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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GATAATATTCAGTCCACTATGGCTCTTTCATGGTATTGTTGCACGCGGAAGGTTTTCAATGCCTGCCCCTTCTTTGCCTCATGGCCGTCATgtgagatttacatatcggcttgtctattaaaactgaccttctcactgtttgcattaccattgttcattttgcatccaattagcctgatatgtttattttcttctttcag

Basic information

species Zea mays
transcript GRMZM2G024690_T02
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G024690_T03 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os03g49900.1 (Oryza sativa), 5'ss of exon 2
GATAATATTCAGTCCACTATGGCTCTTTCATGGTATTGTTGCACGCGGAAGGTTTTCAATGCCTGCCCCTTCTTTGCCTCATGGCCGTCATgtgagatttacatatcggcttgtcta-ttaaaactgaccttctcactgtttgcattaccattgttcattttgcatccaattagcctgatatgtttattttcttctttcag
||| |||||||  || |||||||| |||||||| |||||||| || ||||||||||||||||| ||||||||  | ||||||||||||||||| ||| ||   ||||   || |||| |||  |   || | || ||      ||||    ||| ||   | |  | | ||| |  ||                       
GATTATATTCATCCCTCTATGGCTATTTCATGGCATTGTTGCCCGTGGAAGGTTTTCAATGCCAGCCCCTTCGCTTCCTCATGGCCGTCATgtaagaattg-gtatcaatttctctagttagtatgcacgtgcttacc--ccacatt----ttgatctgatgggtttctatttgtatgtag--------------------
















