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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagttcctggttcttctgcattttgtactttataattgattgcttgaacacgttttaatacctggtaataacatattagGTTAAGAGGATGGAGATAGAGCAGAAGGATTGCTCTTCAATAGTTGATAAGCTAGTCGAGAAATATAATTGGATTGCAACTGAGAAACAATTGTTTGGGA

Basic information

species Zea mays
transcript GRMZM2G006452_T02
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G006452_T02 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os01g67740.1 (Oryza sativa), 3'ss of exon 14
-------gtagttcctggttcttctgcat-tttgtactttataattga--ttgcttgaacacgttttaatacctggtaataacatat------tagGTTAAGAGGATGGAGATAGAGCAGAAGGATTGCTCTTCAATAGTTGATAAGCTAGTCGAGAAATATAATTGGATTGCAACTGAGAAACAATTGTTTGGGA
        | |||      ||| || ||| ||| | |||||||  |||    |       |  ||||  | |     |||  ||| |      |||||||||||||||||||| ||||||||||||||||||||||  ||||||||| |||| ||||| || | ||||||||||||||| ||||| |||||||| |
gtaactgttggttgtaatctctgctacatatttctgctttataggtgaagcagaccttttattttttttttctaaacaattgcatgtaacatgtagGTTAAGAGGATGGAGATTGAGCAGAAGGATTGCTCTTCAAAGGTTGATAAGTTAGTAGAGAAGTACAGTTGGATTGCAACTGAAAAACAGTTGTTTGGAA
















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|211188348|gb|FL216446.1|FL216446
EST:     AGAAAATGGAAAATGAG                         GTTAAGAGGATGGAGATAGAGCAGAAGGATTGCTCTTCAATAGTCGATAAG
genomic: AGAAAATGGAAAATGAGgtagttcctg ... aacatattagGTTAAGAGGATGGAGATAGAGCAGAAGGATTGCTCTTCAATAGTTGATAAG
EST: gi|211188349|gb|FL216447.1|FL216447
EST:     AGAAAATGGAAAATGAG                         GTTAATAGGATGGAGATAGAGCAGAAGGATTGCTCTTCAATAGTCGATAAG
genomic: AGAAAATGGAAAATGAGgtagttcctg ... aacatattagGTTAAGAGGATGGAGATAGAGCAGAAGGATTGCTCTTCAATAGTTGATAAG

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), 48 (downstream exon)
Score: 236

GGAATGTGACTCACAGATAAACCGTATGGCCAAGGAACAGCAGAAACTTCAACAGAAGTTAAGTGATTCAAATGTTGAGAGGAAGAAAATGGAAAATGAGgtagttcctg ... aacatattagGTTAAGAGGATGGAGATAGAGCAGAAGGATTGCTCTTCAATAGTTGATAAGCTAGTCGAGAAATATAATTGGATTGCAACTGAGAAACAATTGTTTGGGA


Block sizes: 49 (upstream exon), 43 (downstream exon)
Score: 33

GGAATGTGACTCACAGATAAACCGTATGGCCAAGGAACAGCAGAAACTTCAACAGAAGTTAAGTGATTCAAATGTTGAGAGGAAGAAAATGGAAAATGAGgtagttcctg ... aacatattagGTTAAGAGGATGGAGATAGAGCAGAAGGATTGCTCTTCAATAGTTGATAAGCTAGTCGAGAAATATAATTGGATTGCAACTGAGAAACAATTGTTTGGGA


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 53

GGAATGTGACTCACAGATAAACCGTATGGCCAAGGAACAGCAGAAACTTCAACAGAAGTTAAGTGATTCAAATGTTGAGAGGAAGAAAATGGAAAATGAGgtagttcctg ... aacatattagGTTAAGAGGATGGAGATAGAGCAGAAGGATTGCTCTTCAATAGTTGATAAGCTAGTCGAGAAATATAATTGGATTGCAACTGAGAAACAATTGTTTGGGA


Block sizes: 44 (upstream exon), 46 (downstream exon)
Score: 14

GGAATGTGACTCACAGATAAACCGTATGGCCAAGGAACAGCAGAAACTTCAACAGAAGTTAAGTGATTCAAATGTTGAGAGGAAGAAAATGGAAAATGAGgtagttcctg ... aacatattagGTTAAGAGGATGGAGATAGAGCAGAAGGATTGCTCTTCAATAGTTGATAAGCTAGTCGAGAAATATAATTGGATTGCAACTGAGAAACAATTGTTTGGGA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtactttataattgattgcttgaacacgttttaatacctggtaataacatattagGTTAAGAGGATGGAGATAGAGCAGAAGGATTGCTCTTCAATAGTTGATAAGCTAGTCGAGAAATATAATTGGATTGCAACTGAGAAACAATTGTTTGGGA
                                         taataac  putative branch site (score: 14)
                                         taataacatatta  TA-rich tract