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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTGGGCATGATGATAAGAAGCTGATGATTCCTACTACAGTAATTTTAAGGCACATGTTCACTCCTGCTGAGTTAAGAgtaagtagctgaaatatgcttggcgcctcctgcaatatgtgctcttttgatctgagacagctcttgtacttgattgcacattagatcattcagattgttcacatgaggtgttcattcttcagagcaactttattttcattcttattggattaaccaataatatccttcag

Basic information

species Zea mays
transcript GRMZM2G074351_T01
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G074351_T01 (Zea mays), 5'ss of exon 10
lower sequence: LOC_Os04g41910.2 (Oryza sativa), 5'ss of exon 10
GTGGGCATGATGATAAGAAGCTGATGATTCCTACTACAGTAATTTTAAGGCACATGTTCACTCCTGCTGAGTTAAGAgtaagtagctgaaatatgctt-ggcgcctcctgcaatatgtgctcttttgatctgagacagctcttgtacttgattgcacattagatcattcagattgttcacatgaggtgttcattcttcagagcaactttattttcattcttattggattaaccaataatatcct--tcag-----
|||| |||||||| |||||| ||| |||| | |||||||| ||||| ||||| ||||||||||||||||| ||  ||||||||| |||||  |||||| | ||  | |   ||  ||||| ||| ||||     |||  |      ||| ||||             |  ||||  || ||||   |  ||||| | || ||||||||   ||   || |  ||||||| |  || || ||| |  |||      
GTGGACATGATGACAAGAAGGTGACGATTACAACTACAGTTATTTTGAGGCATATGTTCACTCCTGCTGAATTGCGAgtaagtaactgaagcatgctttgacgtatgccagaa-gtgtgcccttctgat-----acaattt-----cttaattg-------------tttgattagtcccatggatt--tcattatgcatagcaacttc--ttatgttttatttggattgaggaagaaaatcttgatcatttcag
















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|211121225|gb|FL444926.1|FL444926
EST:     TTAAGGCACATGTTCACTCCTGCTGAGTTAAGA                         GCTGATGAAGAGCTTCTTTCTGAGCTTGAGACTGATGTTAGAGAGGAATGC
genomic: TTAAGGCACATGTTCACTCCTGCTGAGTTAAGAgtaagtagct ... tatccttcagGCTGATGAAGAGCTTCTTTCTGAGCTTGAGACTGATGTTAGAGAGGAATGC
EST: gi|60339717|gb|DN206690.1|DN206690
EST:     TTCCTACTACAGTAATTTTAAGGCACATGTTCACTCCTGCTGAGTTAAGA                         GCTGATGAAGAGCTTCTTTCTGAGCTTGAGACTGATGTTAGAGAGGAATGC
genomic: TTCCTACTACAGTAATTTTAAGGCACATGTTCACTCCTGCTGAGTTAAGAgtaagtagct ... tatccttcagGCTGATGAAGAGCTTCTTTCTGAGCTTGAGACTGATGTTAGAGAGGAATGC
EST: gi|32837936|gb|CD977614.1|CD977614
EST:     TTCCTACTACAGTAATTTTAAGGCACATGTTCACTCCTGCTGAGTTAAGA                         GCTGATGAAGAGCTTCTTTCTGAGCTTGAGACTGATGTTAGAGAGGAATGC
genomic: TTCCTACTACAGTAATTTTAAGGCACATGTTCACTCCTGCTGAGTTAAGAgtaagtagct ... tatccttcagGCTGATGAAGAGCTTCTTTCTGAGCTTGAGACTGATGTTAGAGAGGAATGC
EST: gi|211013609|gb|FL363381.1|FL363381
EST:     TTCCTACTACAGTAATTTTAAGGCACATGTTCACTCCTGCTGAGTTAAGA                         GCTGATGAAGAGCTTCTTTCTGAGCTTGAGACTGATGTTAGAGAGGAATGC
genomic: TTCCTACTACAGTAATTTTAAGGCACATGTTCACTCCTGCTGAGTTAAGAgtaagtagct ... tatccttcagGCTGATGAAGAGCTTCTTTCTGAGCTTGAGACTGATGTTAGAGAGGAATGC
EST: gi|211309996|gb|FL325113.1|FL325113
EST:     TCCTACTACAGTACATTTTAAGGCACATGTTCACTCCTGCTGAGTTAAGA                         GCTGATGAAGAGCTTCTTTCTGAGCTTGAGACTGATGTTAGAGAGGAATGC
genomic: TCCTACTACAGTA-ATTTTAAGGCACATGTTCACTCCTGCTGAGTTAAGAgtaagtagct ... tatccttcagGCTGATGAAGAGCTTCTTTCTGAGCTTGAGACTGATGTTAGAGAGGAATGC
EST: gi|32933834|gb|CF038646.1|CF038646
EST:     ACAGTAATTTTAAGGCACATGTTCACTCCTGCTGAGTTAAGA                         GCTGATGAAGAGCTTCTTTCTGAGCTTGAGACTGATGTTAGAGAGGAATGC
genomic: ACAGTAATTTTAAGGCACATGTTCACTCCTGCTGAGTTAAGAgtaagtagct ... tatccttcagGCTGATGAAGAGCTTCTTTCTGAGCTTGAGACTGATGTTAGAGAGGAATGC

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: 77

GTGGGCATGATGATAAGAAGCTGATGATTCCTACTACAGTAATTTTAAGGCACATGTTCACTCCTGCTGAGTTAAGAgtaagtagct ... tatccttcagGCTGATGAAGAGCTTCTTTCTGAGCTTGAGACTGATGTTAGAGAGGAATGCATCAAGTTTGGTCCTGTGGATAATGTCAAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 63

GTGGGCATGATGATAAGAAGCTGATGATTCCTACTACAGTAATTTTAAGGCACATGTTCACTCCTGCTGAGTTAAGAgtaagtagct ... tatccttcagGCTGATGAAGAGCTTCTTTCTGAGCTTGAGACTGATGTTAGAGAGGAATGCATCAAGTTTGGTCCTGTGGATAATGTCAAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 71

GTGGGCATGATGATAAGAAGCTGATGATTCCTACTACAGTAATTTTAAGGCACATGTTCACTCCTGCTGAGTTAAGAgtaagtagct ... tatccttcagGCTGATGAAGAGCTTCTTTCTGAGCTTGAGACTGATGTTAGAGAGGAATGCATCAAGTTTGGTCCTGTGGATAATGTCAAG


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 43

GTGGGCATGATGATAAGAAGCTGATGATTCCTACTACAGTAATTTTAAGGCACATGTTCACTCCTGCTGAGTTAAGAgtaagtagct ... tatccttcagGCTGATGAAGAGCTTCTTTCTGAGCTTGAGACTGATGTTAGAGAGGAATGCATCAAGTTTGGTCCTGTGGATAATGTCAAG