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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCGCAGGAGGCCACCACGCTGGGGGGTGTGAGGTGGCTGCAGATGCAGAGCGCGTCCGATCTCgtaagacagttcgtcttcctgttatgccttgtggtagagttttgtgtactctggatagcatgctgattgtgtttctgcaaatgcag

Basic information

species Zea mays
transcript GRMZM2G063851_T01
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G063851_T02 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os02g10070.1 (Oryza sativa), 5'ss of exon 3
GCGCAGGAGGCCACCACGCTGGGGGGTGTGAGGTGGCTGCAGATGCAGAGCGCGTCCGATCTCgtaagacagttcgtcttcct--gttatgccttgtggtagagttttgtgtactctggatagcatgctgattgtgtttctg--caaatgcag-----------------------------------------------------
|| ||||||||||||||||| || |||||| | |||||||||||||||||||| || ||||| ||||| || || || ||  |  |||    ||    ||   |||     |||     |     |||    ||||  |  |  | || |  |                                                     
GCACAGGAGGCCACCACGCTTGGTGGTGTGCGATGGCTGCAGATGCAGAGCGCATCTGATCTTgtaagtcaattagtttttgttcgttcgtgctaaatgtgtggttgaaactaccagttactatgtgccatctgtggctaggctcgaaagtggggaatgtgctctgaaaaaagatgtttgattgtgtttctaaatattatatgcag

upper sequence: GRMZM2G063851_T02 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os11g33240.3 (Oryza sativa), 5'ss of exon 2
GCGCAGGAGGCCACCACGCTGGGGGGTGTGAGGTGGCTGCAGATGCAGAGCGCGTCCGATCTCgtaagacagt--tcgtcttcctgttatgccttgtggtaga--gttttgtgtac-tctggatagc--atgctgattgt--gtttctgcaaatgcag----------------------------------------------------------------------------------
|| ||||||||||||||||| || |||||||| |||||||||||||||||  | || ||||| |||||||| |  | || |   ||||      | || | |   ||  | |  |  | || || |   |   |||| ||     |||  |  | | |                                                                                  
GCACAGGAGGCCACCACGCTTGGTGGTGTGAGATGGCTGCAGATGCAGAGTCCATCTGATCTTgtaagacaataatagtttgtttgtttctttgtttgtttgttcgtgctataaatatttgcatggttgaaattgatagttaccctctctaccttctgtggctggctacgattgaaattaagttggaaatgtgctctgaaaaagatgtttgatttgtgttcctaaatattatgctttcag
