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|211453578|gb|FL021062.1|FL021062
EST:     CACGCGGAAGGTTTTCAATGCCTGCCCCTTCTTTGCCTCATGGCCGTCAT                         TGGGCACCATGTCATTCGATTGTTGCGGCGCCTTTACTAATTGCGTTCGAG
genomic: CACGCGGAAGGTTTTCAATGCCTGCCCCTTCTTTGCCTCATGGCCGTCATgtgagattta ... cttctttcagTGGGCACCATGTCATTCGATTGTTGCGGCGCCTTTACTAATTGCGTTCGAG
EST: gi|148938797|gb|EC883136.2|EC883136
EST:     CACGCGGAAGGTTTTCAATGCCTGCCCCTTCTTTGCCTCATGGCCGTCAT                         TGGGCACCATGTCATTCGATTGTTGCGGCGCCTTTACTAATTGCGTTCGAG
genomic: CACGCGGAAGGTTTTCAATGCCTGCCCCTTCTTTGCCTCATGGCCGTCATgtgagattta ... cttctttcagTGGGCACCATGTCATTCGATTGTTGCGGCGCCTTTACTAATTGCGTTCGAG
EST: gi|149070957|gb|EE159363.2|EE159363
EST:     CACGCGGAAGGTTTTCAATGCCTGCCCCTTCTTTGCCTCATGGCCGTCAT                         TGGGCACCATGTCATTCGATTGTTGCGGCGCCTTTACTAATTGCGTTCGAG
genomic: CACGCGGAAGGTTTTCAATGCCTGCCCCTTCTTTGCCTCATGGCCGTCATgtgagattta ... cttctttcagTGGGCACCATGTCATTCGATTGTTGCGGCGCCTTTACTAATTGCGTTCGAG
EST: gi|88756990|gb|DY541131.1|DY541131
EST:     CACGCGGAAGGTTTTCAATGCCTGCCCCTTCTTTGCCTCATGGCCGTCAT                         TGGGCACCATGTCATTCGATTGTTGCGGCGCCTTTACTAATTGCGTTCGAG
genomic: CACGCGGAAGGTTTTCAATGCCTGCCCCTTCTTTGCCTCATGGCCGTCATgtgagattta ... cttctttcagTGGGCACCATGTCATTCGATTGTTGCGGCGCCTTTACTAATTGCGTTCGAG
EST: gi|211453584|gb|FL021068.1|FL021068
EST:     CACGCGGAAGGTTTTCAATGCCTGCCCCTTCTTTGCCTCATGGCCGTCAT                         TGGGCACCATGTCATTCGATTGTTGCGGCGCCTTTACTAATTGCGTTCGAG
genomic: CACGCGGAAGGTTTTCAATGCCTGCCCCTTCTTTGCCTCATGGCCGTCATgtgagattta ... cttctttcagTGGGCACCATGTCATTCGATTGTTGCGGCGCCTTTACTAATTGCGTTCGAG
EST: gi|148931986|gb|EC875260.2|EC875260
EST:     CACGCGGAAGGTTTTCAATGCCTGCCCCTTCTTTGCCTCATGGCCGTCAT                         TGGGCACCATGTCATTCGATTGTTGCGGCGCCTTTACTAATTGCGTTCGAG
genomic: CACGCGGAAGGTTTTCAATGCCTGCCCCTTCTTTGCCTCATGGCCGTCATgtgagattta ... cttctttcagTGGGCACCATGTCATTCGATTGTTGCGGCGCCTTTACTAATTGCGTTCGAG
EST: gi|91870315|gb|EB400812.1|EB400812
EST:     CACGCGGAAGGTTTTCAATGCCTGCCCCTTCTTTGCCTCATGGCCGTCAT                         TGGGCACCATGTCATTCGATTGTTGCGGCGCCTTTACTAATTGCGTTCGAG
genomic: CACGCGGAAGGTTTTCAATGCCTGCCCCTTCTTTGCCTCATGGCCGTCATgtgagattta ... cttctttcagTGGGCACCATGTCATTCGATTGTTGCGGCGCCTTTACTAATTGCGTTCGAG
EST: gi|211374151|gb|FL287201.1|FL287201
EST:     CACGCGGAAGGTTTTCAATGCCTGCCCCTTCTTTGCCTCATGGCCGTCAT                         TGGGCACCATGTCATTCGATTGTTGCGGCGCCTTTACTAATTGCGTTCGAG
genomic: CACGCGGAAGGTTTTCAATGCCTGCCCCTTCTTTGCCTCATGGCCGTCATgtgagattta ... cttctttcagTGGGCACCATGTCATTCGATTGTTGCGGCGCCTTTACTAATTGCGTTCGAG
EST: gi|78117592|gb|DV535979.1|DV535979
EST:     CACGCGGAAGGTTTTCAATGCCTGCCCCTTCTTTGCCTCATGGCCGTCAT                         TGGGCACCATGTCATTCGATTGTTGCGGCGCCTTTACTAATTGCGTTCGAG
genomic: CACGCGGAAGGTTTTCAATGCCTGCCCCTTCTTTGCCTCATGGCCGTCATgtgagattta ... cttctttcagTGGGCACCATGTCATTCGATTGTTGCGGCGCCTTTACTAATTGCGTTCGAG
EST: gi|149104180|gb|EE289614.2|EE289614
EST:     CACGCGGAAGGTTTTCAATGCCTGCCCCTTCTTTGCCTCATGGCCGTCAT                         TGGGCACCATGTCATTCGATTGTTGCGGCGCCTTTACTAATTGCGTTCGAG
genomic: CACGCGGAAGGTTTTCAATGCCTGCCCCTTCTTTGCCTCATGGCCGTCATgtgagattta ... cttctttcagTGGGCACCATGTCATTCGATTGTTGCGGCGCCTTTACTAATTGCGTTCGAG
EST: gi|211453580|gb|FL021064.1|FL021064
EST:     CACGCGGAAGGTTTTCAATGCCTGCCCCTTCTTTGCCTCATGGCCGTCAT                         TGGGCACCATGTCATTCGATTGTTGCGGCGCCTTTACTAATTGCGTTCGAG
genomic: CACGCGGAAGGTTTTCAATGCCTGCCCCTTCTTTGCCTCATGGCCGTCATgtgagattta ... cttctttcagTGGGCACCATGTCATTCGATTGTTGCGGCGCCTTTACTAATTGCGTTCGAG
EST: gi|211374152|gb|FL287202.1|FL287202
EST:     CACGCGGAAGGTTTTCAATGCCTGCCCCTTCTTTGCCTCATGGCCGTCAT                         TGGGCACCATGTCATTCGATTGTTGCGGCGCCTTTACTAATTGCGTTCGAG
genomic: CACGCGGAAGGTTTTCAATGCCTGCCCCTTCTTTGCCTCATGGCCGTCATgtgagattta ... cttctttcagTGGGCACCATGTCATTCGATTGTTGCGGCGCCTTTACTAATTGCGTTCGAG
EST: gi|211453582|gb|FL021066.1|FL021066
EST:     CACGCGGAAGGTTTTCAATGCCTGCCCCTTCTTTGCCTCATGGCCGTCAT                         TGGGCACCATGTCATTCGATTGTTGCGGCGCCTTTACTAATTGCGTTCGAG
genomic: CACGCGGAAGGTTTTCAATGCCTGCCCCTTCTTTGCCTCATGGCCGTCATgtgagattta ... cttctttcagTGGGCACCATGTCATTCGATTGTTGCGGCGCCTTTACTAATTGCGTTCGAG
EST: gi|211453583|gb|FL021067.1|FL021067
EST:     CACGCGGAAGGTTTTCAATGCCTGCCCCTTCTTTGCCTCATGGCCGTCAT                         TGGGCACCATGTCATTCGATTGTTGCGGCGCCTTTACTAATTGCGTTCGAG
genomic: CACGCGGAAGGTTTTCAATGCCTGCCCCTTCTTTGCCTCATGGCCGTCATgtgagattta ... cttctttcagTGGGCACCATGTCATTCGATTGTTGCGGCGCCTTTACTAATTGCGTTCGAG
EST: gi|211374159|gb|FL287209.1|FL287209
EST:     CACGCGGAAGGTTTTCAATGCCTGCCCCTTCTTTGCCTCATGGCCGTCAT                         TGGGCACCATGTCATTCGATTGTTGCGGCGCCTTTACTAATTGCGTTCGAG
genomic: CACGCGGAAGGTTTTCAATGCCTGCCCCTTCTTTGCCTCATGGCCGTCATgtgagattta ... cttctttcagTGGGCACCATGTCATTCGATTGTTGCGGCGCCTTTACTAATTGCGTTCGAG

