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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaggagtagttcgctaccttgagttgaagagtctgtagtatgtgattgaccagatttgcgtgcatctttactcagGACTTTACCTAGGAGCGGCTCGGCGCGCAACATGTGAAGGCATGTAGGAATTGACCGAATATGGCTTTGATGATCCTTACTTGGATTAGGACTGGTGACT

Basic information

species Zea mays
transcript GRMZM2G017525_T01
intron # 6
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|12046320|gb|BF728459.1|BF728459
EST:     TTTGGTAGTTCAAGCGGNTCTGCCAGCAGTTCGCAGCTCCCACCTGGCAG                         GACTTTACCTAAGAGCGGCTCGGCGCGCAACATGTGAAGGCAT
genomic: TTTGGTAGTTCAAGCGGTTCTGCCAGCAGTTCGCAGCTCCCACCTGGCAGgtaggagtag ... ctttactcagGACTTTACCTAGGAGCGGCTCGGCGCGCAACATGTGAAGGCAT
EST: gi|60396927|gb|DN229746.1|DN229746
EST:     TTTGGTAGTTCAAGCGGTTCTGCCAGCAGTTCGCAGCTCCCACCTGGCAG                         GACTTTACCTAAGAGCGGCTCGGCGCGCAACATGTGAAGGCATGTAGGAAT
genomic: TTTGGTAGTTCAAGCGGTTCTGCCAGCAGTTCGCAGCTCCCACCTGGCAGgtaggagtag ... ctttactcagGACTTTACCTAGGAGCGGCTCGGCGCGCAACATGTGAAGGCATGTAGGAAT
EST: gi|37393909|gb|CF634221.1|CF634221
EST:     TTTGGTAGTTCAAGCGGTTCTGCCAGCAGTTCGCAGCTCCCACCTGGCAG                         GACTTTACCTAGGAGCGGCTCGGCGCGCAACATGTGAAGGCATGTAGGAAT
genomic: TTTGGTAGTTCAAGCGGTTCTGCCAGCAGTTCGCAGCTCCCACCTGGCAGgtaggagtag ... ctttactcagGACTTTACCTAGGAGCGGCTCGGCGCGCAACATGTGAAGGCATGTAGGAAT
EST: gi|211146570|gb|FL325019.1|FL325019
EST:     TTTGGTAGTTCAAGCGGTTCTGCCAGCAGTTCGCAGCTCCCACCTGGCAG                         GACTTTACCTAGGAGCGGCTCGGCGCGCAACATGTGAAGGCATGTAGGAAT
genomic: TTTGGTAGTTCAAGCGGTTCTGCCAGCAGTTCGCAGCTCCCACCTGGCAGgtaggagtag ... ctttactcagGACTTTACCTAGGAGCGGCTCGGCGCGCAACATGTGAAGGCATGTAGGAAT
EST: gi|60347061|gb|DN214034.1|DN214034
EST:     TTTGGTAGTTCAAGCGGTTCTGCCAGCAGTTCGCAGCTCCCACCTGGCAG                         GACTTTACCTAGGAGCGGCTCGGCGCGCAACATGTGAAGGCATGTAGGAAT
genomic: TTTGGTAGTTCAAGCGGTTCTGCCAGCAGTTCGCAGCTCCCACCTGGCAGgtaggagtag ... ctttactcagGACTTTACCTAGGAGCGGCTCGGCGCGCAACATGTGAAGGCATGTAGGAAT
EST: gi|9953958|gb|BE640541.1|BE640541
EST:     TTTGGTAGTTCAAGCGGTTCTGCCAGCAGTTCGCAGCTCCCACCTGGCAG                         GACTTTACCTAGGAGCGGCTCGGCGCGCAACATGTGAAGGCATGTAGGAAT
genomic: TTTGGTAGTTCAAGCGGTTCTGCCAGCAGTTCGCAGCTCCCACCTGGCAGgtaggagtag ... ctttactcagGACTTTACCTAGGAGCGGCTCGGCGCGCAACATGTGAAGGCATGTAGGAAT
EST: gi|78179137|gb|DV549510.1|DV549510
EST:     TTTGGTAGTTCAAGCGGTTCTGCCAGCAGTTCGCAGCTCCCACCTGGCAG                         GACTTTACCTAGGAGCGGCTCGGCGCGCAACATGTGAAGGCATGTAGGAAT
genomic: TTTGGTAGTTCAAGCGGTTCTGCCAGCAGTTCGCAGCTCCCACCTGGCAGgtaggagtag ... ctttactcagGACTTTACCTAGGAGCGGCTCGGCGCGCAACATGTGAAGGCATGTAGGAAT
EST: gi|76930458|gb|DV172393.1|DV172393
EST:     TTTGGTAGTTCAAGCGGTTCTGCCAGCAGTTCGCAGCTCCCACCTGGCAG                         GACTTTACCTAGGAGCGGCTCGGCGCGCAACATGTGAAGGCATGTAGGAAT
genomic: TTTGGTAGTTCAAGCGGTTCTGCCAGCAGTTCGCAGCTCCCACCTGGCAGgtaggagtag ... ctttactcagGACTTTACCTAGGAGCGGCTCGGCGCGCAACATGTGAAGGCATGTAGGAAT
EST: gi|6918473|gb|AW400003.1|AW400003
EST:     TTTGGTAGTTCAAGCGGTTCTGCCAGCAGTTCGCAGCTCCCACCTGGCAG                         GACTTTACCTAGGAGCGGCTCGGCGCGCAACATGTGAAGGCATGTAGGAAT
genomic: TTTGGTAGTTCAAGCGGTTCTGCCAGCAGTTCGCAGCTCCCACCTGGCAGgtaggagtag ... ctttactcagGACTTTACCTAGGAGCGGCTCGGCGCGCAACATGTGAAGGCATGTAGGAAT

