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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ccaattctgtgtaagctacgtacgtgggagcactcaagatccttgcttctcctctagcgctagtggttcattcatattgatggtataagcattgtcacagGCAAACCACCAGATCACCACAAAGATACAAAGGCGCATTTATGGGCATGCCACAGATGTGGCGATCAGGCCTTTGGATGAGCAGAAAGCTGTTCAAGCTG

Basic information

species Zea mays
transcript GRMZM2G047509_T02
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G047509_T02 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os01g14020.1 (Oryza sativa), 3'ss of exon 1
-ccaattctgtgtaagctacgtacgtgggagcactcaagatccttgcttctcctctagcgctagtggttcattcat--attgatggtataagcattgtcacagGCAAACCACCAGATCACCACAAAGATACAAAGGCGCATTTATGGGCATGCCACAGATGTGGCGATCAGGCCTTTGGATGAGCAGAAAGCTGTTCAAGCTG
  ||| | | | || |    ||  |  |  ||   |     | |||   |      ||  ||      | | | |   ||||    |||||  ||||| ||||   ||||| |   | || |||| ||||||||||||||||||||||||||| ||||||||||  ||||  |||||  ||||| |||||||||| |||||||
ctcaaatgtatttacgtgttgtgggctgtggc---cgtatcctttgtgcccttatgaggtctgacatataactaaccgattgtaactataacaattgttacagATTAACCATCGTGTTACTACAAGGATACAAAGGCGCATTTATGGGCATGCAACAGATGTGGAAATCACACCTTTAAATGAGGAGAAAGCTGTACAAGCTG
















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|211206703|gb|FL036107.1|FL036107
EST:     AGGCCGCCGTCCACCCCAAGTTCCGCAACTTCATCATCGCCATCGCCCAG                         GCAAACCACCAGATCACCACAAAGATACAAAGGCGCATTTATGGGCATGCC
genomic: AGGCCGCCGTCCACCCCAAGTTCCGCAACTTCATCATCGCCATCGCCCAGgtatcctctt ... attgtcacagGCAAACCACCAGATCACCACAAAGATACAAAGGCGCATTTATGGGCATGCC
EST: gi|44900751|gb|CK827296.1|CK827296
EST:     AGGCCGCTGTCCACCCCAAGTTCCGCAACTTCATCATCGCCATCGCCCAG                         GCAAACCACCAGATCACCACAAAGATACAGAGGCGCATTTATGGGCATGCC
genomic: AGGCCGCCGTCCACCCCAAGTTCCGCAACTTCATCATCGCCATCGCCCAGgtatcctctt ... attgtcacagGCAAACCACCAGATCACCACAAAGATACAAAGGCGCATTTATGGGCATGCC
EST: gi|211206710|gb|FL036114.1|FL036114
EST:     AGGCCGCCGTCCACCCCAAGTTCCGCAACTTCATCATCGCCATCGCCCAG                         GCAAACCACCAGATCACCACAAAGATACAAAGGCGCATTTATGGGCATGCC
genomic: AGGCCGCCGTCCACCCCAAGTTCCGCAACTTCATCATCGCCATCGCCCAGgtatcctctt ... attgtcacagGCAAACCACCAGATCACCACAAAGATACAAAGGCGCATTTATGGGCATGCC
EST: gi|94478837|gb|EB707795.1|EB707795
EST:     AGGCCGCCGTCCACCCCAAGTTCCGCAACTTCATCATCGCCATCCCCCAG                         GCAAACCACCAGATCACCACAAAGATACAAAGGCGCATTTATGGGCATGCC
genomic: AGGCCGCCGTCCACCCCAAGTTCCGCAACTTCATCATCGCCATCGCCCAGgtatcctctt ... attgtcacagGCAAACCACCAGATCACCACAAAGATACAAAGGCGCATTTATGGGCATGCC
EST: gi|211206707|gb|FL036111.1|FL036111
EST:     AGGCCGCCGTCCACCCCAAGTTCCGCAACTTCATCATCGCCATCGCCCAG                         GCAAACCACCAGATCACCACAAAGATACAAAGGCGCATTTATGGGCATGCC
genomic: AGGCCGCCGTCCACCCCAAGTTCCGCAACTTCATCATCGCCATCGCCCAGgtatcctctt ... attgtcacagGCAAACCACCAGATCACCACAAAGATACAAAGGCGCATTTATGGGCATGCC
EST: gi|16927681|gb|BM080750.1|BM080750
EST:     CATCATCGCCATCGCCCAG                         GCAAACCACCAGATCACCACAAAGATACAAAGGCGCATTTATGGGCATGCC
genomic: CATCATCGCCATCGCCCAGgtatcctctt ... attgtcacagGCAAACCACCAGATCACCACAAAGATACAAAGGCGCATTTATGGGCATGCC
EST: gi|148965768|gb|EE016647.2|EE016647
EST:     AGGCCGCCGTCCACCCCAAGTTCCGCAACTTCATCATCGCCATCGCCCAG                         GCAAACCACCAGATCACCACAAAGATACAAAGGCGCATTTATGGGCATGCC
genomic: AGGCCGCCGTCCACCCCAAGTTCCGCAACTTCATCATCGCCATCGCCCAGgtatcctctt ... attgtcacagGCAAACCACCAGATCACCACAAAGATACAAAGGCGCATTTATGGGCATGCC
EST: gi|211206702|gb|FL036106.1|FL036106
EST:     AGGCCGCTGTCCACCCCAAGTTCCGCAACTTCATCATCGCCATCGCCCAG                         GCAAACCACCAGATCACCACAAAGATACAGAGGCGCATTTATGGGCATGCC
genomic: AGGCCGCCGTCCACCCCAAGTTCCGCAACTTCATCATCGCCATCGCCCAGgtatcctctt ... attgtcacagGCAAACCACCAGATCACCACAAAGATACAAAGGCGCATTTATGGGCATGCC
EST: gi|211206704|gb|FL036108.1|FL036108
EST:     AGGCCGCCGTCCACCCCAAGTTCCGCAACTTCATCATCGCCATCGCCCAG                         GCAAACCACCAGATCACCACAAAGATACAAAGGCGCATTTATGGGCATGCC
genomic: AGGCCGCCGTCCACCCCAAGTTCCGCAACTTCATCATCGCCATCGCCCAGgtatcctctt ... attgtcacagGCAAACCACCAGATCACCACAAAGATACAAAGGCGCATTTATGGGCATGCC
EST: gi|211206709|gb|FL036113.1|FL036113
EST:     AGGCCGCTGTCCACCCCAAGTTCCGCAACTTCATCATCGCCATCGCCCAG                         GCAAACCACCAGATCACCACAAAGATACAGAGGCGCATTTATGGGCATGCC
genomic: AGGCCGCCGTCCACCCCAAGTTCCGCAACTTCATCATCGCCATCGCCCAGgtatcctctt ... attgtcacagGCAAACCACCAGATCACCACAAAGATACAAAGGCGCATTTATGGGCATGCC
EST: gi|211206708|gb|FL036112.1|FL036112
EST:     AGGCCGCTGTCCACCCCAAGTTCCGCAACTTCATCATCGCCATCGCCCAG                         GCAAACCACCAGATCACCACAAAGATACAGAGGCGCATTTATGGGCATGCC
genomic: AGGCCGCCGTCCACCCCAAGTTCCGCAACTTCATCATCGCCATCGCCCAGgtatcctctt ... attgtcacagGCAAACCACCAGATCACCACAAAGATACAAAGGCGCATTTATGGGCATGCC

