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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GATGAACATGAACTCAAAAAGCAAAGAAGAAAGCAGTCCAATAGGGAGTCTGCACGTAGATCTAGGTTACGTAAACAGgtaattgtttgttcaacttgactgtactgggtactactatgttaactagttgatgatgaacaatgagttttgcag

Basic information

species Zea mays
transcript GRMZM2G088140_T01
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G088140_T03 (Zea mays), 5'ss of exon 11
lower sequence: LOC_Os12g13170.1 (Oryza sativa), 5'ss of exon 11
GATGAACATGAACTCAAAAAGCAAAGAAGAAAGCAGTCCAATAGGGAGTCTGCACGTAGATCTAGGTTACGTAAACAGgtaattgtttgttcaacttga-ctgtactgggtactactatgttaactagt---------tgatgatgaacaa--tgagttttgcag
|||||||  |||||||||| ||| |||||||| || ||||| ||||||||||| || ||||||||||| ||||| |||||| |||||||| ||  |  | || |||||| ||  | ||| ||   ||||         |||||| |   ||  | | || |||||
GATGAACGGGAACTCAAAAGGCAGAGAAGAAAACAATCCAACAGGGAGTCTGCTCGCAGATCTAGGTTGCGTAAGCAGgtatttgtttgtgcatttcaagctatactggatagaattatcttttgtagtgccttcaattgatgaagcctaacttaaattctgcag

upper sequence: GRMZM2G088140_T03 (Zea mays), 5'ss of exon 11
lower sequence: LOC_Os12g13170.3 (Oryza sativa), 5'ss of exon 10
----------------------GATGAACATGAACTCAAAAAGCAAAGAAGAAAGCAGTCCAATAGGGAGTCTGCACGTAGATCTAGGTTACGTAAACAGgtaattgtttgttcaacttga-ctgtactgggtactactatgttaactagt---------tgatgatgaacaa--tgagttttgcag
                      |||||||  |||||||||| ||| |||||||| || ||||| ||||||||||| || ||||||||||| ||||| |||||| |||||||| ||  |  | || |||||| ||  | ||| ||   ||||         |||||| |   ||  | | || |||||
TGTTGACTCTCCCATGATTCAGGATGAACGGGAACTCAAAAGGCAGAGAAGAAAACAATCCAACAGGGAGTCTGCTCGCAGATCTAGGTTGCGTAAGCAGgtatttgtttgtgcatttcaagctatactggatagaattatcttttgtagtgccttcaattgatgaagcctaacttaaattctgcag

upper sequence: GRMZM2G088140_T03 (Zea mays), 5'ss of exon 11
lower sequence: AT2G35530.1 (Arabidopsis thaliana), 5'ss of exon 11
GATGAACATGAACTCAAAAAGCAAAGAAGAAAGCAGTCCAATAGGGAGTCTGCACGTAGATCTAGGTTACGTAAACAGgtaattgtttgttcaacttgactgtactgggtactactatgttaactagttgatgatgaacaatgagttttgcag
|| ||    ||||| ||    || ||| | ||||||||||||||||||||||| || ||||| ||||| ||||||||||||  |     | ||  | ||         | ||  | |||| | | | ||  |||       |  ||  |  ||
GACGATAGAGAACTTAAGCGACAGAGACGGAAGCAGTCCAATAGGGAGTCTGCTCGAAGATCAAGGTTGCGTAAACAGgta-ctaaacatccatttagatcacctctagcacgcccatgtgagcaaattattgacccggtgtttgtgatttag

