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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CGGAGGAGTGAGAGAGCTACTTGTGGGGAAAGACGATGAACTTCTCCAGACTGACACAAAGTCGATTCCTAGAGCCGATGTGGCTGAGGTTTGTGTCCAGgtatatatgctctaaaccaccatctatatagatctgtctgaaagcatctggttatcatgtacggagtatactcatggtccaaggtccattggacagcatggtgagccagccattctgattttaatcccttttcttctctgataatag

Basic information

species Zea mays
transcript GRMZM2G068244_T01
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G068244_T01 (Zea mays), 5'ss of exon 6
lower sequence: LOC_Os03g60740.1 (Oryza sativa), 5'ss of exon 6
CGGAGGAGTGAGAGAGCTACTTGTGGGGAAAGACGATGAACTTCTCCAGACTGACACAAAGTCGATTCCTAGAGCCGATGTGGCTGAGGTTTGTGTCCAGgtata-----tatgctctaaaccaccatc-----tatatagatctgtctg---aaagcatctggttatcatgtacggag----------------tatactcatggtc--caaggtccat---------tggacag---catggtgagccagccattctgattttaatcccttttcttctctgataatag
||| |||||||| ||| |  |||| || || |||||||||||||||||||| ||||| ||||| ||||| ||||| ||||| ||||| |||||||| |||||||      | || || | ||    ||      | | |   | |   |    ||    || ||  || | | |  ||                 | ||||    |||  ||||  || |         |||| ||   |||||||| |   |||||||||||  || |    || | | || |||||||
CGGGGGAGTGAGGGAGTTGATTGTTGGCAATGACGATGAACTTCTCCAGACAGACACGAAGTCAATTCCAAGAGCTGATGTTGCTGAAGTTTGTGTTCAGgtatgatctttgtggtcaatacagtgatagtttatctttgagtttacttagctaagttttccggcgatgaagcattgatgcatcggccatacgtttctactttctgtcaacaagcaccgtgaaaaaatatggatagtcacatggtgaacttaccattctgattgcaaac----ttttccccttataatag
















