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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gattgtatgatactttcaagtttagaaacaggaagcttgttgctatgattgatgtggacaggaaatatgggcataccattattaacaaactcacttgcagAGGTTTTGATGATGAGATGAGAGCTATTGTTGCAAGCAACCTTGAGGGAAGGGGAATCAAGTTGCATCCAGGGACAAATCTCTCTGAG

Basic information

species Zea mays
transcript GRMZM5G806449_T03
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G806449_T01 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os02g56850.1 (Oryza sativa), 3'ss of exon 8
------gattgtatgatactttcaagtttagaaacaggaagcttgttgctatgattgatgtggacaggaaatatgggcataccattattaacaaactcacttgcagAGGTTTTGATGATGAGATGAGAGCTATTGTTGCAAGCAACCTTGAGGGAAGGGGAATCAAGTTGCATCCAGGGACAAATCTCTCTGAG
      ||  | |||  | | |||  ||||  | |   ||  |    |||||   | | |     |   |  |||   |    ||    ||   ||| | |||||||||||| ||||||||||||||  |  |||||||||| ||||||||||||||||||||||  || ||||||||||||||||| ||||||
tatggagaaagaatgccaatgtcatttttattagccaaaatttcaa-gctattgattacggttctatccaccatgatta----atggcgaattgactaa-ttgcagAGGTTTCGATGATGAGATGAGGACGGTTGTTGCAAGTAACCTTGAGGGAAGGGGAATCAGATTACATCCAGGGACAAATCTATCTGAG

upper sequence: GRMZM5G806449_T01 (Zea mays), 3'ss of exon 7
lower sequence: GLYMA16G27210.1 (Glycine max), 3'ss of exon 8
--gattgtatgatactttcaagtttagaaacaggaagcttgttgctatgattgatgtggacaggaaatatgggcataccattattaacaaactcacttgcagAGGTTTTGATGATGAGATGAGAGCTATTGTTGCAAGCAACCTTGAGGGAAGGGGAATCAAGTTGCATCCAGGGACAAATCTCTCTGAG
    || | |||||      | | |             ||      ||  ||| |||    || | |  |       |  | | |||  || ||  ||||||||||||||||||||| |||||||||   || ||||| || ||||| || |||||||| || ||||||||| |||| ||| |  |  ||
gaagttttctgataacactcattattccttagtttttgttaacatcatttttgctgtttgtagcataccttactccccactgaataa--aattctgttgcagAGGTTTTGATGATGAAATGAGAGCTGCAGTGGCAAGAAATCTTGAAGGCAGGGGAATTAATTTGCATCCAAGGACCAATTTGACACAG

upper sequence: GRMZM5G806449_T01 (Zea mays), 3'ss of exon 7
lower sequence: GLYMA02G08180.1 (Glycine max), 3'ss of exon 7
gattgtatgatactttcaagtttagaaacaggaagcttgttgctatgattgatgtggacaggaaatatgggcatacc--attattaac------aaactcacttgcagAGGTTTTGATGATGAGATGAGAGCTATTGTTGCAAGCAACCTTGAGGGAAGGGGAATCAAGTTGCATCCAGGGACAAATCTCTCTGAG
   | |||  ||||  |     ||  || |||  || |  | |  |  ||  ||   |||  |  | | | ||||||  | |    ||      ||| ||  ||||||||||||||||||||| ||||||||| | |||||||| || ||||| || |||||||| || ||||||||| |||| |||||  |  ||
--gtttatactactcac-----tattaataggttgcattattccctagtttttgctaacatcatttttag-cataccttactccccactgaataaaattctgttgcagAGGTTTTGATGATGAAATGAGAGCTGTAGTTGCAAGAAATCTTGAAGGCAGGGGAATTAATTTGCATCCAAGGACCAATCTGACACAG

