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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagccttagagacacaattgatcttgttgcttttagatcctccaccagttctaatgtcttttacacccagGTATCTATCTATGCTTCGGAAAGCTTCTAAGGAGGAAATTGTTGTTGAGCTCACAAATCTATATGACCATTTCTTCCTTACTATGGGGGAATGCAAGGCT

Basic information

species Zea mays
transcript GRMZM2G139977_T01
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G139977_T02 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os02g04490.1 (Oryza sativa), 3'ss of exon 11
gtaag--ccttagagacaca---attgatcttgttgcttttagatcctc-------caccagttctaatgtcttttacacccagGTATCTATCTATGCTTCGGAAAGCTTCTAAGGAGGAAATTGTTGTTGAGCTCACAAATCTATATGACCATTTCTTCCTTACTATGGGGGAATGCAAGGCT
|||||  | ||   |||||     ||  |||  |  ||||||| || ||       ||  | |||| ||||  ||||||| ||||||  ||||||||||||| |||||| | |||||||| |||||||||||||| |||||||||||||||||||||||| ||||||||||||| |||||||||
gtaagacctttgttgacacttctgttactctgctcacttttagctcttctagtttacatgatttctgatgtactttacactcagGTACTTATCTATGCTTCGAAAAGCTACCAAGGAGGAGATTGTTGTTGAGCTGACAAATCTATATGACCATTTCTTCATTACTATGGGGGAGTGCAAGGCT
















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: 43 (upstream exon), 49 (downstream exon)
Score: 122

GTTACATATGGGCTTGTCCACCTTTGAAGGGTGAAGATTACATCTTATATTGCCATCCTGAGATTCAAAAGACTCCGAAATCTGATAAACTGCGTGAGTGgtaagcctta ... ttacacccagGTATCTATCTATGCTTCGGAAAGCTTCTAAGGAGGAAATTGTTGTTGAGCTCACAAATCTATATGACCATTTCTTCCTTACTATGGGGGAATGCAAGGCT


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 103

GTTACATATGGGCTTGTCCACCTTTGAAGGGTGAAGATTACATCTTATATTGCCATCCTGAGATTCAAAAGACTCCGAAATCTGATAAACTGCGTGAGTGgtaagcctta ... ttacacccagGTATCTATCTATGCTTCGGAAAGCTTCTAAGGAGGAAATTGTTGTTGAGCTCACAAATCTATATGACCATTTCTTCCTTACTATGGGGGAATGCAAGGCT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 133

GTTACATATGGGCTTGTCCACCTTTGAAGGGTGAAGATTACATCTTATATTGCCATCCTGAGATTCAAAAGACTCCGAAATCTGATAAACTGCGTGAGTGgtaagcctta ... ttacacccagGTATCTATCTATGCTTCGGAAAGCTTCTAAGGAGGAAATTGTTGTTGAGCTCACAAATCTATATGACCATTTCTTCCTTACTATGGGGGAATGCAAGGCT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 111

GTTACATATGGGCTTGTCCACCTTTGAAGGGTGAAGATTACATCTTATATTGCCATCCTGAGATTCAAAAGACTCCGAAATCTGATAAACTGCGTGAGTGgtaagcctta ... ttacacccagGTATCTATCTATGCTTCGGAAAGCTTCTAAGGAGGAAATTGTTGTTGAGCTCACAAATCTATATGACCATTTCTTCCTTACTATGGGGGAATGCAAGGCT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aattgatcttgttgcttttagatcctccaccagttctaatgtcttttacacccagGTATCTATCTATGCTTCGGAAAGCTTCTAAGGAGGAAATTGTTGTTGAGCTCACAAATCTATATGACCATTTCTTCCTTACTATGGGGGAATGCAAGGCT
                                 ttctaat  putative branch site (score: 111)
                                       tgtctttt  CT-rich tract
               ttttagat  TA-rich tract