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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgcgtgcgccactcccccccatcctcttgctgtctcgcgttggtgtacatgtttcactgatcactgattccatcggtgtggtcgcttcgacatgcagACATACCCGAACCCCCTCCAAGACAACCCGGCGTATTCAGTCGTCAA

Basic information

species Zea mays
transcript GRMZM2G132069_T01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G132069_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os01g09570.1 (Oryza sativa), 3'ss of exon 1
-------gtgcgtgcgccactcccccccatcctcttgctgtctcgcgttggtgtacatgtttcactgatcactgattccatcggtgtggtcgcttcgacatgcagACATACCCGAACCCCCTCCAAGACAACCCGGCGTATTCAGTCGTCAA
        || | |||   | ||  |  ||     ||| || |||  |||     |   ||||    | ||     ||    | |   || |||  ||  ||||||| |||||||| || || |||||||||||||| ||||||||||||||
tcaatttctgtgggcgatgcgcctactgattgagctgcagtatcgttttgac---cccatttcttgaagcaactgctcacctgctactgttgct--gatctgcagACTTACCCGAATCCTCTGCAAGACAACCCGGCTTATTCAGTCGTCAA
















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), 43 (downstream exon)
Score: 25

AGCGGCGAAGTGGGCGGAGAAGAAGAAGCTGGTGGGCGGCGACGCCGGCTACGTGCTCGAGGACGTGCCGCACCTCACGGATTACCTGCCCCAGCTCCCGgtgcgtgcgc ... cgacatgcagACATACCCGAACCCCCTCCAAGACAACCCGGCGTATTCAGTCGTCAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 117

AGCGGCGAAGTGGGCGGAGAAGAAGAAGCTGGTGGGCGGCGACGCCGGCTACGTGCTCGAGGACGTGCCGCACCTCACGGATTACCTGCCCCAGCTCCCGgtgcgtgcgc ... cgacatgcagACATACCCGAACCCCCTCCAAGACAACCCGGCGTATTCAGTCGTCAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 173

AGCGGCGAAGTGGGCGGAGAAGAAGAAGCTGGTGGGCGGCGACGCCGGCTACGTGCTCGAGGACGTGCCGCACCTCACGGATTACCTGCCCCAGCTCCCGgtgcgtgcgc ... cgacatgcagACATACCCGAACCCCCTCCAAGACAACCCGGCGTATTCAGTCGTCAA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 50

AGCGGCGAAGTGGGCGGAGAAGAAGAAGCTGGTGGGCGGCGACGCCGGCTACGTGCTCGAGGACGTGCCGCACCTCACGGATTACCTGCCCCAGCTCCCGgtgcgtgcgc ... cgacatgcagACATACCCGAACCCCCTCCAAGACAACCCGGCGTATTCAGTCGTCAA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtgtacatgtttcactgatcactgattccatcggtgtggtcgcttcgacatgcagACATACCCGAACCCCCTCCAAGACAACCCGGCGTATTCAGTCGTCAA
                   cactgat  putative branch site (score: 50)
                                       tcgcttc  putative PPT