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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagggactctggacttaaatgttagagtggtagtaggatctgtaatatgtattgagacatctctcctgagtcctgactacttgaacacagGTCTTGAGGAACGGATGCATATACTTTGGGACAGCATGGTG

Basic information

species Zea mays
transcript GRMZM2G020002_T01
intron # 9
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|74240936|gb|DT648850.1|DT648850
EST:     GATGATTTTCGGAAGATTCCCAATGGTGTAAATG                         GTC-TGAGGGAACGGATGCATATACTTTGGGACAGCATGGTGGAG
genomic: GATGATTTTCGGAAGATTCCCAATGGTGTAAATGgtagggactc ... ttgaacacagGTCTTGA-GGAACGGATGCATATACTTTGGGACAGCATGGT---G
EST: gi|113703820|gb|EE681324.1|EE681324
EST:     GAAAGCTTTTGGTTCTGATGATTTTCGGAAGATTCCCAATGGTGTAAATG                         GTCTTGAGGAACGGATGCATATACTTTGGGACAGCATGGTGGAG
genomic: GAAAGCTTTTGGTTCTGATGATTTTCGGAAGATTCCCAATGGTGTAAATGgtagggactc ... ttgaacacagGTCTTGAGGAACGGATGCATATACTTTGGGACAGCATGGT---G
EST: gi|78079711|gb|DV508123.1|DV508123
EST:     AAGATTCCCAATGGTGTAAATG                         GTCTTGAGGAACGGATGCATATACTTTGGGACAGCATGGTGGAG
genomic: AAGATTCCCAATGGTGTAAATGgtagggactc ... ttgaacacagGTCTTGAGGAACGGATGCATATACTTTGGGACAGCATGGT---G
EST: gi|148929734|gb|EC876616.2|EC876616
EST:     TCCCAATGGTGTAAATG                         GTCTTGAGGAACGGATGCATATACTTTGGGACAGCATGGTGGAG
genomic: TCCCAATGGTGTAAATGgtagggactc ... ttgaacacagGTCTTGAGGAACGGATGCATATACTTTGGGACAGCATGGT---G

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: 40 (upstream exon), 49 (downstream exon)
Score: 35

CTTGTAGGTACTGATCACTGCACATTCAACTCCACACAGAAAGCTTTTGGTTCTGATGATTTTCGGAAGATTCCCAATGGTGTAAATGgtagggactc ... ttgaacacagGTCTTGAGGAACGGATGCATATACTTTGGGACAGCATGGTG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 155

CTTGTAGGTACTGATCACTGCACATTCAACTCCACACAGAAAGCTTTTGGTTCTGATGATTTTCGGAAGATTCCCAATGGTGTAAATGgtagggactc ... ttgaacacagGTCTTGAGGAACGGATGCATATACTTTGGGACAGCATGGTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 134

CTTGTAGGTACTGATCACTGCACATTCAACTCCACACAGAAAGCTTTTGGTTCTGATGATTTTCGGAAGATTCCCAATGGTGTAAATGgtagggactc ... ttgaacacagGTCTTGAGGAACGGATGCATATACTTTGGGACAGCATGGTG


Block sizes: 47 (upstream exon), 48 (downstream exon)
Score: 80

CTTGTAGGTACTGATCACTGCACATTCAACTCCACACAGAAAGCTTTTGGTTCTGATGATTTTCGGAAGATTCCCAATGGTGTAAATGgtagggactc ... ttgaacacagGTCTTGAGGAACGGATGCATATACTTTGGGACAGCATGGTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggatctgtaatatgtattgagacatctctcctgagtcctgactacttgaacacagGTCTTGAGGAACGGATGCATATACTTTGGGACAGCATGGTG
                                   tcctgac  putative branch site (score: 80)
       taatatgtatt  TA-rich tract