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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACTAAACCAAAAGCGAGGGGCCTGGATATCAGACTTGAACTTCTGAAGTTTTACAAGAATTATTCAGCAAACGTTATGCACCTTGTTGTTTATGGAAAGGgtaagtattgcaaattagtacattggagtacataagcctatttgttactgataaaatgattttgtag

Basic information

species Zea mays
transcript GRMZM2G054905_T01
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G054905_T01 (Zea mays), 5'ss of exon 9
lower sequence: LOC_Os01g57082.1 (Oryza sativa), 5'ss of exon 8
ACTAAACCAAAAGCGAGGGGCCTGGATATCAGACTTGAACTTCTGAAGTTTTACAAGAATTATTCAGCAAACGTTATGCACCTTGTTGTTTATGGAAAGGgtaagtattgcaaattagtacattggagtacataagcctatttgttactgataaaatgattttgtag------
|| |||||||||| ||||||  |||| || ||||  || ||||||||||| ||  ||||||||||||||||| ||||||||||||||||||||||||||||||| |||| |   ||||| ||||    ||||  | | ||| ||||||||| |  ||   ||| |        
ACAAAACCAAAAGAGAGGGGATTGGACATTAGACAGGAGCTTCTGAAGTTCTATGAGAATTATTCAGCAAACCTTATGCACCTTGTTGTTTATGGAAAGGgtaaatattactggttagtccattctcataca--aacttatctgttactgagattatttatttattttggtag

upper sequence: GRMZM2G054905_T01 (Zea mays), 5'ss of exon 9
lower sequence: LOC_Os01g57073.1 (Oryza sativa), 5'ss of exon 8
ACTAAACCAAAAGCGAGGGGCCTGGATATCAGACTTGAACTTCTGAAGTTTTACAAGAATTATTCAGCAAACGTTATGCACCTTGTTGTTTATGGAAAGGgtaagtattgcaaattagtacattggagtacataagcctatttgttactgataaaatgattttgtag-------
|| |||||||||| ||||||  |||| || ||||  || ||||||||||| ||  ||||||||||||||||| | ||||||||||||||||||||||||||||| |||| |   ||||| ||||     ||| || | ||| |||||||||     |  |||| |         
ACAAAACCAAAAGAGAGGGGATTGGACATTAGACAGGAGCTTCTGAAGTTCTATGAGAATTATTCAGCAAACCTGATGCACCTTGTTGTTTATGGAAAGGgtaaatattactggttagtccattct--cacacaaacttatctgttactgaggtttttttttttttttgggtag
