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: 49 (upstream exon), 48 (downstream exon)
Score: 236

AGCTGGCAGCTGTGCGCTTGGAGAAAGAGCAGGATAACAGGGCAAGACGTTTTGGTAGTTCAAGCGGTTCTGCCAGCAGTTCGCAGCTCCCACCTGGCAGgtaggagtag ... ctttactcagGACTTTACCTAGGAGCGGCTCGGCGCGCAACATGTGAAGGCATGTAGGAATTGACCGAATATGGCTTTGATGATCCTTACTTGGATTAGGACTGGTGACT


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 79

AGCTGGCAGCTGTGCGCTTGGAGAAAGAGCAGGATAACAGGGCAAGACGTTTTGGTAGTTCAAGCGGTTCTGCCAGCAGTTCGCAGCTCCCACCTGGCAGgtaggagtag ... ctttactcagGACTTTACCTAGGAGCGGCTCGGCGCGCAACATGTGAAGGCATGTAGGAATTGACCGAATATGGCTTTGATGATCCTTACTTGGATTAGGACTGGTGACT


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 106

AGCTGGCAGCTGTGCGCTTGGAGAAAGAGCAGGATAACAGGGCAAGACGTTTTGGTAGTTCAAGCGGTTCTGCCAGCAGTTCGCAGCTCCCACCTGGCAGgtaggagtag ... ctttactcagGACTTTACCTAGGAGCGGCTCGGCGCGCAACATGTGAAGGCATGTAGGAATTGACCGAATATGGCTTTGATGATCCTTACTTGGATTAGGACTGGTGACT


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 128

AGCTGGCAGCTGTGCGCTTGGAGAAAGAGCAGGATAACAGGGCAAGACGTTTTGGTAGTTCAAGCGGTTCTGCCAGCAGTTCGCAGCTCCCACCTGGCAGgtaggagtag ... ctttactcagGACTTTACCTAGGAGCGGCTCGGCGCGCAACATGTGAAGGCATGTAGGAATTGACCGAATATGGCTTTGATGATCCTTACTTGGATTAGGACTGGTGACT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gagttgaagagtctgtagtatgtgattgaccagatttgcgtgcatctttactcagGACTTTACCTAGGAGCGGCTCGGCGCGCAACATGTGAAGGCATGTAGGAATTGACCGAATATGGCTTTGATGATCCTTACTTGGATTAGGACTGGTGACT
                       gattgac  putative branch site (score: 128)
                                            tctttactc  putative PPT
                                           atcttta  TA-rich tract