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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttgacattttctgactagattctatgatacacaagatataagctgatctccacaacctgaaaagttcaacaatcttaaacctctttattttattcagATGGAACTGCTGATTCAGGCACATCTCACTCGTGAGTCATTTGCTTTGACCCCAGCACTTCTTAAAGATTACAGACACATGCTTGAACTTGCACCTCGTC

Basic information

species Zea mays
transcript GRMZM2G167868_T01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G167868_T01 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os04g24180.1 (Oryza sativa), 3'ss of exon 7
gttgacattttctgactagattctatgatacacaagatataagctgatctccacaacctgaaaagttcaacaatcttaaacctctttattttattc----agATGGAACTGCTGATTCAGGCACATCTCACTCGTGAGTCATTTGCTTTGACCCCAGCACTTCTTAAAGATTACAGACACATGCTTGAACTTGCACCTCGTC
||||   ||||    |||  |  ||||  ||||||        || || ||    || ||| || |    ||| || |||  ||| |  | || ||    ||||||| ||  |||||||||| || |||||| | ||||||||||||||||| |||||  | || || |||||||| |||||||||||||||||||||||||
gttggtctttttctgctaagtgttatggcacacaaa-------cttatatctgtgacatgacaaatcttgcaagctcaaatatctgtcatctactcttgcagATGGAGCTTTTGATTCAGGCTCACCTCACTGGAGAGTCATTTGCTTTGACACCAGCGTTACTGAAGGATTACAGGCACATGCTTGAACTTGCACCTCGTC
















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: 47 (upstream exon), 49 (downstream exon)
Score: 169

AAAATTGTTTGTAGCTGTTAGAAGTGAGTTAAATCTGGACTTAAAGAACATTAAGACAGAACAAGCAAAGTTCTGGAAGCAGCATCCATCCCTAGTAAAGgttgacattt ... ttttattcagATGGAACTGCTGATTCAGGCACATCTCACTCGTGAGTCATTTGCTTTGACCCCAGCACTTCTTAAAGATTACAGACACATGCTTGAACTTGCACCTCGTC


Block sizes: 47 (upstream exon), 47 (downstream exon)
Score: 156

AAAATTGTTTGTAGCTGTTAGAAGTGAGTTAAATCTGGACTTAAAGAACATTAAGACAGAACAAGCAAAGTTCTGGAAGCAGCATCCATCCCTAGTAAAGgttgacattt ... ttttattcagATGGAACTGCTGATTCAGGCACATCTCACTCGTGAGTCATTTGCTTTGACCCCAGCACTTCTTAAAGATTACAGACACATGCTTGAACTTGCACCTCGTC


Block sizes: 47 (upstream exon), 48 (downstream exon)
Score: 136

AAAATTGTTTGTAGCTGTTAGAAGTGAGTTAAATCTGGACTTAAAGAACATTAAGACAGAACAAGCAAAGTTCTGGAAGCAGCATCCATCCCTAGTAAAGgttgacattt ... ttttattcagATGGAACTGCTGATTCAGGCACATCTCACTCGTGAGTCATTTGCTTTGACCCCAGCACTTCTTAAAGATTACAGACACATGCTTGAACTTGCACCTCGTC


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 279

AAAATTGTTTGTAGCTGTTAGAAGTGAGTTAAATCTGGACTTAAAGAACATTAAGACAGAACAAGCAAAGTTCTGGAAGCAGCATCCATCCCTAGTAAAGgttgacattt ... ttttattcagATGGAACTGCTGATTCAGGCACATCTCACTCGTGAGTCATTTGCTTTGACCCCAGCACTTCTTAAAGATTACAGACACATGCTTGAACTTGCACCTCGTC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctgatctccacaacctgaaaagttcaacaatcttaaacctctttattttattcagATGGAACTGCTGATTCAGGCACATCTCACTCGTGAGTCATTTGCTTTGACCCCAGCACTTCTTAAAGATTACAGACACATGCTTGAACTTGCACCTCGTC
 agctgat  putative branch site (score: 279)
                                     cctctttattttattc  putative PPT
                                       tctttattttattca  TA-rich tract