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|14191057|gb|BG833287.1|BG833287
EST:     TTACAAGAATTATTCAGCAAACGTTATGCACCTTGTTGTTTATGGAAAGG                         AGAACCTCGATTGCATTCAGGGCTTGGTTGAGCGTATGTTTAGTGACATAA
genomic: TTACAAGAATTATTCAGCAAACGTTATGCACCTTGTTGTTTATGGAAAGGgtaagtattg ... gattttgtagAGAACCTCGATTGCATTCAGGGCTTGGTTGAGCGTATGTTTAGTGACATAA
EST: gi|19272565|gb|BM888821.1|BM888821
EST:     TTACAAGAATTATTCAGCATACGTTATGCACCTTGTTGTTTATGGAAAGG                         AGAACCTCGATTGCATTCAGGGCTTGGTTGAGCGTATGTTTAGTGACAT
genomic: TTACAAGAATTATTCAGCAAACGTTATGCACCTTGTTGTTTATGGAAAGGgtaagtattg ... gattttgtagAGAACCTCGATTGCATTCAGGGCTTGGTTGAGCGTATGTTTAGTGACAT
EST: gi|22491542|gb|BU051465.1|BU051465
EST:     TTACAAGAATTATTCAGCAAACGTTATGCACCTTGTTGTTTATGGAAAGG                         AGAACCTCGATTGCATTCAGGGCTTGGTTGAGCGTATGTTTAGTGACATAA
genomic: TTACAAGAATTATTCAGCAAACGTTATGCACCTTGTTGTTTATGGAAAGGgtaagtattg ... gattttgtagAGAACCTCGATTGCATTCAGGGCTTGGTTGAGCGTATGTTTAGTGACATAA
EST: gi|19272510|gb|BM888766.1|BM888766
EST:     TTACAAGAATTATTCAGCAAACGTTATGCACCTTGTTGTTTATGGAAAGG                         AGAACCTCGATTGCATTCAGGGCTCGGTTGAGCGTATGTTTAGTGACATAA
genomic: TTACAAGAATTATTCAGCAAACGTTATGCACCTTGTTGTTTATGGAAAGGgtaagtattg ... gattttgtagAGAACCTCGATTGCATTCAGGGCTTGGTTGAGCGTATGTTTAGTGACATAA
EST: gi|87152720|gb|DY397509.1|DY397509
EST:     TTACAAGAATTATTCAGCAAACGTTATGCACCTTGTTGTTTATGGAAAGG                         AGAACCTCGATTGCATTCAGGGCTTGGTTGAGCGTATGTTTAGTGACATAA
genomic: TTACAAGAATTATTCAGCAAACGTTATGCACCTTGTTGTTTATGGAAAGGgtaagtattg ... gattttgtagAGAACCTCGATTGCATTCAGGGCTTGGTTGAGCGTATGTTTAGTGACATAA
EST: gi|19351400|gb|BM895932.1|BM895932
EST:     TTACAAGAATTATTCAGCAAACGTTATGCACCTTGTTGTTTATGGAAAGG                         AGAACCTCGATTGCATTCAGGGCTTGGTTGAGCGTATGTTTAGTGACATAA
genomic: TTACAAGAATTATTCAGCAAACGTTATGCACCTTGTTGTTTATGGAAAGGgtaagtattg ... gattttgtagAGAACCTCGATTGCATTCAGGGCTTGGTTGAGCGTATGTTTAGTGACATAA
EST: gi|22491318|gb|BU051241.1|BU051241
EST:     TTACAAGAATTATTCAGCAAACGTTATGCACCTTGTTGTTTATGGAAAGG                         AGAACCTCGATTGCATTCAGGGCTTGGTTGAGCGTATGTTTAGTGACATAA
genomic: TTACAAGAATTATTCAGCAAACGTTATGCACCTTGTTGTTTATGGAAAGGgtaagtattg ... gattttgtagAGAACCTCGATTGCATTCAGGGCTTGGTTGAGCGTATGTTTAGTGACATAA
EST: gi|87153579|gb|DY398368.1|DY398368
EST:     TTACAAGAATTATTCAGCAAACGTTATGCACCTTGTTGTTTATGGAAAGG                         AGAACCTCGATTGCATTCAGGGCTTGGTTGAGCGTATGTTTAGTGACATAA
genomic: TTACAAGAATTATTCAGCAAACGTTATGCACCTTGTTGTTTATGGAAAGGgtaagtattg ... gattttgtagAGAACCTCGATTGCATTCAGGGCTTGGTTGAGCGTATGTTTAGTGACATAA
EST: gi|19351432|gb|BM895949.1|BM895949
EST:     TTACAAGAATTATTCAGCAAACGTTATGCACCTTGTTGTTTATGGAAAGG                         AGAACCTCGATTGCATTCAGGGCTTGGTTGAGCGTATGTTTAGTGACATAA
genomic: TTACAAGAATTATTCAGCAAACGTTATGCACCTTGTTGTTTATGGAAAGGgtaagtattg ... gattttgtagAGAACCTCGATTGCATTCAGGGCTTGGTTGAGCGTATGTTTAGTGACATAA

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: 48 (upstream exon), 48 (downstream exon)
Score: 111

ACTAAACCAAAAGCGAGGGGCCTGGATATCAGACTTGAACTTCTGAAGTTTTACAAGAATTATTCAGCAAACGTTATGCACCTTGTTGTTTATGGAAAGGgtaagtattg ... gattttgtagAGAACCTCGATTGCATTCAGGGCTTGGTTGAGCGTATGTTTAGTGACATAAAAAACACTGATCAGAGAAGCTTGAAATGTCCAAGTCATCCTCTTTCAGA


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 104

ACTAAACCAAAAGCGAGGGGCCTGGATATCAGACTTGAACTTCTGAAGTTTTACAAGAATTATTCAGCAAACGTTATGCACCTTGTTGTTTATGGAAAGGgtaagtattg ... gattttgtagAGAACCTCGATTGCATTCAGGGCTTGGTTGAGCGTATGTTTAGTGACATAAAAAACACTGATCAGAGAAGCTTGAAATGTCCAAGTCATCCTCTTTCAGA


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 185

ACTAAACCAAAAGCGAGGGGCCTGGATATCAGACTTGAACTTCTGAAGTTTTACAAGAATTATTCAGCAAACGTTATGCACCTTGTTGTTTATGGAAAGGgtaagtattg ... gattttgtagAGAACCTCGATTGCATTCAGGGCTTGGTTGAGCGTATGTTTAGTGACATAAAAAACACTGATCAGAGAAGCTTGAAATGTCCAAGTCATCCTCTTTCAGA


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

ACTAAACCAAAAGCGAGGGGCCTGGATATCAGACTTGAACTTCTGAAGTTTTACAAGAATTATTCAGCAAACGTTATGCACCTTGTTGTTTATGGAAAGGgtaagtattg ... gattttgtagAGAACCTCGATTGCATTCAGGGCTTGGTTGAGCGTATGTTTAGTGACATAAAAAACACTGATCAGAGAAGCTTGAAATGTCCAAGTCATCCTCTTTCAGA