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|60397802|gb|DN230618.1|DN230618
EST:     CTGACACAAAGTCGATTCCTAGAGCCGATGTGGCTGAGGTTTGTGTCCAG                         GCTCTGCAGTACGAAGAGGCCAAGTTCAAGGCATTTGATTTGGCCTCAAAG
genomic: CTGACACAAAGTCGATTCCTAGAGCCGATGTGGCTGAGGTTTGTGTCCAGgtatatatgc ... ctgataatagGCTCTGCAGTACGAAGAGGCCAAGTTCAAGGCATTTGATTTGGCCTCAAAG
EST: gi|211113405|gb|FL349341.1|FL349341
EST:     CTGACACAAAGTCGATTCCTAGAGCCGATGTGGCTGAGGTTTGTGTCCAG                         GCTCTGCAGTACGAAGAGGCCAAGTTCAAGGCATTTGATTTGGCCTCAAAG
genomic: CTGACACAAAGTCGATTCCTAGAGCCGATGTGGCTGAGGTTTGTGTCCAGgtatatatgc ... ctgataatagGCTCTGCAGTACGAAGAGGCCAAGTTCAAGGCATTTGATTTGGCCTCAAAG
EST: gi|60339573|gb|DN206546.1|DN206546
EST:     CTGACACAAAGTCGATTCCTAGAGCCGATGTGGCTGAGGTTTGTGTCCAG                         GCTCTGCAGTACGAAGAGGCCAAGTTCAAGGCATTTGATTTGGCCTCAAAG
genomic: CTGACACAAAGTCGATTCCTAGAGCCGATGTGGCTGAGGTTTGTGTCCAGgtatatatgc ... ctgataatagGCTCTGCAGTACGAAGAGGCCAAGTTCAAGGCATTTGATTTGGCCTCAAAG
EST: gi|211283841|gb|FL366659.1|FL366659
EST:     CTGACACAAAGTCGATTCCTAGAGCCGATGTGGCTGAAGTTTGTGTCCAG                         GCTCTGCAGTACGAAGAGGGCAAGTTCAAGGCATTTGATTTGGGCTCAAAG
genomic: CTGACACAAAGTCGATTCCTAGAGCCGATGTGGCTGAGGTTTGTGTCCAGgtatatatgc ... ctgataatagGCTCTGCAGTACGAAGAGGCCAAGTTCAAGGCATTTGATTTGGCCTCAAAG
EST: gi|60343124|gb|DN210097.1|DN210097
EST:     CTGACACAAAGTCGATTCCTAGAGCCGATGTGGCTGAGGTTTGTGTCCAG                         GCTCTGCAGTACGAAGAGGCCAAGTTCAAGGCATTTGATTTGGCCTCAAAG
genomic: CTGACACAAAGTCGATTCCTAGAGCCGATGTGGCTGAGGTTTGTGTCCAGgtatatatgc ... ctgataatagGCTCTGCAGTACGAAGAGGCCAAGTTCAAGGCATTTGATTTGGCCTCAAAG
EST: gi|211278086|gb|FL458575.1|FL458575
EST:     CTGACACAAAGTCGATTCCTAGAGCCGATGTGGCTGAGGTTTGTGTCCAG                         GCTCTGCAGTACGAAGAGGCCAAGTTCAAGGCATTTGATTTGGCCTCAAAG
genomic: CTGACACAAAGTCGATTCCTAGAGCCGATGTGGCTGAGGTTTGTGTCCAGgtatatatgc ... ctgataatagGCTCTGCAGTACGAAGAGGCCAAGTTCAAGGCATTTGATTTGGCCTCAAAG
EST: gi|211193544|gb|FL459435.1|FL459435
EST:     CTGACACAAAGTCGATTCCTAGAGCCGATGTGGCTGAGGTTTGTGTCCAG                         GCTCTGCAGTACGAAGAGGCCAAGTTCAAGGCATTTGATTTGGCCTCAAAG
genomic: CTGACACAAAGTCGATTCCTAGAGCCGATGTGGCTGAGGTTTGTGTCCAGgtatatatgc ... ctgataatagGCTCTGCAGTACGAAGAGGCCAAGTTCAAGGCATTTGATTTGGCCTCAAAG
EST: gi|32911901|gb|CF016713.1|CF016713
EST:     CTGACACAAAGTCGATTCCTAGAGCCGATGTGGCTGAGGTTTGTGTCCAG                         GCTCTGCAGTACGAAGAGGCCAAGTTCAAGGCATTTGATTTGGCCTCAAAG
genomic: CTGACACAAAGTCGATTCCTAGAGCCGATGTGGCTGAGGTTTGTGTCCAGgtatatatgc ... ctgataatagGCTCTGCAGTACGAAGAGGCCAAGTTCAAGGCATTTGATTTGGCCTCAAAG
EST: gi|32844239|gb|CD983920.1|CD983920
EST:     CTGACACAAAGTCGATTCCTAGAGCCGATGTGGCTGAGGTTTGTGTCCAG                         GCTCTGCAGTA
genomic: CTGACACAAAGTCGATTCCTAGAGCCGATGTGGCTGAGGTTTGTGTCCAGgtatatatgc ... ctgataatagGCTCTGCAGTA
EST: gi|16379519|gb|BI993001.1|BI993001
EST:     CTGACCCAAAGTCGATTCCTAGAGCCGATGTGGCTGAGGTTTGTGTCCAG                         GCTCTGCAGTACGAAGAGGCCAAGTTCAAGGCATTTGATTTGGCCTCAAAG
genomic: CTGACACAAAGTCGATTCCTAGAGCCGATGTGGCTGAGGTTTGTGTCCAGgtatatatgc ... ctgataatagGCTCTGCAGTACGAAGAGGCCAAGTTCAAGGCATTTGATTTGGCCTCAAAG
EST: gi|60396304|gb|DN229173.1|DN229173
EST:     CTGACACAAAGTCGATTCCTAGAGCCGATGTGGCTGAGGTTTGTGTCCAG                         GCTCTGCAGTACGAAGAGGCCAAGTTCAAGGCATTTGATTTGGCCTCAAAG
genomic: CTGACACAAAGTCGATTCCTAGAGCCGATGTGGCTGAGGTTTGTGTCCAGgtatatatgc ... ctgataatagGCTCTGCAGTACGAAGAGGCCAAGTTCAAGGCATTTGATTTGGCCTCAAAG
EST: gi|78023137|gb|DV491524.1|DV491524
EST:     CTGACACAAAGTCGATTCCTAGAGCCGATGTGGCTGAGGTTTGTGTCCAG                         GCTCTGCAGTACGAAGAGGCCAAGTTCAAGGCATTTGATTTGGCCTCAAAG
genomic: CTGACACAAAGTCGATTCCTAGAGCCGATGTGGCTGAGGTTTGTGTCCAGgtatatatgc ... ctgataatagGCTCTGCAGTACGAAGAGGCCAAGTTCAAGGCATTTGATTTGGCCTCAAAG
EST: gi|32920219|gb|CF025031.1|CF025031
EST:     CTAACACAAAGTCGATTCCTAGAGCCGATGTGGCTGAGGTTTGTGTCCAG                         GCTCTGCAGTA
genomic: CTGACACAAAGTCGATTCCTAGAGCCGATGTGGCTGAGGTTTGTGTCCAGgtatatatgc ... ctgataatagGCTCTGCAGTA
EST: gi|116825576|gb|EC869314.1|EC869314
EST:     CTGACACAAAGTCGATTCCTAGAGCCGATGTGGCTGAGGTTTGTGTCCAG                         GCTCTGCAGTACGAAGAGGCCAAGTTCAAGGCATTTGATTTGGCCTCAAAG
genomic: CTGACACAAAGTCGATTCCTAGAGCCGATGTGGCTGAGGTTTGTGTCCAGgtatatatgc ... ctgataatagGCTCTGCAGTACGAAGAGGCCAAGTTCAAGGCATTTGATTTGGCCTCAAAG

