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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttggaagttgatcacaatattacttcatctcttcattagaatgattccacacagtttgttcctgtgatttttcttgttttgatgctgttgcaactgtgcagGCACTTCCTTCAAGTTGGAAAGAAGTGATTGAACTTCTTGACATATTATTAAGGTGGTTTGTCTTACGCTTTTGTGAATCGAACACAACATGTTTGTTGA

Basic information

species Zea mays
transcript GRMZM2G068755_T03
intron # 32
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G068755_T01 (Zea mays), 3'ss of exon 34
lower sequence: LOC_Os01g60040.2 (Oryza sativa), 3'ss of exon 34
gttggaagttgatcacaatattacttcatctcttcattagaatgattccacacagtttgttcctgtgatttttcttgttttgatgctgttgcaactgtgcagGCACTTCCTTCAAGTTGGAAAGAAGTGATTGAACTTCTTGACATATTATTAAGGTGGTTTGTCTTACGCTTTTGTGAATCGAACACAACATGTTTGTTGA
|||||||    || |  || ||      | | |||||   | |  | | ||  |   | ||  |   |||||  || |||| ||| | ||   | | |||||||| | ||||| ||| |||||||||||||||| ||||| || ||| ||||||||||||||||||| || ||||||||||| ||||||||||||||| |||
gttggaaa--aatgatcatcttggaagtttttttcatgccact--tgctacgtaacctatttttacaattttattttttttaatgatattcttattatgcagGCATTGCCTTCTAGTAGGAAAGAAGTGATTGAGCTTCTCGATATACTATTAAGGTGGTTTGTCTTGCGATTTTGTGAATCTAACACAACATGTTTGCTGA
















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|33770951|gb|CF273245.1|CF273245
EST:     GGAACTCAGACTTTAAGAGGCAAATTGATGGTATTGAATTGCTACAAAAG                         GCACTTCCTTCAGGTTGGAAAGAAGTGATTGAACTTCTTGACATATTATTA
genomic: GGAACTCAGACTTTAAGAGGCAAATCGATGGTATTGAATTGCTACAAAAGgttggaagtt ... aactgtgcagGCACTTCCTTCAAGTTGGAAAGAAGTGATTGAACTTCTTGACATATTATTA




















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: 101

ATTGATTTGTTTAAGCATTTCCGAGAAGATGTAAGCCTGCGATTATGGAACTCAGACTTTAAGAGGCAAATCGATGGTATTGAATTGCTACAAAAGgttggaagtt ... aactgtgcagGCACTTCCTTCAAGTTGGAAAGAAGTGATTGAACTTCTTGACATATTATTAAGGTGGTTTGTCTTACGCTTTTGTGAATCGAACACAACATGTTTGTTGA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 36

ATTGATTTGTTTAAGCATTTCCGAGAAGATGTAAGCCTGCGATTATGGAACTCAGACTTTAAGAGGCAAATCGATGGTATTGAATTGCTACAAAAGgttggaagtt ... aactgtgcagGCACTTCCTTCAAGTTGGAAAGAAGTGATTGAACTTCTTGACATATTATTAAGGTGGTTTGTCTTACGCTTTTGTGAATCGAACACAACATGTTTGTTGA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 52

ATTGATTTGTTTAAGCATTTCCGAGAAGATGTAAGCCTGCGATTATGGAACTCAGACTTTAAGAGGCAAATCGATGGTATTGAATTGCTACAAAAGgttggaagtt ... aactgtgcagGCACTTCCTTCAAGTTGGAAAGAAGTGATTGAACTTCTTGACATATTATTAAGGTGGTTTGTCTTACGCTTTTGTGAATCGAACACAACATGTTTGTTGA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 76

ATTGATTTGTTTAAGCATTTCCGAGAAGATGTAAGCCTGCGATTATGGAACTCAGACTTTAAGAGGCAAATCGATGGTATTGAATTGCTACAAAAGgttggaagtt ... aactgtgcagGCACTTCCTTCAAGTTGGAAAGAAGTGATTGAACTTCTTGACATATTATTAAGGTGGTTTGTCTTACGCTTTTGTGAATCGAACACAACATGTTTGTTGA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccacacagtttgttcctgtgatttttcttgttttgatgctgttgcaactgtgcagGCACTTCCTTCAAGTTGGAAAGAAGTGATTGAACTTCTTGACATATTATTAAGGTGGTTTGTCTTACGCTTTTGTGAATCGAACACAACATGTTTGTTGA
                              ttttgat  putative branch site (score: 76)
                    atttttcttgtttt  TA-rich tract