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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagcctctctcgctcggtccgccgtaggccgtagccccaggttctagctctaatccatcggtctttctaatcttgtgctgctctgttctgttctttctgcagGGTTTGCTCGTGCATGCAG

Basic information

species Zea mays
transcript GRMZM2G065696_T01
intron # 7
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|14243119|gb|BG840835.2|BG840835
EST:     TCGGAGGCCGCGCACGTCATCTCCTGCATGTCGAATCTGGTCTACTGGAC                         GGTTTGCTCGTGCATGCAG
genomic: TCGGAGGCCGCGCACGTCATCTCCTGCATGTCGAATCTGGTCTACTGGACgtaagcctct ... ctttctgcagGGTTTGCTCGTGCATGCAG
EST: gi|51592820|gb|CV071966.1|CV071966
EST:     TCGGAGGCCGCGCACGTCATCTCCTGCATGTCGAATCTGGTCTACTGGAC                         GGTTTGCTCGTGCATGCAG
genomic: TCGGAGGCCGCGCACGTCATCTCCTGCATGTCGAATCTGGTCTACTGGACgtaagcctct ... ctttctgcagGGTTTGCTCGTGCATGCAG
EST: gi|51592771|gb|CV071917.1|CV071917
EST:     TCGGAGGCCGCGCACGTCATCTCCTGCATGTCGAATCTGGTCTACTGGAC                         GGTTTGCTCGTGCATGCAG
genomic: TCGGAGGCCGCGCACGTCATCTCCTGCATGTCGAATCTGGTCTACTGGACgtaagcctct ... ctttctgcagGGTTTGCTCGTGCATGCAG
EST: gi|211148105|gb|FL448499.1|FL448499
EST:     TCGGAGGCCGCGCACGTCATCTCCTGCATGTCGAATCTGGTCTACTGGAC                         GGTTTGCTCGTGCATGCAG
genomic: TCGGAGGCCGCGCACGTCATCTCCTGCATGTCGAATCTGGTCTACTGGACgtaagcctct ... ctttctgcagGGTTTGCTCGTGCATGCAG
EST: gi|16918930|gb|BM073956.1|BM073956
EST:     TCGGAGGCCGCGCACGTCATCTCCTGCATGTCGAATCTGGTCTACTGGAC                         GGTTTGCTCGTGCATGCAG
genomic: TCGGAGGCCGCGCACGTCATCTCCTGCATGTCGAATCTGGTCTACTGGACgtaagcctct ... ctttctgcagGGTTTGCTCGTGCATGCAG
EST: gi|32919835|gb|CF024647.1|CF024647
EST:     TCGGAGGCCGCTCACGTCATCTCCTGCATGTCGAATCTGGTCTACTGGAC                         GGTTTGCTCGTGCATGCAG
genomic: TCGGAGGCCGCGCACGTCATCTCCTGCATGTCGAATCTGGTCTACTGGACgtaagcctct ... ctttctgcagGGTTTGCTCGTGCATGCAG
EST: gi|47961905|gb|CN844614.1|CN844614
EST:     TCGGAGGCCGCGCACGTCATCTCCTGCATGTCGAATCTGGTCTACTGGAC                         GGTTTGCTCGTGCATGCAG
genomic: TCGGAGGCCGCGCACGTCATCTCCTGCATGTCGAATCTGGTCTACTGGACgtaagcctct ... ctttctgcagGGTTTGCTCGTGCATGCAG
EST: gi|32919836|gb|CF024648.1|CF024648
EST:     TCGGAGGCCGCTCACGTCATCTCCTGCATGTCGAATCTGGTCTACTGGAC                         GGTTTGCTCGTGCATGCAGACGCAGCA
genomic: TCGGAGGCCGCGCACGTCATCTCCTGCATGTCGAATCTGGTCTACTGGACgtaagcctct ... ctttctgcagGGTTTGCTCGTGCATGCAGACGCAGCA

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 3 RNA-Seq libraries.


Block sizes: 44 (upstream exon), 19 (downstream exon)
Score: 5

TGGCCTGCATCTGCTCCCTGGTCGCCTGCATCGTCGGCAACAGCGAGCTCTCGGAGGCCGCGCACGTCATCTCCTGCATGTCGAATCTGGTCTACTGGACgtaagcctct ... ctttctgcagGGTTTGCTCGTGCATGCAG


Block sizes: 47 (upstream exon), 19 (downstream exon)
Score: 188

TGGCCTGCATCTGCTCCCTGGTCGCCTGCATCGTCGGCAACAGCGAGCTCTCGGAGGCCGCGCACGTCATCTCCTGCATGTCGAATCTGGTCTACTGGACgtaagcctct ... ctttctgcagGGTTTGCTCGTGCATGCAG


Block sizes: 49 (upstream exon), 44 (downstream exon)
Score: 251

TGGCCTGCATCTGCTCCCTGGTCGCCTGCATCGTCGGCAACAGCGAGCTCTCGGAGGCCGCGCACGTCATCTCCTGCATGTCGAATCTGGTCTACTGGACgtaagcctct ... ctttctgcagGGTTTGCTCGTGCATGCAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctctaatccatcggtctttctaatcttgtgctgctctgttctgttctttctgcagGGTTTGCTCGTGCATGCAG
                 ttctaat  putative branch site (score: 251)
                              ctgctctgttctgttc  putative PPT
                tttctaat  TA-rich tract