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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagcaactgtcttgcacgttaaattaattatgtgatgaacgatttttaacgcagttagtgtttgtctatacagGTGATTGGCACATGGCTTATATCTGCTTGTACAAAGCCCGCATGGCAGAATCAAAGAGTTAGGTCGAATTGGTTCTACATTTCTGTATTGCGAATGCAAC

Basic information

species Zea mays
transcript GRMZM2G028733_T02
intron # 17
splice site 3'
intron type U2

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|5608231|gb|AI901898.1|AI901898
EST:     CAATCCGAACATTCGCAAGGATGAAGACATTTTGAAACTTTCTGGTGGAG                         GTGATTGGCACATGGCTTATATCTGCTTGTACAAAGCCCGCATGGCAGAAT
genomic: CAATCCGAACATTCGCAAGGATGAAGACATTTTGAAACTTTCTGGTGGAGgtgagcaact ... gtctatacagGTGATTGGCACATGGCTTATATCTGCTTGTACAAAGCCCGCATGGCAGAAT




















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), 48 (downstream exon)
Score: 102

GAAAATGGATCGAGTTTGATGATGACAATCCGAACATTCGCAAGGATGAAGACATTTTGAAACTTTCTGGTGGAGgtgagcaact ... gtctatacagGTGATTGGCACATGGCTTATATCTGCTTGTACAAAGCCCGCATGGCAGAATCAAAGAGTTAGGTCGAATTGGTTCTACATTTCTGTATTGCGAATGCAAC


Block sizes: 46 (upstream exon), 48 (downstream exon)
Score: 35

GAAAATGGATCGAGTTTGATGATGACAATCCGAACATTCGCAAGGATGAAGACATTTTGAAACTTTCTGGTGGAGgtgagcaact ... gtctatacagGTGATTGGCACATGGCTTATATCTGCTTGTACAAAGCCCGCATGGCAGAATCAAAGAGTTAGGTCGAATTGGTTCTACATTTCTGTATTGCGAATGCAAC


Block sizes: 46 (upstream exon), 48 (downstream exon)
Score: 39

GAAAATGGATCGAGTTTGATGATGACAATCCGAACATTCGCAAGGATGAAGACATTTTGAAACTTTCTGGTGGAGgtgagcaact ... gtctatacagGTGATTGGCACATGGCTTATATCTGCTTGTACAAAGCCCGCATGGCAGAATCAAAGAGTTAGGTCGAATTGGTTCTACATTTCTGTATTGCGAATGCAAC


Block sizes: 47 (upstream exon), 48 (downstream exon)
Score: 34

GAAAATGGATCGAGTTTGATGATGACAATCCGAACATTCGCAAGGATGAAGACATTTTGAAACTTTCTGGTGGAGgtgagcaact ... gtctatacagGTGATTGGCACATGGCTTATATCTGCTTGTACAAAGCCCGCATGGCAGAATCAAAGAGTTAGGTCGAATTGGTTCTACATTTCTGTATTGCGAATGCAAC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttaaattaattatgtgatgaacgatttttaacgcagttagtgtttgtctatacagGTGATTGGCACATGGCTTATATCTGCTTGTACAAAGCCCGCATGGCAGAATCAAAGAGTTAGGTCGAATTGGTTCTACATTTCTGTATTGCGAATGCAAC
                         ttttaac  putative branch site (score: 34)
                                          tttgtct  putative PPT
     ttaattatgt  TA-rich tract