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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagttcgtaactcaactctatttcaacatgtccacctttctacactgttaattctatttcatgcttatgccctacctttttccagACTATTTTGAGGGCACTATCACAAGCAGTATCCAAGATAGACACCGTGTATCATCATGCACTTCTACACAAT

Basic information

species Zea mays
transcript GRMZM2G415846_T01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G415846_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os06g47350.1 (Oryza sativa), 3'ss of exon 3
gtaagttcgtaac-tcaactctatttcaacatg-tccacctttctacactgttaattctatttcatgcttatgccctacct--ttttccagACTATTTTGAGGGCACTATCACAAGCAGTATCCAAGATAGACACCGTGTATCATCATGCACTTCTACACAAT
|||||| | |||| | |  |  | ||    ||  | | | |   ||    |  | |  |||   |     |||   | |||  |||||||||| | |||||  ||||||||| ||||||| ||||||||||| | | |||| |||||||| ||| |  |||||
gtaagtgcttaacattagtttcactttcctatccttcgcatgcttatgaagcaactcttatgataaatgcatgtatttcctgcttttccagACAACTTTGAAAGCACTATCAGAAGCAGTGTCCAAGATAGATATCATGTACCATCATGCTCTTTTGAACAAT
















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: 159

GTTTTTAATTGACATAAGGGACAAAGATTATTATGATTACATGCTAGGCATTATAGACCCTACCAAGAAAAGGAGTACAGATGATGAAGCTATGTTTGTTgtaagttcgt ... ctttttccagACTATTTTGAGGGCACTATCACAAGCAGTATCCAAGATAGACACCGTGTATCATCATGCACTTCTACACAAT


Block sizes: 49 (upstream exon), 42 (downstream exon)
Score: 108

GTTTTTAATTGACATAAGGGACAAAGATTATTATGATTACATGCTAGGCATTATAGACCCTACCAAGAAAAGGAGTACAGATGATGAAGCTATGTTTGTTgtaagttcgt ... ctttttccagACTATTTTGAGGGCACTATCACAAGCAGTATCCAAGATAGACACCGTGTATCATCATGCACTTCTACACAAT


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 166

GTTTTTAATTGACATAAGGGACAAAGATTATTATGATTACATGCTAGGCATTATAGACCCTACCAAGAAAAGGAGTACAGATGATGAAGCTATGTTTGTTgtaagttcgt ... ctttttccagACTATTTTGAGGGCACTATCACAAGCAGTATCCAAGATAGACACCGTGTATCATCATGCACTTCTACACAAT


Block sizes: 47 (upstream exon), 43 (downstream exon)
Score: 86

GTTTTTAATTGACATAAGGGACAAAGATTATTATGATTACATGCTAGGCATTATAGACCCTACCAAGAAAAGGAGTACAGATGATGAAGCTATGTTTGTTgtaagttcgt ... ctttttccagACTATTTTGAGGGCACTATCACAAGCAGTATCCAAGATAGACACCGTGTATCATCATGCACTTCTACACAAT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tccacctttctacactgttaattctatttcatgcttatgccctacctttttccagACTATTTTGAGGGCACTATCACAAGCAGTATCCAAGATAGACACCGTGTATCATCATGCACTTCTACACAAT
               tgttaat  putative branch site (score: 86)
                                     tgccctacctttttcc  putative PPT
                 ttaattctatttcat  TA-rich tract