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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgattttttgttgttgccagcttttgtgcgagtttattgacttgacatgcctttgttgttctggtgcagGTTCGTTTGAATGGTGTCGCTACTTTTATTGGAATGGTTGGACTTTCTGTTGCCCTTGCAGTTCTTGTTGTACTTTTGGCCAG

Basic information

species Zea mays
transcript GRMZM2G391042_T01
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G391042_T02 (Zea mays), 3'ss of exon 12
lower sequence: LOC_Os04g51610.3 (Oryza sativa), 3'ss of exon 12
gtttgattttttgttgttgccagcttttgtgcgagtttattgacttgacatgcctttgttgttctggtgcagGTTCGTTTGAATGGTGTCGCTACTTTTATTGGAATGGTTGGACTTTCTGTTGCCCTTGCAGTTCTTGTTGTACTTTTGGCCAG
||||||||||||    |||    ||||||  |||||| || || ||||||||  ||| ||||||||| | ||||||| ||||| ||||| || || || |||||||||||||||||||||||||| || || ||||||||||| ||| |||||||
gtttgattttttaac-ttgttgacttttgcacgagttcat-gagttgacatgaatttattgttctggagtagGTTCGCTTGAACGGTGTTGCCACCTTCATTGGAATGGTTGGACTTTCTGTTGCTCTCGCCGTTCTTGTTGTCCTTCTGGCCAG
















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), 47 (downstream exon)
Score: 118

GTAACTGCTGTTGGAATTAACACTGAATGGGGGTTGCTAATGGCAAGCATATCTGAAGATTCGGGTGAAGAGACACCACTTCAGgtttgatttt ... tctggtgcagGTTCGTTTGAATGGTGTCGCTACTTTTATTGGAATGGTTGGACTTTCTGTTGCCCTTGCAGTTCTTGTTGTACTTTTGGCCAG


Block sizes: 48 (upstream exon), 42 (downstream exon)
Score: 25

GTAACTGCTGTTGGAATTAACACTGAATGGGGGTTGCTAATGGCAAGCATATCTGAAGATTCGGGTGAAGAGACACCACTTCAGgtttgatttt ... tctggtgcagGTTCGTTTGAATGGTGTCGCTACTTTTATTGGAATGGTTGGACTTTCTGTTGCCCTTGCAGTTCTTGTTGTACTTTTGGCCAG


Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 32

GTAACTGCTGTTGGAATTAACACTGAATGGGGGTTGCTAATGGCAAGCATATCTGAAGATTCGGGTGAAGAGACACCACTTCAGgtttgatttt ... tctggtgcagGTTCGTTTGAATGGTGTCGCTACTTTTATTGGAATGGTTGGACTTTCTGTTGCCCTTGCAGTTCTTGTTGTACTTTTGGCCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 119

GTAACTGCTGTTGGAATTAACACTGAATGGGGGTTGCTAATGGCAAGCATATCTGAAGATTCGGGTGAAGAGACACCACTTCAGgtttgatttt ... tctggtgcagGTTCGTTTGAATGGTGTCGCTACTTTTATTGGAATGGTTGGACTTTCTGTTGCCCTTGCAGTTCTTGTTGTACTTTTGGCCAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgccagcttttgtgcgagtttattgacttgacatgcctttgttgttctggtgcagGTTCGTTTGAATGGTGTCGCTACTTTTATTGGAATGGTTGGACTTTCTGTTGCCCTTGCAGTTCTTGTTGTACTTTTGGCCAG
                                         ttgttct  CT-rich tract
                agtttatt  TA-rich tract