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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaattgagtgctaaatttacagcagctacaactgtctcagtgagctggaatgcatgtgcctgacttgcggcggcatggttttgaaattctcagGCCAACTTTCCTTCGCTCGAGAGCTTGATAGAGAGAATTCACGAGGATGGAAGAGTAGCAGAGAAGGCACTAGACCTGCCAATGTATGCCAAGTACAAAG

Basic information

species Zea mays
transcript GRMZM2G027115_T01
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G027115_T02 (Zea mays), 3'ss of exon 10
lower sequence: LOC_Os10g14814.1 (Oryza sativa), 3'ss of exon 9
gtaattgagtgctaa---atttacagcagctacaactgtctcagtgagctg-gaatgcatgtgcctgacttgcggcggcatggttttgaaattctcagGCCAACTTTCCTTCGCTCGAGAGCTTGATAGAGAGAATTCACGAGGATGGAAGAGTAGCAGAGAAGGCACTAGACCTGCCAATGTATGCCAAGTACAAAG
|||||| ||  | |    ||||| | | || | | |  || || |     | |||| ||||| |||||||||   ||   |  | |  |||| |  |||||||||||||||| || ||||||||||||||||| ||||||||||||| |||  ||||||||||||| ||  |  | ||| | || |||||||| | ||
gtaatttagaaccagactatttata-ctgcaaaagccatcccactatatggtgaattcatgttcctgacttgtcacgttgt--tatgaaaatgcctagGCCAACTTTCCTTCACTAGAGAGCTTGATAGAGAGGATTCACGAGGATGCAAGGATAGCAGAGAAGGCCCTGAATTTACCATTATACGCCAAGTATACAG

upper sequence: GRMZM2G027115_T02 (Zea mays), 3'ss of exon 10
lower sequence: LOC_Os10g32730.2 (Oryza sativa), 3'ss of exon 10
gtaattgagtgctaa---atttacagcagctacaactgtctcagtgagctggaatgcatgtgcctgacttgcggcggcatggttttgaaattctcagGCCAACTTTCCTTCGCTCGAGAGCTTGATAGAGAGAATTCACGAGGATGGAAGAGTAGCAGAGAAGGCACTAGACCTGCCAATGTATGCCAAGTACAAAG
|||||| ||  | |    ||||| | | ||   | |  || || |        |||||||| |||||||||   ||   |  | |  |||| |  |||||||||||||||| || ||||||||||||||||| ||||||||||||| |||  || |||| ||||| ||  |  | ||| | || |||||||| ||||
gtaatttaggaccagactatttata-ctgcagaagccatcccactatatgttgatgcatgttcctgacttgtcacgttgt--tatgaaaatgcctagGCCAACTTTCCTTCACTTGAGAGCTTGATAGAGAGGATTCACGAGGATGCAAGGATATCAGATAAGGCCCTGAATTTACCATTATACGCCAAGTATAAAG
