upper sequence: GRMZM2G088140_T03 (Zea mays), 5'ss of exon 11
lower sequence: AT1G32150.1 (Arabidopsis thaliana), 5'ss of exon 11
GATGAACATGAACTCAAAAAGCAAAGAAGAAAGCAGTCCAATAGGGAGTCTGCACGTAGATCTAGGTTACGTAAACAGgtaatt---gtttgttcaacttgactgtactgggtactactatgttaactagttgatgatgaacaatgagttttgcag-----------------
|||||    ||  | ||    || ||| | ||||| ||||||||||| ||||| |||||||| ||||| |||||||||||||        ||||        ||| |    | |  |  |||   |  |  |    |||| |||    |||| |                   
GATGAGAGAGAGATTAAGCGACAGAGACGGAAGCAATCCAATAGGGAATCTGCTCGTAGATCCAGGTTGCGTAAACAGgtaacataaacatgtttcttcaagctg-atctagcatcatcatgcctatcaagtatgaatgatcaaaagcttttccttttctcttctgtgttcag

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|60358086|gb|DN225059.1|DN225059
EST:     GAAAGCAGTCCAATAGGGAGTCTGCACGTAGATCTAGGTTACGTAAACAG                         GCTGAATGTGAGGAATTGGCTCAACGTGCTGATGTTTTAAAGCAGGAAAAT
genomic: GAAAGCAGTCCAATAGGGAGTCTGCACGTAGATCTAGGTTACGTAAACAGgtaattgttt ... agttttgcagGCTGAATGTGAGGAATTGGCTCAACGTGCTGATGTTTTAAAGCAGGAAAAT
EST: gi|60345747|gb|DN212720.1|DN212720
EST:     GAAAGCAGTCCAATAGGGAGTCTGCACGTAGATCTAGGTTACGTAAACAG                         GCTGAATGTGAGGAATTGGCTCAACGTGCTGATGTTTTAAAGCAGGAAAAT
genomic: GAAAGCAGTCCAATAGGGAGTCTGCACGTAGATCTAGGTTACGTAAACAGgtaattgttt ... agttttgcagGCTGAATGTGAGGAATTGGCTCAACGTGCTGATGTTTTAAAGCAGGAAAAT
EST: gi|60350100|gb|DN217073.1|DN217073
EST:     GAAAGCAGTCCAATAGGGAGTCTGCACGTAGATCTAGGTTACGTAAACAG                         GCTGAATGTGAGGAATTGGCTCAACGTGCTGATGTTTTAAAGCAGGAAAAT
genomic: GAAAGCAGTCCAATAGGGAGTCTGCACGTAGATCTAGGTTACGTAAACAGgtaattgttt ... agttttgcagGCTGAATGTGAGGAATTGGCTCAACGTGCTGATGTTTTAAAGCAGGAAAAT
EST: gi|32867163|gb|CF006845.1|CF006845
EST:     GAAAGCAGTCCAATAGGGAGTCTGCACGTAGATCTAGGTTACGTAAACAG                         GCTGAATGTGAGGAATTGGCTCAACGTGCTGATGTTTTAAAGCAGGAAAAT
genomic: GAAAGCAGTCCAATAGGGAGTCTGCACGTAGATCTAGGTTACGTAAACAGgtaattgttt ... agttttgcagGCTGAATGTGAGGAATTGGCTCAACGTGCTGATGTTTTAAAGCAGGAAAAT
EST: gi|211353575|gb|FL066643.1|FL066643
EST:     GAAAGCAGTCCAATAGGGAGTCTGCACGTAGATCTAGGTTACGTAAACAG                         GCTGAATGTGAGGAATTGGCTCAACGTGCTGATGTTTTAAAGCAGGAAAAT
genomic: GAAAGCAGTCCAATAGGGAGTCTGCACGTAGATCTAGGTTACGTAAACAGgtaattgttt ... agttttgcagGCTGAATGTGAGGAATTGGCTCAACGTGCTGATGTTTTAAAGCAGGAAAAT
EST: gi|60353486|gb|DN220459.1|DN220459
EST:     GAAAGCAGTCCAATAGGGAGTCTGCACGTAGATCTAGGTTACGTAAACAG                         GCTGAATGTGAGGAATTGGCTCAACGTGCTGATGTTTTAAAGCAGGAAAAT
genomic: GAAAGCAGTCCAATAGGGAGTCTGCACGTAGATCTAGGTTACGTAAACAGgtaattgttt ... agttttgcagGCTGAATGTGAGGAATTGGCTCAACGTGCTGATGTTTTAAAGCAGGAAAAT
EST: gi|211496290|gb|FL041702.1|FL041702
EST:     GAAAGCAGTCCAATAGGGAGTCTGCACGTAGATCTAGGTTACGTAAACAG                         GCTGAATGTGAGGAATTGGCTCAACGTGCTGATGTTTTAAAGCAGGAAAAT
genomic: GAAAGCAGTCCAATAGGGAGTCTGCACGTAGATCTAGGTTACGTAAACAGgtaattgttt ... agttttgcagGCTGAATGTGAGGAATTGGCTCAACGTGCTGATGTTTTAAAGCAGGAAAAT
EST: gi|71772544|gb|DR970475.1|DR970475
EST:     GAAAGCAGTCCAATAGGGAGTCTGCACGTAGATCTAGGTTACGTAAACAG                         GCTGAATGTGAGGAATTGGCTCAACGTGCTGATGTTTTAAAGCAGGAAAAT
genomic: GAAAGCAGTCCAATAGGGAGTCTGCACGTAGATCTAGGTTACGTAAACAGgtaattgttt ... agttttgcagGCTGAATGTGAGGAATTGGCTCAACGTGCTGATGTTTTAAAGCAGGAAAAT
EST: gi|32847056|gb|CD986737.1|CD986737
EST:     GAAAGCAGTCCAATAGGGAGTCTGCACGTAGATCTAGGTTACGTAAACAG                         GCTGAATGTGAGGAATTGGCTCAACGTGCTGATGTTTTAAAGCAGGAAAAT
genomic: GAAAGCAGTCCAATAGGGAGTCTGCACGTAGATCTAGGTTACGTAAACAGgtaattgttt ... agttttgcagGCTGAATGTGAGGAATTGGCTCAACGTGCTGATGTTTTAAAGCAGGAAAAT