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|211287654|gb|FL367858.1|FL367858
EST:     GGGATGGGTGCTGAAGTAGATTTGTTTTATCGAAGAGATCTTCCTCTAAG                         AGGTTTTGATGATGAGATGAGAGCTATTGTTGCAAGCAACCTTGAGGGAAG
genomic: GGGATGGGTGCTGAAGTAGATTTGTTTTATCGAAGAGATCTTCCTCTAAGgtttgtaatt ... tcacttgcagAGGTTTTGATGATGAGATGAGAGCTATTGTTGCAAGCAACCTTGAGGGAAG
EST: gi|148994377|gb|EE034060.2|EE034060
EST:     GGGATGGGTGCTGAAGTAGATTTGTTTTATCGAAGAGATCTTCCTCTA-G                         AAGGTTTTGATGATGAGATGAGAGCTATTGTTGCAAGCAACCTTTGAGG
genomic: GGGATGGGTGCTGAAGTAGATTTGTTTTATCGAAGAGATCTTCCTCTAAGgtttgtaatt ... tcacttgcagA-GGTTTTGATGATGAGATGAGAGCTATTGTTGCAAGCAACCTT-GAGG
EST: gi|211462691|gb|FL336836.1|FL336836
EST:     GGGATGGGTGCTGAAGTAGATTTGTTTTATCGAAGAGATCTTCCTCTAAG                         AGGTTTTGATGATGAGATGAGAGCTATTGTTGCAAGCAACCTTGAGGGAAG
genomic: GGGATGGGTGCTGAAGTAGATTTGTTTTATCGAAGAGATCTTCCTCTAAGgtttgtaatt ... tcacttgcagAGGTTTTGATGATGAGATGAGAGCTATTGTTGCAAGCAACCTTGAGGGAAG
EST: gi|211123447|gb|FL321141.1|FL321141
EST:     GGGATGGGTGCTGAAGTAGATTTGTTTTATCGAAGAGATCTTCCTCTAAG                         AGGTTTTGATGATGAGATGAGAGCTATTGTTGCAAGCAACCTTGAGGGAAG
genomic: GGGATGGGTGCTGAAGTAGATTTGTTTTATCGAAGAGATCTTCCTCTAAGgtttgtaatt ... tcacttgcagAGGTTTTGATGATGAGATGAGAGCTATTGTTGCAAGCAACCTTGAGGGAAG
EST: gi|67026810|gb|CO455559.1|CO455559
EST:     GGGATGGGTGCTGAAGTAGATTTGTTTTATCGAAAAGATCTTCCTTTAAG                         AGGTTTTGATGATGAGATGAGAGCTATTGTTGCAAGCAACCTTGAGGGAAG
genomic: GGGATGGGTGCTGAAGTAGATTTGTTTTATCGAAGAGATCTTCCTCTAAGgtttgtaatt ... tcacttgcagAGGTTTTGATGATGAGATGAGAGCTATTGTTGCAAGCAACCTTGAGGGAAG
EST: gi|24934176|gb|CA452394.1|CA452394
EST:     GGGATGGGTGCTGAAGTAGATTTGTTNTATCGAAGAGATCTTCCTCTAAG                         AAGTTTTGATGATGAGATGAGAGCTATTGTTGCCAGCAACCTTGAGGGAAG
genomic: GGGATGGGTGCTGAAGTAGATTTGTTTTATCGAAGAGATCTTCCTCTAAGgtttgtaatt ... tcacttgcagAGGTTTTGATGATGAGATGAGAGCTATTGTTGCAAGCAACCTTGAGGGAAG
EST: gi|211135367|gb|FL349825.1|FL349825
EST:     GGGATGGGTGCTGAAGTAGATTTGTTTTATCGAAGAGATCTTCCTCTAAG                         ANGTTTTGATGATGAGATGAGAGCTATTGTTGCAAGCAACCTTGAGGGAAG
genomic: GGGATGGGTGCTGAAGTAGATTTGTTTTATCGAAGAGATCTTCCTCTAAGgtttgtaatt ... tcacttgcagAGGTTTTGATGATGAGATGAGAGCTATTGTTGCAAGCAACCTTGAGGGAAG
EST: gi|32794339|gb|CD946575.1|CD946575
EST:     GATCTTCCTCTAAG                         AGGTTTTGATGATGAGATGAGAGCTATTGTTGCAAGCAACCTTGAGGGAAG
genomic: GATCTTCCTCTAAGgtttgtaatt ... tcacttgcagAGGTTTTGATGATGAGATGAGAGCTATTGTTGCAAGCAACCTTGAGGGAAG
EST: gi|24934507|gb|CA452725.1|CA452725
EST:     GGGATGGGTGCTGAAGTAGATTTGTTTTATCGAAGAGATCTTCCTCTAAG                         AGGTTTTGATGATGAGATGAGAGCTATTGTTGCAAGCAACCTTGAGGGAAG
genomic: GGGATGGGTGCTGAAGTAGATTTGTTTTATCGAAGAGATCTTCCTCTAAGgtttgtaatt ... tcacttgcagAGGTTTTGATGATGAGATGAGAGCTATTGTTGCAAGCAACCTTGAGGGAAG