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: 107

CGGAGGAGTGAGAGAGCTACTTGTGGGGAAAGACGATGAACTTCTCCAGACTGACACAAAGTCGATTCCTAGAGCCGATGTGGCTGAGGTTTGTGTCCAGgtatatatgc ... ctgataatagGCTCTGCAGTACGAAGAGGCCAAGTTCAAGGCATTTGATTTGGCCTCAAAGCCTGAAGGTGTGGGCACGCCAACAAAGGACTTTAGGGCACTGTTCTCCC


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 86

CGGAGGAGTGAGAGAGCTACTTGTGGGGAAAGACGATGAACTTCTCCAGACTGACACAAAGTCGATTCCTAGAGCCGATGTGGCTGAGGTTTGTGTCCAGgtatatatgc ... ctgataatagGCTCTGCAGTACGAAGAGGCCAAGTTCAAGGCATTTGATTTGGCCTCAAAGCCTGAAGGTGTGGGCACGCCAACAAAGGACTTTAGGGCACTGTTCTCCC


Block sizes: 49 (upstream exon), 42 (downstream exon)
Score: 22

CGGAGGAGTGAGAGAGCTACTTGTGGGGAAAGACGATGAACTTCTCCAGACTGACACAAAGTCGATTCCTAGAGCCGATGTGGCTGAGGTTTGTGTCCAGgtatatatgc ... ctgataatagGCTCTGCAGTACGAAGAGGCCAAGTTCAAGGCATTTGATTTGGCCTCAAAGCCTGAAGGTGTGGGCACGCCAACAAAGGACTTTAGGGCACTGTTCTCCC


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 120

CGGAGGAGTGAGAGAGCTACTTGTGGGGAAAGACGATGAACTTCTCCAGACTGACACAAAGTCGATTCCTAGAGCCGATGTGGCTGAGGTTTGTGTCCAGgtatatatgc ... ctgataatagGCTCTGCAGTACGAAGAGGCCAAGTTCAAGGCATTTGATTTGGCCTCAAAGCCTGAAGGTGTGGGCACGCCAACAAAGGACTTTAGGGCACTGTTCTCCC