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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgggacctgtcttgaatgcacacgctattggtcacactatcgtatgaaaagtagttattatattagtttttgttgtctgatgtcagAAAGCAACAAAATGGTCTGAGAGAAGGGATGCTGTGGCAGAATTAACCAAGCTTGGTTCGGCAAAAAAAATTGCTCCTGGTGATTTTCATGAAATTTGCC

Basic information

species Zea mays
transcript GRMZM2G068755_T02
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G068755_T02 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os01g60040.1 (Oryza sativa), 3'ss of exon 8
gtatgggacctgtcttgaatgca-------cacgctattggtcacactatcgta-tgaaaagtagttattatattagt-------ttttgttgtctgatgtcagAAAGCAACAAAATGGTCTGAGAGAAGGGATGCTGTGGCAGAATTAACCAAGCTTGGTTCGGCAAAAAAAATTGCTCCTGGTGATTTTCATGAAATTTGCC
||||| |  |||  |||| ||||        ||  | |   |||||  ||  || |||||  | ||  |  | | | |       ||||||| ||||||  |||||||| || || |||||||| |||||||||||||| || ||  ||||||| |||| |||  | |||||||||||||| ||||||||||||||||| ||||
gtatgtg--ctgatttgagtgcagcattgatacattgtccatcacaacattatagtgaaatattgtcctcttttgaatgattctattttgttatctgataccagAAAGCTACCAAGTGGTCTGAAAGAAGGGATGCTGTTGCCGAGCTAACCAAACTTGCTTCAACCAAAAAAATTGCTCCCGGTGATTTTCATGAAATCTGCC
















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|211517040|gb|FL438272.1|FL438272
EST:     CTGTAGACATTTTAACCCCACTAGAAAAGTCTGGATTCTGGGACGGTGTG                         AAAGCAACAAAATGGTCTGAGAGAAGGGATGCTGTGGCAGAATTAACCAAG
genomic: CTGTAGACATTTTAACCCCACTAGAAAAGTCTGGATTCTGGGACGGTGTGgtatgggacc ... ctgatgtcagAAAGCAACAAAATGGTCTGAGAGAAGGGATGCTGTGGCAGAATTAACCAAG
EST: gi|18963448|gb|BM660440.1|BM660440
EST:     CTGTAGACATTTTAACCCCACTAGAAAAGTCTGGATTCTGGGACGGTGTG                         AAAGCAACAAAATGGTCTGAGAGAAGGGATGCTGTGGCAGAATTAACCAAG
genomic: CTGTAGACATTTTAACCCCACTAGAAAAGTCTGGATTCTGGGACGGTGTGgtatgggacc ... ctgatgtcagAAAGCAACAAAATGGTCTGAGAGAAGGGATGCTGTGGCAGAATTAACCAAG
EST: gi|32934909|gb|CF039721.1|CF039721
EST:     CTGTAGACATTTTAACCCCACTAGAAAAGTCTGGATTCTGGGACGGTGTG                         AAAGCAACAAAATGGTCTGAGAGAAGGGATGCTGTGGCAGAATTAACCAAG
genomic: CTGTAGACATTTTAACCCCACTAGAAAAGTCTGGATTCTGGGACGGTGTGgtatgggacc ... ctgatgtcagAAAGCAACAAAATGGTCTGAGAGAAGGGATGCTGTGGCAGAATTAACCAAG

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: 47 (upstream exon), 49 (downstream exon)
Score: 122

CCCCTGTGGAGATCGATGAATATGACCTTGTTGATCCTGTAGACATTTTAACCCCACTAGAAAAGTCTGGATTCTGGGACGGTGTGgtatgggacc ... ctgatgtcagAAAGCAACAAAATGGTCTGAGAGAAGGGATGCTGTGGCAGAATTAACCAAGCTTGGTTCGGCAAAAAAAATTGCTCCTGGTGATTTTCATGAAATTTGCC


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 47

CCCCTGTGGAGATCGATGAATATGACCTTGTTGATCCTGTAGACATTTTAACCCCACTAGAAAAGTCTGGATTCTGGGACGGTGTGgtatgggacc ... ctgatgtcagAAAGCAACAAAATGGTCTGAGAGAAGGGATGCTGTGGCAGAATTAACCAAGCTTGGTTCGGCAAAAAAAATTGCTCCTGGTGATTTTCATGAAATTTGCC


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 46

CCCCTGTGGAGATCGATGAATATGACCTTGTTGATCCTGTAGACATTTTAACCCCACTAGAAAAGTCTGGATTCTGGGACGGTGTGgtatgggacc ... ctgatgtcagAAAGCAACAAAATGGTCTGAGAGAAGGGATGCTGTGGCAGAATTAACCAAGCTTGGTTCGGCAAAAAAAATTGCTCCTGGTGATTTTCATGAAATTTGCC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 99

CCCCTGTGGAGATCGATGAATATGACCTTGTTGATCCTGTAGACATTTTAACCCCACTAGAAAAGTCTGGATTCTGGGACGGTGTGgtatgggacc ... ctgatgtcagAAAGCAACAAAATGGTCTGAGAGAAGGGATGCTGTGGCAGAATTAACCAAGCTTGGTTCGGCAAAAAAAATTGCTCCTGGTGATTTTCATGAAATTTGCC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcacactatcgtatgaaaagtagttattatattagtttttgttgtctgatgtcagAAAGCAACAAAATGGTCTGAGAGAAGGGATGCTGTGGCAGAATTAACCAAGCTTGGTTCGGCAAAAAAAATTGCTCCTGGTGATTTTCATGAAATTTGCC
                                           gtctgat  putative branch site (score: 99)
           tatgaaaagtagttat  TA-rich tract