EST: gi|211396212|gb|FL320934.1|FL320934
EST:     GGGATGGGTGCTGAAGTAGATTTGTTTTATCGAAGAGATCTTCCTCTAAG                         AGGTTTTGATGATGAGATGAGAGCTATTGTTGCAAGCAACCTTGAGGGAAG
genomic: GGGATGGGTGCTGAAGTAGATTTGTTTTATCGAAGAGATCTTCCTCTAAGgtttgtaatt ... tcacttgcagAGGTTTTGATGATGAGATGAGAGCTATTGTTGCAAGCAACCTTGAGGGAAG
EST: gi|47961736|gb|CN844445.1|CN844445
EST:     GGTGCTGAAGTAGATTTGTTTTATCGAAAAGATCTTCCTTTAAG                         AGGTTTTGATGATGAGATGAGAGCTATTGTTGCAAGCAACCTTGAGGGAAG
genomic: GGTGCTGAAGTAGATTTGTTTTATCGAAGAGATCTTCCTCTAAGgtttgtaatt ... tcacttgcagAGGTTTTGATGATGAGATGAGAGCTATTGTTGCAAGCAACCTTGAGGGAAG
EST: gi|211460047|gb|FL333663.1|FL333663
EST:     GGGATGGGTGCTGAAGTAGATTTGTTTTATCGAAGAGATCTTCCTCTAAG                         AGGTTTTGATGATGAGATGAGAGCTATTGTTGCAAGCAACCTTGAGGGAAG
genomic: GGGATGGGTGCTGAAGTAGATTTGTTTTATCGAAGAGATCTTCCTCTAAGgtttgtaatt ... tcacttgcagAGGTTTTGATGATGAGATGAGAGCTATTGTTGCAAGCAACCTTGAGGGAAG
EST: gi|76293305|gb|DV032873.1|DV032873
EST:     GGGATGGGTGCTGAAGTAGATTTGTTTTATCGAAGAGATCTTCCTCTAAG                         AGGTTTTGATGATG
genomic: GGGATGGGTGCTGAAGTAGATTTGTTTTATCGAAGAGATCTTCCTCTAAGgtttgtaatt ... tcacttgcagAGGTTTTGATGATG
EST: gi|51593048|gb|CV072194.1|CV072194
EST:     GGGATGGGTGCTGAAGTAGATTTGTTTTATCGAAAAGATCTTCCTTTAAG                         AGGTTTTGATGATGAGATGAGAGCTATTGTTGCAAGCAACCTTGAGGGAAG
genomic: GGGATGGGTGCTGAAGTAGATTTGTTTTATCGAAGAGATCTTCCTCTAAGgtttgtaatt ... tcacttgcagAGGTTTTGATGATGAGATGAGAGCTATTGTTGCAAGCAACCTTGAGGGAAG
EST: gi|33942527|gb|CF349127.1|CF349127
EST:     GGGATGGGTGCTGAAGTAGATTTGTTTTATCGAAAAGATCTTCCTTTAAG                         AGGTTTTGATGATGAGATGAGAGCTATTGTTGCAAGCAACCTTGAGGGAAG
genomic: GGGATGGGTGCTGAAGTAGATTTGTTTTATCGAAGAGATCTTCCTCTAAGgtttgtaatt ... tcacttgcagAGGTTTTGATGATGAGATGAGAGCTATTGTTGCAAGCAACCTTGAGGGAAG
EST: gi|211540781|gb|FL336428.1|FL336428
EST:     GGGATGGGTGCTGAAGTAGATTTGTTTTATCGAAGAGATCTTCCTCTAAG                         AGGTTTTGATGATGAGATGAGAGCTATTGTTGCAAGCAACCTTGAGGGAAG
genomic: GGGATGGGTGCTGAAGTAGATTTGTTTTATCGAAGAGATCTTCCTCTAAGgtttgtaatt ... tcacttgcagAGGTTTTGATGATGAGATGAGAGCTATTGTTGCAAGCAACCTTGAGGGAAG
EST: gi|211318389|gb|FL341246.1|FL341246
EST:     GGGATGGGTGCTGAAGTAGATTTGTTTTATCGAAGAGATCTTCCTCTAAG                         ANGTTTTGATGATGAGATGAGAGCTATTGTTGCAAGCAACCTTGAGGGAAG
genomic: GGGATGGGTGCTGAAGTAGATTTGTTTTATCGAAGAGATCTTCCTCTAAGgtttgtaatt ... tcacttgcagAGGTTTTGATGATGAGATGAGAGCTATTGTTGCAAGCAACCTTGAGGGAAG
EST: gi|24934516|gb|CA452734.1|CA452734
EST:     GGGATGGGTGCTGAAGTAGATTTGTTTTATCGAAGAGATCTTCCTCTAAG                         AGGTTTTGATGATGAGATGAGAGCTATTGTTGCAAGCAACCTTGAGGGAAG
genomic: GGGATGGGTGCTGAAGTAGATTTGTTTTATCGAAGAGATCTTCCTCTAAGgtttgtaatt ... tcacttgcagAGGTTTTGATGATGAGATGAGAGCTATTGTTGCAAGCAACCTTGAGGGAAG

