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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAGATAAAAAGTGAAGGTCTTCACAATGAGGTGTGCCAGATTCTGAATGGCTACAAGCAGgtaaagctggcctcctccttttgcatctgcataatggcgatggtaaatgatgctaaatagttattgtttttgttgttgtctag

Basic information

species Zea mays
transcript GRMZM5G869572_T01
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G869572_T01 (Zea mays), 5'ss of exon 8
lower sequence: LOC_Os04g59494.2 (Oryza sativa), 5'ss of exon 28
GAGATAAAAAGTGAAGGTCTTCACAATGAGGTGTGCCAGATTCTGAATGGCTACAAGCAGgtaaagctggcctcctccttttgcatctgcataatggcgatggtaaatgatgctaaatagttattgtttttgttgttgtctag
|||||||| ||||||||| | |||||||| |||||||||||| ||||||| |||||||||||| |  |    |  |   || |     | | || |            | | ||  ||                         
GAGATAAAGAGTGAAGgt-tacacaatgaagtgtgccagattttgaatggatacaagcaggtata--tatttttttttcttagggcgggtaaaacgattcctcattgcggttctgtatc------------------------

upper sequence: GRMZM5G869572_T01 (Zea mays), 5'ss of exon 8
lower sequence: LOC_Os04g59494.4 (Oryza sativa), 5'ss of exon 28
GAGATAAAAAGTGAAGGTCTTCACAATGAGGTGTGCCAGATTCTGAATGGCTACAAGCAGgtaaagctggcctcctccttttgcatctgcataatggcgatggtaaatgatgctaaatagttattgtttttgttgttgtctag-------------------
|||||||| ||||||||| | |||||||| |||||||||||| ||||||| |||||||||||| |  |    |  |   || |     | | || |            | | ||  || | ||  ||   ||       |||                    
GAGATAAAGAGTGAAGGT-TACACAATGAAGTGTGCCAGATTTTGAATGGATACAAGCAGgtata--tatttttttttcttagggcgggtaaaacgattcctcattgcggttctgtatcggtaccgtacatgcaacaaactaacaaaaaacattttccatag
