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|32921306|gb|CF026118.1|CF026118
EST:     TCTATGGCGAGGAGGTGCGCCTTGCCATCGTTGGCTACATAAGACCTGAG                         GCCAACTTTCCTTCGCTCGAGAGCTTGATAGAGAGAATTCACGAGGATGGA
genomic: TCTATGGCGAGGAGGTGCGCCTTGCCATCGTTGGCTACATAAGACCTGAGgtaattgagt ... aaattctcagGCCAACTTTCCTTCGCTCGAGAGCTTGATAGAGAGAATTCACGAGGATGGA
EST: gi|211114268|gb|FL244779.1|FL244779
EST:     TCTATGGCGAGGAGGTGCGCCTTGCCATCGTTGGCTACATAAGACCTGAG                         GCCAACTTTCCTTCGCTCGAGAGCTTGATAGAGAGAATTCACGAGGATGGA
genomic: TCTATGGCGAGGAGGTGCGCCTTGCCATCGTTGGCTACATAAGACCTGAGgtaattgagt ... aaattctcagGCCAACTTTCCTTCGCTCGAGAGCTTGATAGAGAGAATTCACGAGGATGGA
EST: gi|76018985|gb|DT946155.1|DT946155
EST:     TCTATGGCGAGGAGGTGCGCCTTGCCATCGTTGGCTACATAAGACCTGAG                         GCCAACTTTCCTTCGCTCGAGAGCTTGA
genomic: TCTATGGCGAGGAGGTGCGCCTTGCCATCGTTGGCTACATAAGACCTGAGgtaattgagt ... aaattctcagGCCAACTTTCCTTCGCTCGAGAGCTTGA
EST: gi|18169104|gb|BM338944.1|BM338944
EST:     TCTATGGCGAGGAGGTGCGCCTTGCCATCGTTGGCTACATAAGACCTGAG                         GCCAACTTTCCTTCGCTCGAGAGCTTGATAGAGAGAATTCACGATGATGGA
genomic: TCTATGGCGAGGAGGTGCGCCTTGCCATCGTTGGCTACATAAGACCTGAGgtaattgagt ... aaattctcagGCCAACTTTCCTTCGCTCGAGAGCTTGATAGAGAGAATTCACGAGGATGGA
EST: gi|15499363|gb|BI595876.1|BI595876
EST:     TCTATGGCGAGGAGGTGCGCCTTGCCATCGTTGGCTACATAAGACCTGAG                         GCCAACTTTCCTTCGCTCGAGAGCTTGATAGAGAGAATTCACGAGGATGGA
genomic: TCTATGGCGAGGAGGTGCGCCTTGCCATCGTTGGCTACATAAGACCTGAGgtaattgagt ... aaattctcagGCCAACTTTCCTTCGCTCGAGAGCTTGATAGAGAGAATTCACGAGGATGGA
EST: gi|18169085|gb|BM338925.1|BM338925
EST:     TCTATGGCGAGGAGGTGCGCCTTGCCATCGTTGGCTACATAAGACCTGAT                         GCCAACTTTCCTTCGCTCGAGAGCTTGATAGAG
genomic: TCTATGGCGAGGAGGTGCGCCTTGCCATCGTTGGCTACATAAGACCTGAGgtaattgagt ... aaattctcagGCCAACTTTCCTTCGCTCGAGAGCTTGATAGAG
EST: gi|15426986|gb|BI542808.1|BI542808
EST:     TCTATGGCGAGGAGGTGCGCCTTGCCATCGTTGGCTACATAAGACCTGAG                         GCCAACTTTCCTTCGCTCGAGAGCTTGATAGAGAGAATTCACGAGGATGGA
genomic: TCTATGGCGAGGAGGTGCGCCTTGCCATCGTTGGCTACATAAGACCTGAGgtaattgagt ... aaattctcagGCCAACTTTCCTTCGCTCGAGAGCTTGATAGAGAGAATTCACGAGGATGGA
EST: gi|71447208|gb|DR828258.1|DR828258
EST:     TCTATGGCGAGGAGGTGCGCCTTGCCATCGTTGGCTACATAAGACCTGAG                         GCCAACTTTCCTTCGCTCGAGAGCTTGA
genomic: TCTATGGCGAGGAGGTGCGCCTTGCCATCGTTGGCTACATAAGACCTGAGgtaattgagt ... aaattctcagGCCAACTTTCCTTCGCTCGAGAGCTTGA
EST: gi|211114263|gb|FL244774.1|FL244774
EST:     TCTATGGCGAGGAGGTGCGCCTTGCCATCGTTGGCTACATAAGACCTGAG                         GCCAACTTTCCTTCGCTCGAGAGCTTGATAGAGAGAATTCACGAGGATGGA
genomic: TCTATGGCGAGGAGGTGCGCCTTGCCATCGTTGGCTACATAAGACCTGAGgtaattgagt ... aaattctcagGCCAACTTTCCTTCGCTCGAGAGCTTGATAGAGAGAATTCACGAGGATGGA

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), 48 (downstream exon)
Score: 149

GAACCTTGGCTGCTTCATAATTTCGGCGAGGACTTCTATGGCGAGGAGGTGCGCCTTGCCATCGTTGGCTACATAAGACCTGAGgtaattgagt ... aaattctcagGCCAACTTTCCTTCGCTCGAGAGCTTGATAGAGAGAATTCACGAGGATGGAAGAGTAGCAGAGAAGGCACTAGACCTGCCAATGTATGCCAAGTACAAAG


Block sizes: 48 (upstream exon), 45 (downstream exon)
Score: 69

GAACCTTGGCTGCTTCATAATTTCGGCGAGGACTTCTATGGCGAGGAGGTGCGCCTTGCCATCGTTGGCTACATAAGACCTGAGgtaattgagt ... aaattctcagGCCAACTTTCCTTCGCTCGAGAGCTTGATAGAGAGAATTCACGAGGATGGAAGAGTAGCAGAGAAGGCACTAGACCTGCCAATGTATGCCAAGTACAAAG


Block sizes: 48 (upstream exon), 47 (downstream exon)
Score: 54

GAACCTTGGCTGCTTCATAATTTCGGCGAGGACTTCTATGGCGAGGAGGTGCGCCTTGCCATCGTTGGCTACATAAGACCTGAGgtaattgagt ... aaattctcagGCCAACTTTCCTTCGCTCGAGAGCTTGATAGAGAGAATTCACGAGGATGGAAGAGTAGCAGAGAAGGCACTAGACCTGCCAATGTATGCCAAGTACAAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 68

GAACCTTGGCTGCTTCATAATTTCGGCGAGGACTTCTATGGCGAGGAGGTGCGCCTTGCCATCGTTGGCTACATAAGACCTGAGgtaattgagt ... aaattctcagGCCAACTTTCCTTCGCTCGAGAGCTTGATAGAGAGAATTCACGAGGATGGAAGAGTAGCAGAGAAGGCACTAGACCTGCCAATGTATGCCAAGTACAAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agtgagctggaatgcatgtgcctgacttgcggcggcatggttttgaaattctcagGCCAACTTTCCTTCGCTCGAGAGCTTGATAGAGAGAATTCACGAGGATGGAAGAGTAGCAGAGAAGGCACTAGACCTGCCAATGTATGCCAAGTACAAAG
                   gcctgac  putative branch site (score: 68)
                                                ttctc  putative PPT
                                        ttttgaaatt  TA-rich tract