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), 49 (downstream exon)
Score: 52

CCTAGCGCTGCGGACGCTGTCCAAGCCCATCGCCAGCCGCCTCAAGAGCCAGGCCGCCGTCCACCCCAAGTTCCGCAACTTCATCATCGCCATCGCCCAGgtatcctctt ... attgtcacagGCAAACCACCAGATCACCACAAAGATACAAAGGCGCATTTATGGGCATGCCACAGATGTGGCGATCAGGCCTTTGGATGAGCAGAAAGCTGTTCAAGCTG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 133

CCTAGCGCTGCGGACGCTGTCCAAGCCCATCGCCAGCCGCCTCAAGAGCCAGGCCGCCGTCCACCCCAAGTTCCGCAACTTCATCATCGCCATCGCCCAGgtatcctctt ... attgtcacagGCAAACCACCAGATCACCACAAAGATACAAAGGCGCATTTATGGGCATGCCACAGATGTGGCGATCAGGCCTTTGGATGAGCAGAAAGCTGTTCAAGCTG


Block sizes: 44 (upstream exon), 49 (downstream exon)
Score: 81

CCTAGCGCTGCGGACGCTGTCCAAGCCCATCGCCAGCCGCCTCAAGAGCCAGGCCGCCGTCCACCCCAAGTTCCGCAACTTCATCATCGCCATCGCCCAGgtatcctctt ... attgtcacagGCAAACCACCAGATCACCACAAAGATACAAAGGCGCATTTATGGGCATGCCACAGATGTGGCGATCAGGCCTTTGGATGAGCAGAAAGCTGTTCAAGCTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 133

CCTAGCGCTGCGGACGCTGTCCAAGCCCATCGCCAGCCGCCTCAAGAGCCAGGCCGCCGTCCACCCCAAGTTCCGCAACTTCATCATCGCCATCGCCCAGgtatcctctt ... attgtcacagGCAAACCACCAGATCACCACAAAGATACAAAGGCGCATTTATGGGCATGCCACAGATGTGGCGATCAGGCCTTTGGATGAGCAGAAAGCTGTTCAAGCTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttctcctctagcgctagtggttcattcatattgatggtataagcattgtcacagGCAAACCACCAGATCACCACAAAGATACAAAGGCGCATTTATGGGCATGCCACAGATGTGGCGATCAGGCCTTTGGATGAGCAGAAAGCTGTTCAAGCTG
                             tattgat  putative branch site (score: 133)
                        attcatatt  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ccaattctgtgtaagctacgtacgtgggagcactcaagatccttgcttctcctctagcgctagtggttcattcatattgatggtataagcattgtcacagGCAAACCACCAGATCACCACAAAGATACAAAGGCGCATTTATGGGCATGCCACAGATGTGGCGATCAGGCCTTTGGATGAGCAGAAAGCTGTTCAAGCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG