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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CATGATAGCTTCAAGAGTAGTGATGTTTCTTCCTCGCAACATTGACCTAAACCAATTGGCGGACATGTCCTTGTCTGTGGATCCCCCGTGGGCAGTTGAGgtaagcccatttttgctgattttgtgccaagctgacgtttcctatagatgtcacagtggtctctctctctgcag

Basic information

species Zea mays
transcript GRMZM2G347808_T02
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G347808_T01 (Zea mays), 5'ss of exon 10
lower sequence: LOC_Os03g27930.1 (Oryza sativa), 5'ss of exon 11
CATGATAGCTTCAAGAGTAGTGATGTTTCTTCCTCGCAACATTGACCTAAACCAATTGGCGGACATGTCCTTGTCTGTGGATCCCCCGTGGGCAGTTGAGgtaagcccatttttgctgattttgtgccaagctgacgtttcctatagatgtcacagtggtctctctctctgcag-------------------------------------------------------------------------------------------------------------------
    || ||||| || || ||||||||||||||||| |||||||||| ||| |||||||| ||||||| | |||| || ||||| || |||||||||||||||   ||||||    |||||| |||   ||||||| ||  | | | | |  |  || |   | || | || ||                                                                                                                   
ATCAATCGCTTCGAGGGTGGTGATGTTTCTTCCTCGTAACATTGACCAAAATCAATTGGCAGACATGTGCCTGTCAGTTGATCCTCCTTGGGCAGTTGAGgtatatccatttcctgtgattt-gtgtatagctgac-ttggccacaaaaga-agggttgatgcact-tgtggagcttaattgtttatccatggtcttttcttctgatgcacttacttgtggaacttaattgtttatccatggtcttttcttctgatgctaagtggtcttttcctattactttctggcag
















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|32824820|gb|CD964542.1|CD964542
EST:     GATCTCCCGTGGGCAGTTGAG                         GTCGAGAAGAACTTCCTCAACGGAAAGCTGAAAGCCATAACAGCTTACTTT
genomic: GATCCCCCGTGGGCAGTTGAGgtaagcccat ... ctctctgcagGTCGAGAAGAACTTCCTCAACGGAAAGCTGAAAGCCATAACAGCTTACTTT
EST: gi|76015415|gb|DT942585.1|DT942585
EST:     ACCAATTGGCGGACATGTCCTTGTCTGTGGATCCCCCGTGGGCAGTTGAG                         GTCGAGAAGAACTTCCTCAACGGAAAGCTGAAAGCCATAACAGCTTACTTT
genomic: ACCAATTGGCGGACATGTCCTTGTCTGTGGATCCCCCGTGGGCAGTTGAGgtaagcccat ... ctctctgcagGTCGAGAAGAACTTCCTCAACGGAAAGCTGAAAGCCATAACAGCTTACTTT
EST: gi|89248734|gb|DY620520.1|DY620520
EST:     ACCAATTGGCGGACATGTCCTTGTCTGTGGATCCCCCGTGGGCAGTTGAG                         GTCGAGAAGAACTTCCTCAACGGAAAGCTGAAAGCCATAACAGCTTACTTT
genomic: ACCAATTGGCGGACATGTCCTTGTCTGTGGATCCCCCGTGGGCAGTTGAGgtaagcccat ... ctctctgcagGTCGAGAAGAACTTCCTCAACGGAAAGCTGAAAGCCATAACAGCTTACTTT
EST: gi|211522968|gb|FL454638.1|FL454638
EST:     GTGGGCAGTTGAG                         GTCGAGAAGAACTTCCTCAACGGAAAGCTGAAAGCCATAACAGCTTACTTT
genomic: GTGGGCAGTTGAGgtaagcccat ... ctctctgcagGTCGAGAAGAACTTCCTCAACGGAAAGCTGAAAGCCATAACAGCTTACTTT
EST: gi|71762989|gb|DR960926.1|DR960926
EST:     ACCAATTGGCGGACATGTCCTTGTCTGTGGATCCCCCGTGGGCAGTTGAG                         GTCGAGAAGAACTTCCTCAACGGAAAGCTGAAAGCCATAACAGCTTACTTT
genomic: ACCAATTGGCGGACATGTCCTTGTCTGTGGATCCCCCGTGGGCAGTTGAGgtaagcccat ... ctctctgcagGTCGAGAAGAACTTCCTCAACGGAAAGCTGAAAGCCATAACAGCTTACTTT
EST: gi|76020625|gb|DT947795.1|DT947795
EST:     ACCAATTGGCGGACATGTCCTTGTCTGTGGATCCCCCGTGGGCAGTTGAG                         GTCGAGAAGAACTTCCTCAACGGAAAGCTGAAAGCCATAACAGCTTACTTT
genomic: ACCAATTGGCGGACATGTCCTTGTCTGTGGATCCCCCGTGGGCAGTTGAGgtaagcccat ... ctctctgcagGTCGAGAAGAACTTCCTCAACGGAAAGCTGAAAGCCATAACAGCTTACTTT
EST: gi|60394235|gb|DN227105.1|DN227105
EST:     ACCAATTGGCGGACATGTCCTTGTCTGTGGATCCCCCGTGGGCAGTTGAG                         GTCGAGAAGAACTTCCTCAACGGAAAGCTGAAAGCCATAACAGCTTACTTT
genomic: ACCAATTGGCGGACATGTCCTTGTCTGTGGATCCCCCGTGGGCAGTTGAGgtaagcccat ... ctctctgcagGTCGAGAAGAACTTCCTCAACGGAAAGCTGAAAGCCATAACAGCTTACTTT
EST: gi|76020624|gb|DT947794.1|DT947794
EST:     ACCAATTGGCGGACATGTCCTTGTCTGTGGATCCCCCGTGGGCAGTTGAG                         GTCGAGAAGAACTTCCTCAACGGAAAGCTGAAAGCCATAACAGCTTACTTT
genomic: ACCAATTGGCGGACATGTCCTTGTCTGTGGATCCCCCGTGGGCAGTTGAGgtaagcccat ... ctctctgcagGTCGAGAAGAACTTCCTCAACGGAAAGCTGAAAGCCATAACAGCTTACTTT

