAGGATATCAGTAATGCTTATGAGgttgggccca ... atgtctgtagGTTCTGTCTGATGATGAGAAGCGATCGATCTATGATAAATATGGAGAAGCA
EST: gi|211525859|gb|FL340350.1|FL340350
EST:     AGATCCTGGTGCTGAACAAAAGTTCAAGGATATCAGTAATGCTTATGAG                         GTTCTGTCTGATGATGAGAAGCGATCGATCTATGATAAATATGGAGAAGCA
genomic: AGATCCTGGTGCTGAACAAAAGTTCAAGGATATCAGTAATGCTTATGAGgttgggccca ... atgtctgtagGTTCTGTCTGATGATGAGAAGCGATCGATCTATGATAAATATGGAGAAGCA
EST: gi|149051735|gb|EE155859.2|EE155859
EST:     AGATCCTGGTGCTGAACAAAAGTTCAAGGATATCAGTAATGCTTATGAG                         GTTCTGTCTGATGATGAGAAGCGATCGATCTATGATAAATATGGAGAAGCA
genomic: AGATCCTGGTGCTGAACAAAAGTTCAAGGATATCAGTAATGCTTATGAGgttgggccca ... atgtctgtagGTTCTGTCTGATGATGAGAAGCGATCGATCTATGATAAATATGGAGAAGCA
EST: gi|211152737|gb|FL348042.1|FL348042
EST:     AGATCCTGGTGCTGAACAAAAGTTCAAGGATATCAGTAATGCTTATGAG                         GTTCTGTCTGATGATGAGAAGCGATCGATCTATGATAAATATGGAGAAGCA
genomic: AGATCCTGGTGCTGAACAAAAGTTCAAGGATATCAGTAATGCTTATGAGgttgggccca ... atgtctgtagGTTCTGTCTGATGATGAGAAGCGATCGATCTATGATAAATATGGAGAAGCA
EST: gi|71769003|gb|DR966940.1|DR966940
EST:     AGATCCTGGTGCTGAACAAAAGTTCAAGGATATCAGTAATGCTTATGAG                         GTTCTGTCTGATGATGAGAAGCGATCGATCTATGATAAATATGGAGAAGCA
genomic: AGATCCTGGTGCTGAACAAAAGTTCAAGGATATCAGTAATGCTTATGAGgttgggccca ... atgtctgtagGTTCTGTCTGATGATGAGAAGCGATCGATCTATGATAAATATGGAGAAGCA

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: 151

AGATCCTGGTGCTGAACAAAAGTTCAAGGATATCAGTAATGCTTATGAGgttgggccca ... atgtctgtagGTTCTGTCTGATGATGAGAAGCGATCGATCTATGATAAATATGGAGAAGCAGGTCTGAAGGGTGCTGGCATGGGCACAGGA


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 279

AGATCCTGGTGCTGAACAAAAGTTCAAGGATATCAGTAATGCTTATGAGgttgggccca ... atgtctgtagGTTCTGTCTGATGATGAGAAGCGATCGATCTATGATAAATATGGAGAAGCAGGTCTGAAGGGTGCTGGCATGGGCACAGGA


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 85

AGATCCTGGTGCTGAACAAAAGTTCAAGGATATCAGTAATGCTTATGAGgttgggccca ... atgtctgtagGTTCTGTCTGATGATGAGAAGCGATCGATCTATGATAAATATGGAGAAGCAGGTCTGAAGGGTGCTGGCATGGGCACAGGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 159

AGATCCTGGTGCTGAACAAAAGTTCAAGGATATCAGTAATGCTTATGAGgttgggccca ... atgtctgtagGTTCTGTCTGATGATGAGAAGCGATCGATCTATGATAAATATGGAGAAGCAGGTCTGAAGGGTGCTGGCATGGGCACAGGA