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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagttgcgattcctattgttcagctatatatagccgtcccggccgtactcttttgatttgtgtgtacgtacatacagGAGATAAAAAGTGAAGGTCTTCACAATGAGGTGTGCCAGATTCTGAATGGCTACAAGCAG

Basic information

species Zea mays
transcript GRMZM5G869572_T01
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G869572_T01 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os04g59494.4 (Oryza sativa), 3'ss of exon 27
gtgagttgcgattcctattgttca-gctatatatagccgtcccggccgtactcttttgatttgtgtgtacgtacatacagGAGATAAAAAGTGAAGGTCTTCACAATGAGGTGTGCCAGATTCTGAATGGCTACAAGCAG
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gtgagattcctgtcatattagacatgctttctgcaccagt----attctgcaccgaagctcacgatatttgtttatacagGAGATAAAGAGTGAAGGT-TACACAATGAAGTGTGCCAGATTTTGAATGGATACAAGCAG
















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|211163358|gb|FK967901.1|FK967901
EST:     GAGGCGCCGGTTCATTAGCTTACATCTGCCAGGCCTGTGCGAGTTGGACT                         GAGATAAAAAGTGAAGGTCTTCACAATGAGGTGTGCCAGATTCTGAATGGC
genomic: GAGGCGCCGGTTCATTAGCTTACATCTGCCAGGCCTGTGCGAGTTGGACTgtgagttgcg ... gtacatacagGAGATAAAAAGTGAAGGTCTTCACAATGAGGTGTGCCAGATTCTGAATGGC
EST: gi|31363389|gb|CD447746.1|CD447746
EST:     GAGGCGCCGGTTCATTAGCTTACATCTGCCAGGCCTGTGCGAGTTGGACT                         GAGATAAAAAGTGAAGGTCTTCACAATGAGGTGTGCCAGATTCTGAATGGC
genomic: GAGGCGCCGGTTCATTAGCTTACATCTGCCAGGCCTGTGCGAGTTGGACTgtgagttgcg ... gtacatacagGAGATAAAAAGTGAAGGTCTTCACAATGAGGTGTGCCAGATTCTGAATGGC
EST: gi|89250982|gb|DY622768.1|DY622768
EST:     GAGGCGCCGGTTCATTAGCTTACATCTGCCAGGCCTGTGCGAGTTGGACT                         GAGATAAAAAGTGAAGGTCTTCACAATGAGGTGTGCCAGATTCTGAATGGC
genomic: GAGGCGCCGGTTCATTAGCTTACATCTGCCAGGCCTGTGCGAGTTGGACTgtgagttgcg ... gtacatacagGAGATAAAAAGTGAAGGTCTTCACAATGAGGTGTGCCAGATTCTGAATGGC
EST: gi|6918339|gb|AW399869.1|AW399869
EST:     GAGGCGCCGGTTCATTAGCTTACATCTGCCAGGCCTGTGCGAGTTGGACT                         GAGATAAAAAGTGAAGGTCTTNACAATGAGGTGTGCCAGATTCTGAATGGC
genomic: GAGGCGCCGGTTCATTAGCTTACATCTGCCAGGCCTGTGCGAGTTGGACTgtgagttgcg ... gtacatacagGAGATAAAAAGTGAAGGTCTTCACAATGAGGTGTGCCAGATTCTGAATGGC
EST: gi|211163359|gb|FK967902.1|FK967902
EST:     GAGGCGCCGGTTCATTAGCTTACATCTGCCAGGCCTGTGCGAGTTGGACT                         GAGATAAAAAGTGAAGGTCTTCACAATGAGGTGTGCCAGATTCTGAATGGC
genomic: GAGGCGCCGGTTCATTAGCTTACATCTGCCAGGCCTGTGCGAGTTGGACTgtgagttgcg ... gtacatacagGAGATAAAAAGTGAAGGTCTTCACAATGAGGTGTGCCAGATTCTGAATGGC
EST: gi|6918594|gb|AW400124.1|AW400124
EST:     GAGGCGCCGGTTCATTAGCTTACATCTGGCAGGCCTGTGCGAGTTGGACT                         GAGATAAAAAGTGAAGGTCTTCACAATGAGGTGTGCCAGATTCTGAATGGC
genomic: GAGGCGCCGGTTCATTAGCTTACATCTGCCAGGCCTGTGCGAGTTGGACTgtgagttgcg ... gtacatacagGAGATAAAAAGTGAAGGTCTTCACAATGAGGTGTGCCAGATTCTGAATGGC
EST: gi|60338787|gb|DN205760.1|DN205760
EST:     GAGGCGCCGGTTCATTAGCTTACATCTGCCAGGCCTGTGCGAGTTGGACT                         GAGATAAAAAGTGAAGGTCTTCACAATGAGGTGTGCCAGATTCTGAATGGC
genomic: GAGGCGCCGGTTCATTAGCTTACATCTGCCAGGCCTGTGCGAGTTGGACTgtgagttgcg ... gtacatacagGAGATAAAAAGTGAAGGTCTTCACAATGAGGTGTGCCAGATTCTGAATGGC

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: 47 (upstream exon), 48 (downstream exon)
Score: 168

GTGGCAGCAAACCCTACAGGAGGCGCCGGTTCATTAGCTTACATCTGCCAGGCCTGTGCGAGTTGGACTgtgagttgcg ... gtacatacagGAGATAAAAAGTGAAGGTCTTCACAATGAGGTGTGCCAGATTCTGAATGGCTACAAGCAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 138

GTGGCAGCAAACCCTACAGGAGGCGCCGGTTCATTAGCTTACATCTGCCAGGCCTGTGCGAGTTGGACTgtgagttgcg ... gtacatacagGAGATAAAAAGTGAAGGTCTTCACAATGAGGTGTGCCAGATTCTGAATGGCTACAAGCAG


Block sizes: 47 (upstream exon), 48 (downstream exon)
Score: 122

GTGGCAGCAAACCCTACAGGAGGCGCCGGTTCATTAGCTTACATCTGCCAGGCCTGTGCGAGTTGGACTgtgagttgcg ... gtacatacagGAGATAAAAAGTGAAGGTCTTCACAATGAGGTGTGCCAGATTCTGAATGGCTACAAGCAG


Block sizes: 47 (upstream exon), 48 (downstream exon)
Score: 137

GTGGCAGCAAACCCTACAGGAGGCGCCGGTTCATTAGCTTACATCTGCCAGGCCTGTGCGAGTTGGACTgtgagttgcg ... gtacatacagGAGATAAAAAGTGAAGGTCTTCACAATGAGGTGTGCCAGATTCTGAATGGCTACAAGCAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gctatatatagccgtcccggccgtactcttttgatttgtgtgtacgtacatacagGAGATAAAAAGTGAAGGTCTTCACAATGAGGTGTGCCAGATTCTGAATGGCTACAAGCAG
                            ttttgat  putative branch site (score: 137)
                            ttttgattt  TA-rich tract