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: 93

GATGAACATGAACTCAAAAAGCAAAGAAGAAAGCAGTCCAATAGGGAGTCTGCACGTAGATCTAGGTTACGTAAACAGgtaattgttt ... agttttgcagGCTGAATGTGAGGAATTGGCTCAACGTGCTGATGTTTTAAAGCAGGAAAATGCTTCACTTAGAGATGAAGTAAACCGTATCAGAAAAGAGTACGAGGAAC


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 45

GATGAACATGAACTCAAAAAGCAAAGAAGAAAGCAGTCCAATAGGGAGTCTGCACGTAGATCTAGGTTACGTAAACAGgtaattgttt ... agttttgcagGCTGAATGTGAGGAATTGGCTCAACGTGCTGATGTTTTAAAGCAGGAAAATGCTTCACTTAGAGATGAAGTAAACCGTATCAGAAAAGAGTACGAGGAAC


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 39

GATGAACATGAACTCAAAAAGCAAAGAAGAAAGCAGTCCAATAGGGAGTCTGCACGTAGATCTAGGTTACGTAAACAGgtaattgttt ... agttttgcagGCTGAATGTGAGGAATTGGCTCAACGTGCTGATGTTTTAAAGCAGGAAAATGCTTCACTTAGAGATGAAGTAAACCGTATCAGAAAAGAGTACGAGGAAC


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 122

GATGAACATGAACTCAAAAAGCAAAGAAGAAAGCAGTCCAATAGGGAGTCTGCACGTAGATCTAGGTTACGTAAACAGgtaattgttt ... agttttgcagGCTGAATGTGAGGAATTGGCTCAACGTGCTGATGTTTTAAAGCAGGAAAATGCTTCACTTAGAGATGAAGTAAACCGTATCAGAAAAGAGTACGAGGAAC