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: 47 (upstream exon), 44 (downstream exon)
Score: 99

CATGATAGCTTCAAGAGTAGTGATGTTTCTTCCTCGCAACATTGACCTAAACCAATTGGCGGACATGTCCTTGTCTGTGGATCCCCCGTGGGCAGTTGAGgtaagcccat ... ctctctgcagGTCGAGAAGAACTTCCTCAACGGAAAGCTGAAAGCCATAACAGCTTACTTTGAAGAACAGGATCGTTGAACCAAGCATCGGCGCTGGTGATACAAATCAT


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 62

CATGATAGCTTCAAGAGTAGTGATGTTTCTTCCTCGCAACATTGACCTAAACCAATTGGCGGACATGTCCTTGTCTGTGGATCCCCCGTGGGCAGTTGAGgtaagcccat ... ctctctgcagGTCGAGAAGAACTTCCTCAACGGAAAGCTGAAAGCCATAACAGCTTACTTTGAAGAACAGGATCGTTGAACCAAGCATCGGCGCTGGTGATACAAATCAT


Block sizes: 41 (upstream exon), 47 (downstream exon)
Score: 43

CATGATAGCTTCAAGAGTAGTGATGTTTCTTCCTCGCAACATTGACCTAAACCAATTGGCGGACATGTCCTTGTCTGTGGATCCCCCGTGGGCAGTTGAGgtaagcccat ... ctctctgcagGTCGAGAAGAACTTCCTCAACGGAAAGCTGAAAGCCATAACAGCTTACTTTGAAGAACAGGATCGTTGAACCAAGCATCGGCGCTGGTGATACAAATCAT


Block sizes: 49 (upstream exon), 44 (downstream exon)
Score: 40

CATGATAGCTTCAAGAGTAGTGATGTTTCTTCCTCGCAACATTGACCTAAACCAATTGGCGGACATGTCCTTGTCTGTGGATCCCCCGTGGGCAGTTGAGgtaagcccat ... ctctctgcagGTCGAGAAGAACTTCCTCAACGGAAAGCTGAAAGCCATAACAGCTTACTTTGAAGAACAGGATCGTTGAACCAAGCATCGGCGCTGGTGATACAAATCAT