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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTCACCGCAGAATCTTTCATTGATGGAGGATTCTTCAAGACAGGTGATACAGTAACTGTAGATGAGGAAGGATACTTCATAATTTTGGGACgtaagtaacagtttttatgcacatgcacgcacgcttatgtccttctagttgctgttttcatcacctcgtggtgttactgcctagggtcagcttcggtttgcttgtagcctcatttgcattaccttgtgcag

Basic information

species Zea mays
transcript GRMZM2G460078_T02
intron # 13
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G460078_T01 (Zea mays), 5'ss of exon 13
lower sequence: LOC_Os01g55590.1 (Oryza sativa), 5'ss of exon 13
GTCACCGCAGAATCTTTCATTGATGGAGGATTCTTCAAGACAGGTGATACAGTAACTGTAGATGAGGAAGGATACTTCATAATTTTGGGACgtaagtaacagtttttatgcacatgcacgcacgcttatgtccttctagttgctgttttcatcacctcgtggtgttactgccta---gggtcagcttcggtttgcttgtagcctcatttgcattaccttgtgcag
|| || |||||||| || |||||||| || ||||||||||| |||||||||||||||||||| || |||||||| ||||||||||| || |||||| | ||   || ||     | |||      || |||  || |  ||            |  | |||||| ||||| |||   |     | || || ||   |||   |||||||| |||| | |||| ||
GTTACTGCAGAATCATTTATTGATGGTGGGTTCTTCAAGACTGGTGATACAGTAACTGTAGACGATGAAGGATATTTCATAATTTTAGGGCgtaaggacca--cttcatcgttttccac---tagttgtgtttttttgttt------------aagttgtggtgctactgtctatttgtaatcgttttgggttatctgt---ctcatttgtattatcctgtgtag

upper sequence: GRMZM2G460078_T01 (Zea mays), 5'ss of exon 13
lower sequence: Vv09s0002g04170.t01 (Vitis vinifera), 5'ss of exon 13
GTCACCGCAGAATCTTTCATTGATGGAGGATTCTTCAAGACAGGTGATACAGTAACTGTAGATGAGGAAGGATACTTCATAATTTTGGGACgtaagtaa---cagtttttatgcacatgcacgcacg----cttatgtccttctagttgctgttttcatcacctcgtggtgttactgcctagggtcagcttcggtttgcttgtagcctcatttgcattaccttgtgcag
|| ||    ||||| || |||||||| || ||||||||||| |||||| | || |  || ||||| || ||||||| ||| || ||||||||||||||     || |  |||   |||| ||  ||     | |||    ||  | | | |  ||   ||  | |    | || |   |||      | |                                       
GTAACTAAGGAATCATTTATTGATGGCGGGTTCTTCAAGACTGGTGATGCTGTTAAAGTGGATGACGATGGATACTACATCATCTTGGGACgtaagtagacctagatcctatatgcatgaaccaacatggtcctattatttttaaatgggttattaactcgtcaccaaattttgccctctatatgtggttg--------------------------------------
















