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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtgtgccctgcataatttatgtcctgtccactagaacatttcagtaagaattggtatcttacaatgatcatttattattcttgcagGTTCTCGAACAATTGGTGTTATCACAAAG

Basic information

species Zea mays
transcript GRMZM2G180335_T01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G180335_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os01g69130.2 (Oryza sativa), 3'ss of exon 2
gtatgtgtgccctgcataatttatgtcctgtccactagaacatttcagtaagaattggtatcttacaatgatc-atttattattcttgcagGTTCTCGAACAATTGGTGTTATCACAAAG
    || | | || || | |  ||   |  |    ||   ||| | | ||    ||| |   |   ||| ||  ||| ||| |||||| |||||||||||||||||||||||| ||||||
----gtattcactacagactcaat---ccattagataattcatgttaatatattttgtttcttattaataattgattcattgttcttgtagGTTCTCGAACAATTGGTGTTATAACAAAG
















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: 41 (upstream exon), 35 (downstream exon)
Score: 131

ATCAAGCACAAGACATGTATCATCTTAGCTGTATCGCCAGCAAATGCAGATTTAGCAAACTCTGACGCTCTTCAAATGGCTCGGGTTGCTGATCCTGATGgtatgtgtgc ... attcttgcagGTTCTCGAACAATTGGTGTTATCACAAAG


Block sizes: 47 (upstream exon), 36 (downstream exon)
Score: 159

ATCAAGCACAAGACATGTATCATCTTAGCTGTATCGCCAGCAAATGCAGATTTAGCAAACTCTGACGCTCTTCAAATGGCTCGGGTTGCTGATCCTGATGgtatgtgtgc ... attcttgcagGTTCTCGAACAATTGGTGTTATCACAAAG


Block sizes: 45 (upstream exon), 29 (downstream exon)
Score: 147

ATCAAGCACAAGACATGTATCATCTTAGCTGTATCGCCAGCAAATGCAGATTTAGCAAACTCTGACGCTCTTCAAATGGCTCGGGTTGCTGATCCTGATGgtatgtgtgc ... attcttgcagGTTCTCGAACAATTGGTGTTATCACAAAG


Block sizes: 45 (upstream exon), 29 (downstream exon)
Score: 180

ATCAAGCACAAGACATGTATCATCTTAGCTGTATCGCCAGCAAATGCAGATTTAGCAAACTCTGACGCTCTTCAAATGGCTCGGGTTGCTGATCCTGATGgtatgtgtgc ... attcttgcagGTTCTCGAACAATTGGTGTTATCACAAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tagaacatttcagtaagaattggtatcttacaatgatcatttattattcttgcagGTTCTCGAACAATTGGTGTTATCACAAAG
                        atcttac  putative branch site (score: 180)
                                           ttattctt  putative PPT
                           ttacaatgatcattta  TA-rich tract