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|71316293|gb|DR794832.1|DR794832
EST:     GTGAAGGTCTTCACAATGAGGTGTGCCAGATTCTGAATGGCTACAAGCAG                         CTGCTTGGAAACGGTGGGTGGGAACAATGCATGGCCACCCTGCAACCGGAT
genomic: GTGAAGGTCTTCACAATGAGGTGTGCCAGATTCTGAATGGCTACAAGCAGgtaaagctgg ... tgttgtctagCTGCTTGGAAACGGTGGGTGGGAACAATGCATGGCCACCCTGCAACCGGAT
EST: gi|211163358|gb|FK967901.1|FK967901
EST:     GTGAAGGTCTTCACAATGAGGTGTGCCAGATTCTGAATGGCTACAAGCAG                         CTGCTTGGAAACGGTGGGTGGGAACAATGCATGGCCACCCTGCAACCGGAT
genomic: GTGAAGGTCTTCACAATGAGGTGTGCCAGATTCTGAATGGCTACAAGCAGgtaaagctgg ... tgttgtctagCTGCTTGGAAACGGTGGGTGGGAACAATGCATGGCCACCCTGCAACCGGAT
EST: gi|31363389|gb|CD447746.1|CD447746
EST:     GTGAAGGTCTTCACAATGAGGTGTGCCAGATTCTGAATGGCTACAAGCAG                         CTGCTTGGAAACGGTGGGTGGGAACAATGCATGGCCACCCTGCAACCGGAT
genomic: GTGAAGGTCTTCACAATGAGGTGTGCCAGATTCTGAATGGCTACAAGCAGgtaaagctgg ... tgttgtctagCTGCTTGGAAACGGTGGGTGGGAACAATGCATGGCCACCCTGCAACCGGAT
EST: gi|89250982|gb|DY622768.1|DY622768
EST:     GTGAAGGTCTTCACAATGAGGTGTGCCAGATTCTGAATGGCTACAAGCAG                         CTGCTTGGAAACGGTGGGTGGGAACAATGCATGGCCACCCTGCAACCGGAT
genomic: GTGAAGGTCTTCACAATGAGGTGTGCCAGATTCTGAATGGCTACAAGCAGgtaaagctgg ... tgttgtctagCTGCTTGGAAACGGTGGGTGGGAACAATGCATGGCCACCCTGCAACCGGAT
EST: gi|6918339|gb|AW399869.1|AW399869
EST:     GTGAAGGTCTTNACAATGAGGTGTGCCAGATTCTGAATGGCTACAAGCAG                         CTGCTTGGAAACGGTGGGTGGGAACAATGCATGGCCACCCTGCAACCGGAT
genomic: GTGAAGGTCTTCACAATGAGGTGTGCCAGATTCTGAATGGCTACAAGCAGgtaaagctgg ... tgttgtctagCTGCTTGGAAACGGTGGGTGGGAACAATGCATGGCCACCCTGCAACCGGAT
EST: gi|6918594|gb|AW400124.1|AW400124
EST:     GTGAAGGTCTTCACAATGAGGTGTGCCAGATTCTGAATGGCTGCAAGCAG                         CTGCTTGGAAACGGTGGGTGGGAACAATGCATGGCCACCCTGCAACCGGAT
genomic: GTGAAGGTCTTCACAATGAGGTGTGCCAGATTCTGAATGGCTACAAGCAGgtaaagctgg ... tgttgtctagCTGCTTGGAAACGGTGGGTGGGAACAATGCATGGCCACCCTGCAACCGGAT
EST: gi|60338787|gb|DN205760.1|DN205760
EST:     GTGAAGGTCTTCACAATGAGGTGTGCCAGATTCTGAATGGCTACAAGCAG                         CTGCTTGGAAACGGTGGGTGGGAACAATGCATGGCCACCCTGCAACCGGAT
genomic: GTGAAGGTCTTCACAATGAGGTGTGCCAGATTCTGAATGGCTACAAGCAGgtaaagctgg ... tgttgtctagCTGCTTGGAAACGGTGGGTGGGAACAATGCATGGCCACCCTGCAACCGGAT

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: 46 (upstream exon), 48 (downstream exon)
Score: 101

GAGATAAAAAGTGAAGGTCTTCACAATGAGGTGTGCCAGATTCTGAATGGCTACAAGCAGgtaaagctgg ... tgttgtctagCTGCTTGGAAACGGTGGGTGGGAACAATGCATGGCCACCCTGCAACCGGATGTTGTGCAGAAATTAGCTAGATACGGAGTATGATGGCAGTGGTCGTGTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 80

GAGATAAAAAGTGAAGGTCTTCACAATGAGGTGTGCCAGATTCTGAATGGCTACAAGCAGgtaaagctgg ... tgttgtctagCTGCTTGGAAACGGTGGGTGGGAACAATGCATGGCCACCCTGCAACCGGATGTTGTGCAGAAATTAGCTAGATACGGAGTATGATGGCAGTGGTCGTGTG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 75

GAGATAAAAAGTGAAGGTCTTCACAATGAGGTGTGCCAGATTCTGAATGGCTACAAGCAGgtaaagctgg ... tgttgtctagCTGCTTGGAAACGGTGGGTGGGAACAATGCATGGCCACCCTGCAACCGGATGTTGTGCAGAAATTAGCTAGATACGGAGTATGATGGCAGTGGTCGTGTG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 48

GAGATAAAAAGTGAAGGTCTTCACAATGAGGTGTGCCAGATTCTGAATGGCTACAAGCAGgtaaagctgg ... tgttgtctagCTGCTTGGAAACGGTGGGTGGGAACAATGCATGGCCACCCTGCAACCGGATGTTGTGCAGAAATTAGCTAGATACGGAGTATGATGGCAGTGGTCGTGTG