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: 48 (upstream exon), 48 (downstream exon)
Score: 109

GATAATATTCAGTCCACTATGGCTCTTTCATGGTATTGTTGCACGCGGAAGGTTTTCAATGCCTGCCCCTTCTTTGCCTCATGGCCGTCATgtgagattta ... cttctttcagTGGGCACCATGTCATTCGATTGTTGCGGCGCCTTTACTAATTGCGTTCGAGCTGCTTCTTTGTATATATCTTGAAAGCATAAGAG


Block sizes: 48 (upstream exon), 47 (downstream exon)
Score: 76

GATAATATTCAGTCCACTATGGCTCTTTCATGGTATTGTTGCACGCGGAAGGTTTTCAATGCCTGCCCCTTCTTTGCCTCATGGCCGTCATgtgagattta ... cttctttcagTGGGCACCATGTCATTCGATTGTTGCGGCGCCTTTACTAATTGCGTTCGAGCTGCTTCTTTGTATATATCTTGAAAGCATAAGAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 63

GATAATATTCAGTCCACTATGGCTCTTTCATGGTATTGTTGCACGCGGAAGGTTTTCAATGCCTGCCCCTTCTTTGCCTCATGGCCGTCATgtgagattta ... cttctttcagTGGGCACCATGTCATTCGATTGTTGCGGCGCCTTTACTAATTGCGTTCGAGCTGCTTCTTTGTATATATCTTGAAAGCATAAGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 98

GATAATATTCAGTCCACTATGGCTCTTTCATGGTATTGTTGCACGCGGAAGGTTTTCAATGCCTGCCCCTTCTTTGCCTCATGGCCGTCATgtgagattta ... cttctttcagTGGGCACCATGTCATTCGATTGTTGCGGCGCCTTTACTAATTGCGTTCGAGCTGCTTCTTTGTATATATCTTGAAAGCATAAGAG