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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagcttaatgttcctctccagttttttcaggcctgtgcgctgagttgctgacacagaacataatttacagatcatttacatgaattaaattatctggtataaattttactgtaacttcaatggtgattaacaacaccttaataaatttgtttttatgccatagGATGATCATGGAAATTCATCGCTTAGCCAGAGCAGTGGAAGTGAAATTGGAAGCTTTCTTGGTTGGGCTATGGCAATGATTTATATGGGTGGGCGGCTTC

Basic information

species Zea mays
transcript GRMZM2G153434_T01
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G153434_T01 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os01g16170.4 (Oryza sativa), 3'ss of exon 8
gtaagcttaatgttcctctccagttttttcaggcctgtgcgctgagttgctgacacagaacataatttacagatcatttacatgaattaaattatctggtataaattttactgtaacttcaatggtgattaacaacaccttaataaatt-tgtttttatgccatagGATGATCATGGAAATTCATCGCTTAGCCAGAGCAGTGGAAGTGAAATTGGAAGCTTTCTTGGTTGGGCTATGGCAATGATTTATATGGGTGGGCGGCTTC
                                                                         | |  | ||  | |  |  ||| | |||| | ||||    ||| | ||| | ||   ||||     || ||| ||| |  | || |  |||||||||| |||| | |||||||  | ||| |  |||||||||||| |||||||||||| |||||||||||||||||  | || ||||||||||| || ||||
------------------------------------------------------------------------gtaagctccagcagtacatctatttagtatgatttttttcataattgcaa-gttg--caacagtgg-ttgatacattataatcttctttcatagGATGACCATGCAGATTCATCTGTCAGCAATGGCAGTGGAAGTGGAATTGGAAGCTTCCTTGGTTGGGCTATGGCGGTAATCTATATGGGTGGACGACTTC
















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|22549090|gb|BU101291.1|BU101291
EST:     TGGCAAGTGGCACTGTCATACCAATTGGAAGAAGGCTTTTACTGCTTGTG                         GATGATCATGGAAATTCATCGCTTAG
genomic: TGGCAAGTGGCACTGTCATACCAATTGGAAGAAGGCTTTTACTGTTTGTGgtaagcttaa ... tatgccatagGATGATCATGGAAATTCATCGCTTAG
EST: gi|211278622|gb|FL264828.1|FL264828
EST:     TGGCAAGTGGCACTGTCATACCAATTGGAAGAAGGCTTTTACTGTTTGTG                         GATGATCATGGAAATTCATCGCTTAGCCAGAGCAGTGGAAGTGAAATTGGA
genomic: TGGCAAGTGGCACTGTCATACCAATTGGAAGAAGGCTTTTACTGTTTGTGgtaagcttaa ... tatgccatagGATGATCATGGAAATTCATCGCTTAGCCAGAGCAGTGGAAGTGAAATTGGA
EST: gi|89106847|gb|DY577064.1|DY577064
EST:     TGGCAAGTGGCACTGTCATACCAATTGGAAGAAGGCTTTTACTGTTTGTG                         GATGATCATGGAAATTCATCGCTTAGCCAGAGCAGTGGAAGTGAAATTGGA
genomic: TGGCAAGTGGCACTGTCATACCAATTGGAAGAAGGCTTTTACTGTTTGTGgtaagcttaa ... tatgccatagGATGATCATGGAAATTCATCGCTTAGCCAGAGCAGTGGAAGTGAAATTGGA
EST: gi|89106878|gb|DY577095.1|DY577095
EST:     TGGCAAGTGGCACTGTCATACCAATTGGAAGAAGGCTTTTACTGTTTGTG                         GATGATCATGGAAATTCATCGCTTAGCCAGAGCAGTGGAAGTGAAATTGGA
genomic: TGGCAAGTGGCACTGTCATACCAATTGGAAGAAGGCTTTTACTGTTTGTGgtaagcttaa ... tatgccatagGATGATCATGGAAATTCATCGCTTAGCCAGAGCAGTGGAAGTGAAATTGGA
EST: gi|26558987|gb|CA831222.1|CA831222
EST:     TGGCAAGTGGCACTGTCATACCAATTGGAAGAAGGCTTTTACTGTTTGTG                         GATGATCATGGAAATTCATCGCTTAGCCAGAGCAGTGGAAGTGAAATTGGA
genomic: TGGCAAGTGGCACTGTCATACCAATTGGAAGAAGGCTTTTACTGTTTGTGgtaagcttaa ... tatgccatagGATGATCATGGAAATTCATCGCTTAGCCAGAGCAGTGGAAGTGAAATTGGA
EST: gi|211278621|gb|FL264827.1|FL264827
EST:     TGGCAAGTGGCACTGTCATACCAATTGGAAGAAGGCTTTTACTGTTTGTG                         GATGATCATGGAAATTCATCGCTTAGCCAGAGCAGTGGAAGTGAAACTGGA
genomic: TGGCAAGTGGCACTGTCATACCAATTGGAAGAAGGCTTTTACTGTTTGTGgtaagcttaa ... tatgccatagGATGATCATGGAAATTCATCGCTTAGCCAGAGCAGTGGAAGTGAAATTGGA

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: 35 (upstream exon), 37 (downstream exon)
Score: 7

ATTGGGTACGTGCCTCTTGCACATTTTGATTGGAAACAAACATAGGGAGATGGCAAGTGGCACTGTCATACCAATTGGAAGAAGGCTTTTACTGTTTGTGgtaagcttaa ... tatgccatagGATGATCATGGAAATTCATCGCTTAGCCAGAGCAGTGGAAGTGAAATTGGAAGCTTTCTTGGTTGGGCTATGGCAATGATTTATATGGGTGGGCGGCTTC


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 35

ATTGGGTACGTGCCTCTTGCACATTTTGATTGGAAACAAACATAGGGAGATGGCAAGTGGCACTGTCATACCAATTGGAAGAAGGCTTTTACTGTTTGTGgtaagcttaa ... tatgccatagGATGATCATGGAAATTCATCGCTTAGCCAGAGCAGTGGAAGTGAAATTGGAAGCTTTCTTGGTTGGGCTATGGCAATGATTTATATGGGTGGGCGGCTTC


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 12

ATTGGGTACGTGCCTCTTGCACATTTTGATTGGAAACAAACATAGGGAGATGGCAAGTGGCACTGTCATACCAATTGGAAGAAGGCTTTTACTGTTTGTGgtaagcttaa ... tatgccatagGATGATCATGGAAATTCATCGCTTAGCCAGAGCAGTGGAAGTGAAATTGGAAGCTTTCTTGGTTGGGCTATGGCAATGATTTATATGGGTGGGCGGCTTC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 45

ATTGGGTACGTGCCTCTTGCACATTTTGATTGGAAACAAACATAGGGAGATGGCAAGTGGCACTGTCATACCAATTGGAAGAAGGCTTTTACTGTTTGTGgtaagcttaa ... tatgccatagGATGATCATGGAAATTCATCGCTTAGCCAGAGCAGTGGAAGTGAAATTGGAAGCTTTCTTGGTTGGGCTATGGCAATGATTTATATGGGTGGGCGGCTTC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctgtaacttcaatggtgattaacaacaccttaataaatttgtttttatgccatagGATGATCATGGAAATTCATCGCTTAGCCAGAGCAGTGGAAGTGAAATTGGAAGCTTTCTTGGTTGGGCTATGGCAATGATTTATATGGGTGGGCGGCTTC
                                     tttgttttt  CT-rich tract
                          accttaataaatttgt  TA-rich tract