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), 49 (downstream exon)
Score: 844

ATATATTGCTGTTGAATTTGCTTCTATCTGGAGGGGGATGGGTGCTGAAGTAGATTTGTTTTATCGAAGAGATCTTCCTCTAAGgtttgtaatt ... tcacttgcagAGGTTTTGATGATGAGATGAGAGCTATTGTTGCAAGCAACCTTGAGGGAAGGGGAATCAAGTTGCATCCAGGGACAAATCTCTCTGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 5944

ATATATTGCTGTTGAATTTGCTTCTATCTGGAGGGGGATGGGTGCTGAAGTAGATTTGTTTTATCGAAGAGATCTTCCTCTAAGgtttgtaatt ... tcacttgcagAGGTTTTGATGATGAGATGAGAGCTATTGTTGCAAGCAACCTTGAGGGAAGGGGAATCAAGTTGCATCCAGGGACAAATCTCTCTGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 4593

ATATATTGCTGTTGAATTTGCTTCTATCTGGAGGGGGATGGGTGCTGAAGTAGATTTGTTTTATCGAAGAGATCTTCCTCTAAGgtttgtaatt ... tcacttgcagAGGTTTTGATGATGAGATGAGAGCTATTGTTGCAAGCAACCTTGAGGGAAGGGGAATCAAGTTGCATCCAGGGACAAATCTCTCTGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 1278

ATATATTGCTGTTGAATTTGCTTCTATCTGGAGGGGGATGGGTGCTGAAGTAGATTTGTTTTATCGAAGAGATCTTCCTCTAAGgtttgtaatt ... tcacttgcagAGGTTTTGATGATGAGATGAGAGCTATTGTTGCAAGCAACCTTGAGGGAAGGGGAATCAAGTTGCATCCAGGGACAAATCTCTCTGAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgattgatgtggacaggaaatatgggcataccattattaacaaactcacttgcagAGGTTTTGATGATGAGATGAGAGCTATTGTTGCAAGCAACCTTGAGGGAAGGGGAATCAAGTTGCATCCAGGGACAAATCTCTCTGAG
                                            ctcactt  CT-rich tract
                                attattaacaaact  TA-rich tract