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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaatatttggcagcgcatctgacatctgccccctccattccccgcttggatatgcagaacactcataccttgtcacctaaagcggggttatactcaaagtaccattgaaattcttttgtgtgttctgttacttgtggaatatgcagCTTATAAAGGAATTGGCACAGCCTGATGTAAGACATGAAATATCTCGGCTAGTAAAGCCCATGACTCAG

Basic information

species Zea mays
transcript GRMZM5G870572_T01
intron # 17
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G870572_T03 (Zea mays), 3'ss of exon 18
lower sequence: LOC_Os08g25060.1 (Oryza sativa), 3'ss of exon 18
gtaaatatttggcagcgcatctgacatctgccccctccattccccgcttggatatgcagaacactcataccttgtcacctaaagcggggttatactcaaagtaccattgaaattcttttgtgtgttctgttacttgtggaatatgcagCTTATAAAGGAATTGGCACAGCCTGATGTAAGACATGAAATATCTCGGCTAGTAAAGCCCATGACTCAG
                                  || ||  |     |  ||| |   | | |||  ||||||||        | |  |  || ||||  | |||  |   |||| | ||  |    |   || ||  | ||||         ||||||||  ||||| |||||||| ||||| ||||||||||  ||||||||||||||||| |||
-----------------------------attgacttcaaactttcttatgatgttatgga-act-gtaccttgtttt----ggtgatgaaattctcactggacccct---attcatatgcataactt-ccacctgcagGATAT---------AAAGGAATCAGCACAACCTGATGTGAGACACGAAATATCTCAACTAGTAAAGCCCATGACCCAG
















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|31348758|gb|CD433115.1|CD433115
EST:     GTTCAAAGAGTTAAAGAAGCTATGACACAGATATATCAAAAGCTGCAG                         CTTATAAAGGAATTGGCACAGCCTGATGTAAGACATGAAATATCTCGGCTA
genomic: GTTCAAAGAGTTAAAGAAGCTATGACACAGATATATCAAAAGCTGCAGgtaaatattt ... gaatatgcagCTTATAAAGGAATTGGCACAGCCTGATGTAAGACATGAAATATCTCGGCTA
EST: gi|29946463|gb|CB816162.1|CB816162
EST:     GTTCAAAGAGTTAAAGAAGCTATGACACAGATATATCAAAAGCTGCAG                         CTTATAAAGGAATTGGCACAGCCTGATGTAAGACATGAAATATCTCGGCTA
genomic: GTTCAAAGAGTTAAAGAAGCTATGACACAGATATATCAAAAGCTGCAGgtaaatattt ... gaatatgcagCTTATAAAGGAATTGGCACAGCCTGATGTAAGACATGAAATATCTCGGCTA
EST: gi|71301572|gb|DR786840.1|DR786840
EST:     GTTCAAAGAGTTAAAGAAGCTATGACACAGATATATCAAAAGCTGCAG                         CTTATAAAGGAATTGGCACAGCCTGATGTAAGACATGAAATATCTCGGCTA
genomic: GTTCAAAGAGTTAAAGAAGCTATGACACAGATATATCAAAAGCTGCAGgtaaatattt ... gaatatgcagCTTATAAAGGAATTGGCACAGCCTGATGTAAGACATGAAATATCTCGGCTA
EST: gi|89247122|gb|DY618908.1|DY618908
EST:     GTTCAAAGAGTTAAAGAAGCTATGACACAGATATATCAAAAGCTGCAG                         CTTATAAAGGAATTGGCACAGCCTGATGTAAGACATGAAATATCTCGGCTA
genomic: GTTCAAAGAGTTAAAGAAGCTATGACACAGATATATCAAAAGCTGCAGgtaaatattt ... gaatatgcagCTTATAAAGGAATTGGCACAGCCTGATGTAAGACATGAAATATCTCGGCTA
EST: gi|74239224|gb|DT647138.1|DT647138
EST:     GTTCAAAGAGTTAAAGAAGCTATGACACAGATATATCAAAAGCTGCAG                         CTTATAAAGGAATTGGCACAGCCTGATGTAAGACATGAAATATCTCGGCTA
genomic: GTTCAAAGAGTTAAAGAAGCTATGACACAGATATATCAAAAGCTGCAGgtaaatattt ... gaatatgcagCTTATAAAGGAATTGGCACAGCCTGATGTAAGACATGAAATATCTCGGCTA
EST: gi|71433412|gb|DR814462.1|DR814462
EST:     GAGTTAAAGAAGCTTTGACCCAGATATTTCAAAAGCTGCAG                         CTTATAAAGGAATTGGCACAGCCTGATGTAAGACATGAAATATCTCGGCTA
genomic: GAGTTAAAGAAGCTATGACACAGATATATCAAAAGCTGCAGgtaaatattt ... gaatatgcagCTTATAAAGGAATTGGCACAGCCTGATGTAAGACATGAAATATCTCGGCTA
EST: gi|5607882|gb|AI901549.1|AI901549
EST:     AGATATATCAAAAGCTGCAG                         CTTATAAAGGAATTGGCNCAGCCTGATGTAAGACATGAAATATCTCGGCTA
genomic: AGATATATCAAAAGCTGCAGgtaaatattt ... gaatatgcagCTTATAAAGGAATTGGCACAGCCTGATGTAAGACATGAAATATCTCGGCTA
EST: gi|24763305|gb|CA398481.1|CA398481
EST:     GTTCAAAGAGTTAAAGAAGCTATGACACAGATATATCAAAAGCTGCAG                         CTTATAAAGGAATTGGCACAGCCTGATGTAAGACATGAAATATCTCGGCTA
genomic: GTTCAAAGAGTTAAAGAAGCTATGACACAGATATATCAAAAGCTGCAGgtaaatattt ... gaatatgcagCTTATAAAGGAATTGGCACAGCCTGATGTAAGACATGAAATATCTCGGCTA
EST: gi|148959669|gb|EE010942.2|EE010942
EST:     GTTCAAAGAGTTAAAGAAGCTATGACACAGATATATCAAAAGCTGCAG                         CTTATAAAGGAATTGGCACAGCCTGATGTAAGACATGAAATATTTCGGTTA
genomic: GTTCAAAGAGTTAAAGAAGCTATGACACAGATATATCAAAAGCTGCAGgtaaatattt ... gaatatgcagCTTATAAAGGAATTGGCACAGCCTGATGTAAGACATGAAATATCTCGGCTA
EST: gi|4967176|gb|AI691877.1|AI691877
EST:     GTTCAAAGAGTTAAAGAAGCTATGACACAGATATATCAAAAGCTGCAG                         CTTATAAAGGAATTGGCACAGCCTGATGTAAGACATGAAATATCTCGGCTA
genomic: GTTCAAAGAGTTAAAGAAGCTATGACACAGATATATCAAAAGCTGCAGgtaaatattt ... gaatatgcagCTTATAAAGGAATTGGCACAGCCTGATGTAAGACATGAAATATCTCGGCTA

