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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacccctgatccctctccggctctccctgtcttcagctctcttcgaatttggcaggctggttcccgcgtttgaatttgactcaatttcgtgcgttggtgctttgtttggtatagATTGCGAGCGGGCACGCAGATGGGAGCATCAGGCTGTGGGACGCGGAAACAGGTGCTTGCGAGGCAACCCTCCACGGCCACCGCTCCGCTGCCTCCGCCC

Basic information

species Zea mays
transcript AC209858.4_FGT002
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AC209858.4_FGT002 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os03g05720.1 (Oryza sativa), 3'ss of exon 1
gtacccctgatccctctccggctctccctgtcttcagctctcttcgaatttggcaggctggttcccgcgtttgaatttgactcaatttcgtgcgttggtgctttgtttggtatagATTGCGAGCGGGCACGCAGATGGGAGCATCAGGCTGTGGGACGCGGAAACAGGTGCTTGCGAGGCAACCCTCCACGGCCACCGCTCCGCTGCCTCCGCCC
         ||| | | | |   || |||  |||   |  | | ||  ||   |   | |  |   | | | |  ||| |    || ||||||| || || || ||||| |  |||||||||| |||||||| ||||||||||||||||| |||||| |||| || ||  | || ||||| |||||||| ||||||||||| || || |||||||
-------gtatcacacgctgaaccttcctccctttccccttttgcggtttaatctctccgcattttgagctgg--tttcatc--atctcgtgcgctg-tg-ttggtttgcttcagATTGCGAGTGGGCACGCCGATGGGAGCATCAGGCTATGGGACACGGAGACCGGCTCCTGTGAGGCGACCCTCCATGGCCACCGCTCTGCGGCTTCCGCCC
















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), 46 (downstream exon)
Score: 11

GCGTGGTCTTCCCTCTGTCTCCTTCGCACCTTCCTCCTCCTCCCCTTCGCTCGCCGTCTCCTGCATCGCTTCCTCCCACTCCGCCGCCGTCTCCTCTTCGgtacccctga ... tttggtatagATTGCGAGCGGGCACGCAGATGGGAGCATCAGGCTGTGGGACGCGGAAACAGGTGCTTGCGAGGCAACCCTCCACGGCCACCGCTCCGCTGCCTCCGCCC


Block sizes: 37 (upstream exon), 46 (downstream exon)
Score: 10

GCGTGGTCTTCCCTCTGTCTCCTTCGCACCTTCCTCCTCCTCCCCTTCGCTCGCCGTCTCCTGCATCGCTTCCTCCCACTCCGCCGCCGTCTCCTCTTCGgtacccctga ... tttggtatagATTGCGAGCGGGCACGCAGATGGGAGCATCAGGCTGTGGGACGCGGAAACAGGTGCTTGCGAGGCAACCCTCCACGGCCACCGCTCCGCTGCCTCCGCCC


Block sizes: 46 (upstream exon), 46 (downstream exon)
Score: 9

GCGTGGTCTTCCCTCTGTCTCCTTCGCACCTTCCTCCTCCTCCCCTTCGCTCGCCGTCTCCTGCATCGCTTCCTCCCACTCCGCCGCCGTCTCCTCTTCGgtacccctga ... tttggtatagATTGCGAGCGGGCACGCAGATGGGAGCATCAGGCTGTGGGACGCGGAAACAGGTGCTTGCGAGGCAACCCTCCACGGCCACCGCTCCGCTGCCTCCGCCC


Block sizes: 47 (upstream exon), 48 (downstream exon)
Score: 9

GCGTGGTCTTCCCTCTGTCTCCTTCGCACCTTCCTCCTCCTCCCCTTCGCTCGCCGTCTCCTGCATCGCTTCCTCCCACTCCGCCGCCGTCTCCTCTTCGgtacccctga ... tttggtatagATTGCGAGCGGGCACGCAGATGGGAGCATCAGGCTGTGGGACGCGGAAACAGGTGCTTGCGAGGCAACCCTCCACGGCCACCGCTCCGCTGCCTCCGCCC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttcccgcgtttgaatttgactcaatttcgtgcgttggtgctttgtttggtatagATTGCGAGCGGGCACGCAGATGGGAGCATCAGGCTGTGGGACGCGGAAACAGGTGCTTGCGAGGCAACCCTCCACGGCCACCGCTCCGCTGCCTCCGCCC
              atttgac  putative branch site (score: 9)
                                        ctttgttt  putative PPT
         tttgaattt  TA-rich tract