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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCTATCAGGTTGAAGAGTGTTATATACCACTTTCGTAAGAATCGAGAATTTTGCCGATTAAGGATTGgtactttctacactcttgccatttagaatttgtttaattttggtggacaagaattcatcctgacttatttag

Basic information

species Zea mays
transcript GRMZM5G896731_T02
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G896731_T02 (Zea mays), 5'ss of exon 7
lower sequence: LOC_Os03g22610.1 (Oryza sativa), 5'ss of exon 6
---------------------------------TCTATCAGGTTGAAGAGTGTTATATACCACTTTCGTAAGAATCGAGAATTTTGCCGATTAAGGATTGgtactttctacactcttgc-catttagaatttgtttaattttggtggacaagaattcatcctgacttatttag
                                   ||||||| |||||||  | |||||||| ||||||||||| ||||||||| | ||||||||||||||||  ||| |||    ||  |||||     |   ||||| | | |  | |    |  |   | ||||||| ||
TTTTTTACATTGACAAAATATTTACCTTTCTAGCTTATCAGGGTGAAGAGCTTGATATACCATTTTCGTAAGAACCGAGAATTTGGTCGATTAAGGATTGgtaggttcgacatctgtgttcatttcc--ctcccttaatgtggataaatattcttatactttaacttattcag

upper sequence: GRMZM5G896731_T02 (Zea mays), 5'ss of exon 7
lower sequence: LOC_Os03g22610.2 (Oryza sativa), 5'ss of exon 7
TCTATCAGGTTGAAGAGTGTTATATACCACTTTCGTAAGAATCGAGAATTTTGCCGATTAAGGATTGgtactttctacactcttgc-catttagaatttgtttaattttggtggacaagaattcatcctgacttatttag
        | |||||||  | |||||||| ||||||||||| ||||||||| | ||||||||||||||||  ||| |||    ||  |||||     |   ||||| | | |  | |    |  |   | ||||||| ||
--------GGTGAAGAGCTTGATATACCATTTTCGTAAGAACCGAGAATTTGGTCGATTAAGGATTGgtaggttcgacatctgtgttcatttcc--ctcccttaatgtggataaatattcttatactttaacttattcag
















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|86468848|gb|DY235218.1|DY235218
EST:     TGTTATATACCACTTTCGTAAGAATCGAGAATTTTGCCGATTAAGGATTG                         GAATTGGACGGCCAGCTGGCCAGATGGATCCTAAAGCCTTTGTTCTTCAGA
genomic: TGTTATATACCACTTTCGTAAGAATCGAGAATTTTGCCGATTAAGGATTGgtactttcta ... acttatttagGAATTGGACGGCCAGCTGGCCAGATGGATCCTAAAGCCTTTGTTCTTCAGA
EST: gi|71438321|gb|DR819371.1|DR819371
EST:     TGTTATATACCACTTTCGTAGGAATCGAGAATTTTGCCGATTAAGGATTG                         GAATTGGACGGCC
genomic: TGTTATATACCACTTTCGTAAGAATCGAGAATTTTGCCGATTAAGGATTGgtactttcta ... acttatttagGAATTGGACGGCC
EST: gi|89250808|gb|DY622594.1|DY622594
EST:     TGTTATATACCACTTTCGTAAGAATCGAGAATTTTGCCGATTAAGGATTG                         GAATTGGACGGCCAGCTGGCCAGATGGATCCTAAAGCCTTTGTTCTTCAGA
genomic: TGTTATATACCACTTTCGTAAGAATCGAGAATTTTGCCGATTAAGGATTGgtactttcta ... acttatttagGAATTGGACGGCCAGCTGGCCAGATGGATCCTAAAGCCTTTGTTCTTCAGA
EST: gi|78109135|gb|DV527552.1|DV527552
EST:     TGTTATATACCACTTTCGTAAGAATCGAGAATTTTGCCGATTAAGGATTG                         GAATTGGACGGCCAGCTGGCCAGATGGATCCTAAAGCCTTTGTTCTTCAGA
genomic: TGTTATATACCACTTTCGTAAGAATCGAGAATTTTGCCGATTAAGGATTGgtactttcta ... acttatttagGAATTGGACGGCCAGCTGGCCAGATGGATCCTAAAGCCTTTGTTCTTCAGA
EST: gi|60358732|gb|DN225705.1|DN225705
EST:     TGTTATATACCACTTTCGTAAGAATCGAGAATTTTGCCGATTAAGGATTG                         GAATTGGACGGCCAGCTGGCCAGATGGATCCTAAAGCCTTTGTTCTTCAGA
genomic: TGTTATATACCACTTTCGTAAGAATCGAGAATTTTGCCGATTAAGGATTGgtactttcta ... acttatttagGAATTGGACGGCCAGCTGGCCAGATGGATCCTAAAGCCTTTGTTCTTCAGA

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), 41 (downstream exon)
Score: 38

TCTATCAGGTTGAAGAGTGTTATATACCACTTTCGTAAGAATCGAGAATTTTGCCGATTAAGGATTGgtactttcta ... acttatttagGAATTGGACGGCCAGCTGGCCAGATGGATCCTAAAGCCTTTGTTCTTCAGAAGTTCAATAGGACTGGTCGTGAACGG


Block sizes: 44 (upstream exon), 47 (downstream exon)
Score: 18

TCTATCAGGTTGAAGAGTGTTATATACCACTTTCGTAAGAATCGAGAATTTTGCCGATTAAGGATTGgtactttcta ... acttatttagGAATTGGACGGCCAGCTGGCCAGATGGATCCTAAAGCCTTTGTTCTTCAGAAGTTCAATAGGACTGGTCGTGAACGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 22

TCTATCAGGTTGAAGAGTGTTATATACCACTTTCGTAAGAATCGAGAATTTTGCCGATTAAGGATTGgtactttcta ... acttatttagGAATTGGACGGCCAGCTGGCCAGATGGATCCTAAAGCCTTTGTTCTTCAGAAGTTCAATAGGACTGGTCGTGAACGG


Block sizes: 49 (upstream exon), 42 (downstream exon)
Score: 20

TCTATCAGGTTGAAGAGTGTTATATACCACTTTCGTAAGAATCGAGAATTTTGCCGATTAAGGATTGgtactttcta ... acttatttagGAATTGGACGGCCAGCTGGCCAGATGGATCCTAAAGCCTTTGTTCTTCAGAAGTTCAATAGGACTGGTCGTGAACGG