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), 46 (downstream exon)
Score: 142

GTTCAAAGAGTTAAAGAAGCTATGACACAGATATATCAAAAGCTGCAGgtaaatattt ... gaatatgcagCTTATAAAGGAATTGGCACAGCCTGATGTAAGACATGAAATATCTCGGCTAGTAAAGCCCATGACTCAG


Block sizes: 47 (upstream exon), 47 (downstream exon)
Score: 139

GTTCAAAGAGTTAAAGAAGCTATGACACAGATATATCAAAAGCTGCAGgtaaatattt ... gaatatgcagCTTATAAAGGAATTGGCACAGCCTGATGTAAGACATGAAATATCTCGGCTAGTAAAGCCCATGACTCAG


Block sizes: 47 (upstream exon), 46 (downstream exon)
Score: 76

GTTCAAAGAGTTAAAGAAGCTATGACACAGATATATCAAAAGCTGCAGgtaaatattt ... gaatatgcagCTTATAAAGGAATTGGCACAGCCTGATGTAAGACATGAAATATCTCGGCTAGTAAAGCCCATGACTCAG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 119

GTTCAAAGAGTTAAAGAAGCTATGACACAGATATATCAAAAGCTGCAGgtaaatattt ... gaatatgcagCTTATAAAGGAATTGGCACAGCCTGATGTAAGACATGAAATATCTCGGCTAGTAAAGCCCATGACTCAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

actcaaagtaccattgaaattcttttgtgtgttctgttacttgtggaatatgcagCTTATAAAGGAATTGGCACAGCCTGATGTAAGACATGAAATATCTCGGCTAGTAAAGCCCATGACTCAG
            attgaaattctttt  TA-rich tract