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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtaaagtcatattaagactttttattgtatttagtttgttatattgaaatattgcatatataatgagcatctcatatatcctcttcttcccacaatttagGCTCTACATGAGTGGAGAGATCGTATAGCTCGTCAGGAAGATGAGAGTACTGGTTATATACTGCCAAATAAGGCTTTAATTGAGATAG

Basic information

species Zea mays
transcript GRMZM2G000749_T02
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G000749_T01 (Zea mays), 3'ss of exon 9
lower sequence: LOC_Os03g06190.1 (Oryza sativa), 3'ss of exon 9
gtaaagtcatattaagactttttattgtatttagtttgttatattgaaatattgcatatataat--gagcatctcatatatcctcttcttcccacaatttagGCTCTACATGAGTGGAGAGATCGTATAGCTCGTCAGGAAGATGAGAGTACTGGTTATATACTGCCAAATAAGGCTTTAATTGAGATAG
  |    |||   | |  |    ||   |  |  | | || | |   |||   |  ||| ||||    |  | | ||| ||      | |  |    |  ||||||||||| | |||||||||  |||||||||| | | ||||||||| ||||||||| |  | |||||||||||||||||||||||||
--atgtccatgccatgtttccaaataacaacttatattttttctaccaattcgggttatttaatttatgtgtgtaataaatatctcacatatctttttgcagGCTCTACATCAATGGAGAGATTATATAGCTCGTGAAGTAGATGAGAGCACTGGTTATGTGTTACCAAATAAGGCTTTAATTGAGATAG
















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|21987416|gb|BQ778944.1|BQ778944
EST:     GTTGCAGGAACATGAACTGGATGCAAGACAGCTGGCTGTTGTTGCT                         GCTCTACATGAGTGGAGAGATCGTATAGCTCGTCAGGAAGATGAGAGTACT
genomic: GTTGCAGGAACATGAACTGGATGCAAGACAGCTGGCTGTTGTTGCTgtaagaacag ... cacaatttagGCTCTACATGAGTGGAGAGATCGTATAGCTCGTCAGGAAGATGAGAGTACT
EST: gi|211021453|gb|FL457596.1|FL457596
EST:     GTTGCAGGAACATGAACTGGATGCAAGACAGCTGGCTGTTGTTGCT                         GCTCTACATGAGTGGAGAGATCGTATAGCTCGTCAGGAAGATGAGAGTACT
genomic: GTTGCAGGAACATGAACTGGATGCAAGACAGCTGGCTGTTGTTGCTgtaagaacag ... cacaatttagGCTCTACATGAGTGGAGAGATCGTATAGCTCGTCAGGAAGATGAGAGTACT
EST: gi|60341236|gb|DN208209.1|DN208209
EST:     GTTGCAGGAACATGAACTGGATGCAAGACAGCTGGCTGTTGTTGCT                         GCTCTACATGAGTGGAGAGATCGTATAGCTCGTCAGGAAGATGAGAGTACT
genomic: GTTGCAGGAACATGAACTGGATGCAAGACAGCTGGCTGTTGTTGCTgtaagaacag ... cacaatttagGCTCTACATGAGTGGAGAGATCGTATAGCTCGTCAGGAAGATGAGAGTACT
EST: gi|22543109|gb|BU093547.1|BU093547
EST:     GACAGCTGGCTGTTGTTGCT                         GCTCTACATGAGTGGAGAGATCGTATAGCTCGTCAGGAAGATGAGAGTACT
genomic: GACAGCTGGCTGTTGTTGCTgtaagaacag ... cacaatttagGCTCTACATGAGTGGAGAGATCGTATAGCTCGTCAGGAAGATGAGAGTACT

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: 40 (upstream exon), 48 (downstream exon)
Score: 89

GTTGCAGGAACATGAACTGGATGCAAGACAGCTGGCTGTTGTTGCTgtaagaacag ... cacaatttagGCTCTACATGAGTGGAGAGATCGTATAGCTCGTCAGGAAGATGAGAGTACTGGTTATATACTGCCAAATAAGGCTTTAATTGAGATAG


Block sizes: 46 (upstream exon), 48 (downstream exon)
Score: 138

GTTGCAGGAACATGAACTGGATGCAAGACAGCTGGCTGTTGTTGCTgtaagaacag ... cacaatttagGCTCTACATGAGTGGAGAGATCGTATAGCTCGTCAGGAAGATGAGAGTACTGGTTATATACTGCCAAATAAGGCTTTAATTGAGATAG


Block sizes: 46 (upstream exon), 48 (downstream exon)
Score: 191

GTTGCAGGAACATGAACTGGATGCAAGACAGCTGGCTGTTGTTGCTgtaagaacag ... cacaatttagGCTCTACATGAGTGGAGAGATCGTATAGCTCGTCAGGAAGATGAGAGTACTGGTTATATACTGCCAAATAAGGCTTTAATTGAGATAG


Block sizes: 46 (upstream exon), 48 (downstream exon)
Score: 152

GTTGCAGGAACATGAACTGGATGCAAGACAGCTGGCTGTTGTTGCTgtaagaacag ... cacaatttagGCTCTACATGAGTGGAGAGATCGTATAGCTCGTCAGGAAGATGAGAGTACTGGTTATATACTGCCAAATAAGGCTTTAATTGAGATAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaaatattgcatatataatgagcatctcatatatcctcttcttcccacaatttagGCTCTACATGAGTGGAGAGATCGTATAGCTCGTCAGGAAGATGAGAGTACTGGTTATATACTGCCAAATAAGGCTTTAATTGAGATAG
                        tctcatatatcctctt  CT-rich tract
     attgcatatataat  TA-rich tract