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|6601765|gb|AW256206.1|AW256206
EST:     AGGTGATACAGTAACTGTAGATGAGGAAGGATACTTCATAATTTTGGGAC                         GCACAAATGCCGACATTATGAAATTTGGCGGTTACAAGCTGTCAGCATTAG
genomic: AGGTGATACAGTAACTGTAGATGAGGAAGGATACTTCATAATTTTGGGACgtaagtaaca ... ccttgtgcagGCACAAATGCCGACATTATGAAATTTGGCGGTTACAAGCTGTCAGCATTAG
EST: gi|5847518|gb|AW000597.1|AW000597
EST:     AGGTGATACAGTAACTGTAGATGAGGAAGGATACTTCATAATTTTGGGAC                         GCACAAATGCCGACATTATGAAATTTGGCGGTTACAAGCTGTCAGCATTAG
genomic: AGGTGATACAGTAACTGTAGATGAGGAAGGATACTTCATAATTTTGGGACgtaagtaaca ... ccttgtgcagGCACAAATGCCGACATTATGAAATTTGGCGGTTACAAGCTGTCAGCATTAG
EST: gi|87153333|gb|DY398122.1|DY398122
EST:     AGGTGATACAGTAACTGTAGATGAGGAAGGATACTTCATAATTTTGGGAC                         GCACAAATGCCGACATTATGAAATTTGGCGGTTACAAGCTGTCAGCATTAG
genomic: AGGTGATACAGTAACTGTAGATGAGGAAGGATACTTCATAATTTTGGGACgtaagtaaca ... ccttgtgcagGCACAAATGCCGACATTATGAAATTTGGCGGTTACAAGCTGTCAGCATTAG
EST: gi|32867326|gb|CF007008.1|CF007008
EST:     GTAGATGAGGAAGGATACTTCATAATTTTGGGAC                         GCACAAATGCCGACATTATGAAATTTGGCGGTTACAAGCTGTCAGCATTAG
genomic: GTAGATGAGGAAGGATACTTCATAATTTTGGGACgtaagtaaca ... ccttgtgcagGCACAAATGCCGACATTATGAAATTTGGCGGTTACAAGCTGTCAGCATTAG
EST: gi|113694423|gb|DW847952.1|DW847952
EST:     TACTTCATAATTTTGGGAC                         GCACAAATAGCCGACATTATGAAATTTGGCGGTTACAAGCTGTCAGCATTA
genomic: TACTTCATAATTTTGGGACgtaagtaaca ... ccttgtgcagGCACAAAT-GCCGACATTATGAAATTTGGCGGTTACAAGCTGTCAGCATTA
EST: gi|37385309|gb|CF629791.1|CF629791
EST:     AGGTGTTACAGTAACTGTAGATGAGGAAGGATACTTCATAATTTTGGGAC                         GCACAAATGCCGACATTATGAAATTTGGCGGTTACAAGCTGTCAGCATTAG
genomic: AGGTGATACAGTAACTGTAGATGAGGAAGGATACTTCATAATTTTGGGACgtaagtaaca ... ccttgtgcagGCACAAATGCCGACATTATGAAATTTGGCGGTTACAAGCTGTCAGCATTAG
EST: gi|17921701|gb|BM259352.1|BM259352
EST:     AGGTGATACAGTAACTGTAGATGAGGAAGGATACTTCATAATTTTGGGAC                         GCACAAATGCCGACATTATGAAATTTGGCGGTTACAAGCTGTCAGCATTAG
genomic: AGGTGATACAGTAACTGTAGATGAGGAAGGATACTTCATAATTTTGGGACgtaagtaaca ... ccttgtgcagGCACAAATGCCGACATTATGAAATTTGGCGGTTACAAGCTGTCAGCATTAG
EST: gi|93012881|gb|EB638401.1|EB638401
EST:     AGGTGATACAGTAACTGTAGATGAGGAAGGATACTTCATAATTTTGGGAC                         GCACAAATGCCGACATTATGAAATTTGGCGGTTACAAGCTGTCAGCATTAG
genomic: AGGTGATACAGTAACTGTAGATGAGGAAGGATACTTCATAATTTTGGGACgtaagtaaca ... ccttgtgcagGCACAAATGCCGACATTATGAAATTTGGCGGTTACAAGCTGTCAGCATTAG
EST: gi|211208064|gb|FL437175.1|FL437175
EST:     AGGTGATACAGTAACTGTAGATGAGGAAGGATACTTCATAATTTTGGGAC                         GCACAAATGCCGACATTATGAAATTTGGCGGTTACAAGCTGTCAGCATTAG
genomic: AGGTGATACAGTAACTGTAGATGAGGAAGGATACTTCATAATTTTGGGACgtaagtaaca ... ccttgtgcagGCACAAATGCCGACATTATGAAATTTGGCGGTTACAAGCTGTCAGCATTAG
EST: gi|17970088|gb|BM276854.1|BM276854
EST:     AGGTGATACAGTAACTGTAGATGAGGAAGGATACTT-ATAATTTTGGGAC                         GCACAAATGCCGACATTATGAAATTTGGCGGTTACAAGCTGTCAGCATTAG
genomic: AGGTGATACAGTAACTGTAGATGAGGAAGGATACTTCATAATTTTGGGACgtaagtaaca ... ccttgtgcagGCACAAATGCCGACATTATGAAATTTGGCGGTTACAAGCTGTCAGCATTAG
EST: gi|78120378|gb|DV538762.1|DV538762
EST:     AGGTGATACAGTAACTGTAGATGAGGAAGGATACTTCATAATTTTGGGAC                         GCACAAATGCCGACATTATGAAATTTGGCGGTTACAAGCTGTCAGCATTAG
genomic: AGGTGATACAGTAACTGTAGATGAGGAAGGATACTTCATAATTTTGGGACgtaagtaaca ... ccttgtgcagGCACAAATGCCGACATTATGAAATTTGGCGGTTACAAGCTGTCAGCATTAG

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), 49 (downstream exon)
Score: 103

GTCACCGCAGAATCTTTCATTGATGGAGGATTCTTCAAGACAGGTGATACAGTAACTGTAGATGAGGAAGGATACTTCATAATTTTGGGACgtaagtaaca ... ccttgtgcagGCACAAATGCCGACATTATGAAATTTGGCGGTTACAAGCTGTCAGCATTAGAAATTGAGGCAGTACTGTTAGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 189

GTCACCGCAGAATCTTTCATTGATGGAGGATTCTTCAAGACAGGTGATACAGTAACTGTAGATGAGGAAGGATACTTCATAATTTTGGGACgtaagtaaca ... ccttgtgcagGCACAAATGCCGACATTATGAAATTTGGCGGTTACAAGCTGTCAGCATTAGAAATTGAGGCAGTACTGTTAGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 97

GTCACCGCAGAATCTTTCATTGATGGAGGATTCTTCAAGACAGGTGATACAGTAACTGTAGATGAGGAAGGATACTTCATAATTTTGGGACgtaagtaaca ... ccttgtgcagGCACAAATGCCGACATTATGAAATTTGGCGGTTACAAGCTGTCAGCATTAGAAATTGAGGCAGTACTGTTAGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 486

GTCACCGCAGAATCTTTCATTGATGGAGGATTCTTCAAGACAGGTGATACAGTAACTGTAGATGAGGAAGGATACTTCATAATTTTGGGACgtaagtaaca ... ccttgtgcagGCACAAATGCCGACATTATGAAATTTGGCGGTTACAAGCTGTCAGCATTAGAAATTGAGGCAGTACTGTTAGAG