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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgcgtacattttataattttcgaatcagctgcacgtttgtagtttttgaagtaaacagctttccccttgccttaatgagcatccctccaacatatgcagGCAGTCCTTCACTTAAGGGGAGTCTCTTTCGGTGGTGTCAGGTAGTCGGGGGAGGCAAGCACAAAAAACTGGTCTTACTGGGCGATCCTGTTGGGAGTCG

Basic information

species Zea mays
transcript AC214119.3_FGT009
intron # 14
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|71317392|gb|DR795407.1|DR795407
EST:     GATAAGAAACGGGCTGTTCGTCGAGTGGCTGTCCGATGCCGGCACACATG                         GCAGTCCTTCACTTAAGGGGAGTCTCTTTCGGTGGTGTCAGGTAGTCGGGG
genomic: GATAAGAAACGGGCTGTTCGTCGAGTGGCTGTCCGATGCCGGCACACATGgtgcgtacat ... acatatgcagGCAGTCCTTCACTTAAGGGGAGTCTCTTTCGGTGGTGTCAGGTAGTCGGGG
EST: gi|91876638|gb|EB406595.1|EB406595
EST:     GATAAGAAACGGGCTGTTCGTCGAGTGGCTGTCCGATGCCGGCACACATG                         GCAGTCCTTCACTTAAGGGGAGTCTCTTTCGGTGGTGTCAGGTAGTCGGGG
genomic: GATAAGAAACGGGCTGTTCGTCGAGTGGCTGTCCGATGCCGGCACACATGgtgcgtacat ... acatatgcagGCAGTCCTTCACTTAAGGGGAGTCTCTTTCGGTGGTGTCAGGTAGTCGGGG
EST: gi|91876639|gb|EB406596.1|EB406596
EST:     GATAAGAAACGGGCTGTTCGTCGAGTGGCTGTCCGATGCCGGCACACATG                         GCAGTCCTTCACTTAAGGGGAGTCTCTTTCGGTGGTGTCAGGTAGTCGGGG
genomic: GATAAGAAACGGGCTGTTCGTCGAGTGGCTGTCCGATGCCGGCACACATGgtgcgtacat ... acatatgcagGCAGTCCTTCACTTAAGGGGAGTCTCTTTCGGTGGTGTCAGGTAGTCGGGG
EST: gi|71317391|gb|DR795406.1|DR795406
EST:     GATAAGAAACGGGCTGTTCGTCGAGTGGCTGTCCGATGCCGGCACACATG                         GCAGTCCTTCACTTAAGGGGAGTCTCTTTCGGTGGTGTCAGGTAGTCGGGG
genomic: GATAAGAAACGGGCTGTTCGTCGAGTGGCTGTCCGATGCCGGCACACATGgtgcgtacat ... acatatgcagGCAGTCCTTCACTTAAGGGGAGTCTCTTTCGGTGGTGTCAGGTAGTCGGGG

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), 49 (downstream exon)
Score: 86

GTTGTGCAGGCAGCAGTCAGGGCTCTCGACGATAAGAAACGGGCTGTTCGTCGAGTGGCTGTCCGATGCCGGCACACATGgtgcgtacat ... acatatgcagGCAGTCCTTCACTTAAGGGGAGTCTCTTTCGGTGGTGTCAGGTAGTCGGGGGAGGCAAGCACAAAAAACTGGTCTTACTGGGCGATCCTGTTGGGAGTCG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 51

GTTGTGCAGGCAGCAGTCAGGGCTCTCGACGATAAGAAACGGGCTGTTCGTCGAGTGGCTGTCCGATGCCGGCACACATGgtgcgtacat ... acatatgcagGCAGTCCTTCACTTAAGGGGAGTCTCTTTCGGTGGTGTCAGGTAGTCGGGGGAGGCAAGCACAAAAAACTGGTCTTACTGGGCGATCCTGTTGGGAGTCG


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

GTTGTGCAGGCAGCAGTCAGGGCTCTCGACGATAAGAAACGGGCTGTTCGTCGAGTGGCTGTCCGATGCCGGCACACATGgtgcgtacat ... acatatgcagGCAGTCCTTCACTTAAGGGGAGTCTCTTTCGGTGGTGTCAGGTAGTCGGGGGAGGCAAGCACAAAAAACTGGTCTTACTGGGCGATCCTGTTGGGAGTCG


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 32

GTTGTGCAGGCAGCAGTCAGGGCTCTCGACGATAAGAAACGGGCTGTTCGTCGAGTGGCTGTCCGATGCCGGCACACATGgtgcgtacat ... acatatgcagGCAGTCCTTCACTTAAGGGGAGTCTCTTTCGGTGGTGTCAGGTAGTCGGGGGAGGCAAGCACAAAAAACTGGTCTTACTGGGCGATCCTGTTGGGAGTCG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttgaagtaaacagctttccccttgccttaatgagcatccctccaacatatgcagGCAGTCCTTCACTTAAGGGGAGTCTCTTTCGGTGGTGTCAGGTAGTCGGGGGAGGCAAGCACAAAAAACTGGTCTTACTGGGCGATCCTGTTGGGAGTCG
                         ccttaat  putative branch site (score: 32)
                           ttaatga  TA-rich tract