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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGTTGTACATGTGTTCCGCTTCCTGTCCGTCGGAAAGCTTCATCGCTTCCTAAAACACCTCCATGTGgttagttaacagactagtattttgctttgtacctaattcatttaggatattgttgttttacatatgctttggttcatttgttgtag

Basic information

species Zea mays
transcript GRMZM2G178822_T01
intron # 16
splice site 5'
intron type U2

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|67015254|gb|CO444003.1|CO444003
EST:     GCTTCCTGTCCGTCGGAAATCTTCATCGCTTCCTAAAACACCTCCATGTG                         TTGGATCAAAGAGAATTTCCGAGAACAGTGTTGCTAGAAGATTCTCGACCG
genomic: GCTTCCTGTCCGTCGGAAAGCTTCATCGCTTCCTAAAACACCTCCATGTGgttagttaac ... tttgttgtagTTGGATCAAAGAGAATTTCCGAGAACAGTGTTGCTAGAAGATTCTCGACCG
EST: gi|67022700|gb|CO451449.1|CO451449
EST:     GCTTCCTGTCCGTCGGAAATCTTCATCGCTTCCTAAAACACCTCCATGTG                         TTGGATCAAAGAGAATTTCCGAGAACAGTGTTGCTAGAAGATTCTCGACCG
genomic: GCTTCCTGTCCGTCGGAAAGCTTCATCGCTTCCTAAAACACCTCCATGTGgttagttaac ... tttgttgtagTTGGATCAAAGAGAATTTCCGAGAACAGTGTTGCTAGAAGATTCTCGACCG
EST: gi|60352824|gb|DN219797.1|DN219797
EST:     GCTTCCTGTCCGTCGGAAAGCTTCATCGCTTCCTAAAACACCTCCATGTG                         TTGGATCAAAGAGAATTTCCGAGAACAGTGTTGCT
genomic: GCTTCCTGTCCGTCGGAAAGCTTCATCGCTTCCTAAAACACCTCCATGTGgttagttaac ... tttgttgtagTTGGATCAAAGAGAATTTCCGAGAACAGTGTTGCT
EST: gi|71311110|gb|DR791868.1|DR791868
EST:     GCTTCCTGTCCGTCGGAAAGCTTCATCGCTTCCTAAAACACCTCCATGTG                         TTGGATCAAAGAGAATTTCCGAGAACAGTGTTGCTAGAAGATTCTCGACCG
genomic: GCTTCCTGTCCGTCGGAAAGCTTCATCGCTTCCTAAAACACCTCCATGTGgttagttaac ... tttgttgtagTTGGATCAAAGAGAATTTCCGAGAACAGTGTTGCTAGAAGATTCTCGACCG
EST: gi|28188021|gb|CB179631.1|CB179631
EST:     GCTTCCTGTCCGTCTGAAAGCTTCATCGCTTCCTAAAACACCTCCATGTG                         TTGGATCAAAGAGAATTTCCGAGAACAGTGTTGCTAGAAGATTCTCGACCG
genomic: GCTTCCTGTCCGTCGGAAAGCTTCATCGCTTCCTAAAACACCTCCATGTGgttagttaac ... tttgttgtagTTGGATCAAAGAGAATTTCCGAGAACAGTGTTGCTAGAAGATTCTCGACCG
EST: gi|6269998|gb|AW157969.1|AW157969
EST:     CTGGCCTGTCCGTCGGAAATCTTCATCGCTTCCTAAAACACCTCCATGTG                         TTGGATCAAAGAGAATTTCCGAGAACAGTGTTGCTAGAAGATTCTCGACCG
genomic: CT-TCCTGTCCGTCGGAAAGCTTCATCGCTTCCTAAAACACCTCCATGTGgttagttaac ... tttgttgtagTTGGATCAAAGAGAATTTCCGAGAACAGTGTTGCTAGAAGATTCTCGACCG

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: 207

GGTTGTACATGTGTTCCGCTTCCTGTCCGTCGGAAAGCTTCATCGCTTCCTAAAACACCTCCATGTGgttagttaac ... tttgttgtagTTGGATCAAAGAGAATTTCCGAGAACAGTGTTGCTAGAAGATTCTCGACCGGGACTCTATCTACGATGAAATCTCATAGCAATGCACCTGCAAAATCAAA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 111

GGTTGTACATGTGTTCCGCTTCCTGTCCGTCGGAAAGCTTCATCGCTTCCTAAAACACCTCCATGTGgttagttaac ... tttgttgtagTTGGATCAAAGAGAATTTCCGAGAACAGTGTTGCTAGAAGATTCTCGACCGGGACTCTATCTACGATGAAATCTCATAGCAATGCACCTGCAAAATCAAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 107

GGTTGTACATGTGTTCCGCTTCCTGTCCGTCGGAAAGCTTCATCGCTTCCTAAAACACCTCCATGTGgttagttaac ... tttgttgtagTTGGATCAAAGAGAATTTCCGAGAACAGTGTTGCTAGAAGATTCTCGACCGGGACTCTATCTACGATGAAATCTCATAGCAATGCACCTGCAAAATCAAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 212

GGTTGTACATGTGTTCCGCTTCCTGTCCGTCGGAAAGCTTCATCGCTTCCTAAAACACCTCCATGTGgttagttaac ... tttgttgtagTTGGATCAAAGAGAATTTCCGAGAACAGTGTTGCTAGAAGATTCTCGACCGGGACTCTATCTACGATGAAATCTCATAGCAATGCACCTGCAAAATCAAA