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|51592469|gb|CV071615.1|CV071615
EST:     CCACGCTGGGGGGTGTGAGGTGGCTGCAGATGCAGAGCGCGTCCGATCTC                         GATCCTAAGTCCCAGTTGCAGGAATTGATTCCGGAACAACAG
genomic: CCACGCTGGGGGGTGTGAGGTGGCTGCAGATGCAGAGCGCGTCCGATCTCgtaagacagt ... gcaaatgcagGATCTTAAGTCCCAGTTGCAGGAATTGATTCCGGAACAACAG
EST: gi|211505526|gb|FL228165.1|FL228165
EST:     CCACGCTGGGGGGTGTGAGGTGGCTGCAGATGCAGAGCGCGTCCGATCTC                         GATCTTAAGTCCCAGTTGCAGGAATTGATTCCGGAACAACAG
genomic: CCACGCTGGGGGGTGTGAGGTGGCTGCAGATGCAGAGCGCGTCCGATCTCgtaagacagt ... gcaaatgcagGATCTTAAGTCCCAGTTGCAGGAATTGATTCCGGAACAACAG
EST: gi|211507876|gb|FL228171.1|FL228171
EST:     CCACGCTGGGGGGTGTGAGGTGGCTGCAGATGCAGAGCGCGTCCGATCTC                         GATCTTAAGTCCCAGTTGCAGGAATTGATTCCGGAACAACAG
genomic: CCACGCTGGGGGGTGTGAGGTGGCTGCAGATGCAGAGCGCGTCCGATCTCgtaagacagt ... gcaaatgcagGATCTTAAGTCCCAGTTGCAGGAATTGATTCCGGAACAACAG
EST: gi|149084983|gb|EE174493.2|EE174493
EST:     CCACGCTGGGGGGTGTGAGGTGGCTGCAGATGCAGAGCGCGTCCGATCTC                         GATCTTAAGTCCCAGTTGCAGGAATTGATTCCGGAACAACAG
genomic: CCACGCTGGGGGGTGTGAGGTGGCTGCAGATGCAGAGCGCGTCCGATCTCgtaagacagt ... gcaaatgcagGATCTTAAGTCCCAGTTGCAGGAATTGATTCCGGAACAACAG
EST: gi|211507874|gb|FL228169.1|FL228169
EST:     CCACGCTGGGGGGTGTGAGGTGGCTGCAGATGCAGAGCGCGTCCGATCTC                         GATCTTAAGTCCCAGTTGCAGGAATTGATTCCGGAACAACAG
genomic: CCACGCTGGGGGGTGTGAGGTGGCTGCAGATGCAGAGCGCGTCCGATCTCgtaagacagt ... gcaaatgcagGATCTTAAGTCCCAGTTGCAGGAATTGATTCCGGAACAACAG
EST: gi|211059244|gb|FL131321.1|FL131321
EST:     CCACGCTGGGGGGTGTGAGGTGGCTGCAGATGCAGAGCGCGTCCGATCTC                         GATCTTAAGTCCCAGTTGCAGGAATTGATTCCGGAACAACAG
genomic: CCACGCTGGGGGGTGTGAGGTGGCTGCAGATGCAGAGCGCGTCCGATCTCgtaagacagt ... gcaaatgcagGATCTTAAGTCCCAGTTGCAGGAATTGATTCCGGAACAACAG
EST: gi|148932412|gb|EC876097.2|EC876097
EST:     CCACGCTGGGGGGTGTGAGGTGGCTGCAGATGCAGAGCGCGTCCGATCTC                         GATCTTAAGTCCCAGTTGCAGGAATTGATTCCGGAACAACAG
genomic: CCACGCTGGGGGGTGTGAGGTGGCTGCAGATGCAGAGCGCGTCCGATCTCgtaagacagt ... gcaaatgcagGATCTTAAGTCCCAGTTGCAGGAATTGATTCCGGAACAACAG
EST: gi|211507879|gb|FL228174.1|FL228174
EST:     CCACGCTGGGGGGTGTGAGGTGGCTGCAGATGCAGAGCGCGTCCGATCTC                         GATCTTAAGTCCCAGTTGCAGGAATTGATTCCGGAACAACAG
genomic: CCACGCTGGGGGGTGTGAGGTGGCTGCAGATGCAGAGCGCGTCCGATCTCgtaagacagt ... gcaaatgcagGATCTTAAGTCCCAGTTGCAGGAATTGATTCCGGAACAACAG
EST: gi|67013663|gb|CO442412.1|CO442412
EST:     CCACGCTGGGGGGTGTGAGGTGGCTGCAGATGCAGAGCGCGTCCGATCTC                         GATCTTAAGTCCCAGTTGCAGGAATTGATTCCGGAACAACAG
genomic: CCACGCTGGGGGGTGTGAGGTGGCTGCAGATGCAGAGCGCGTCCGATCTCgtaagacagt ... gcaaatgcagGATCTTAAGTCCCAGTTGCAGGAATTGATTCCGGAACAACAG
EST: gi|149100799|gb|EE186893.2|EE186893
EST:     CCACGCTGGGGGGTGTGAGGTGGCTGCAGATGCAGAGCGCGTCCGATCTC                         GATCTTAAGTCCCAGTTGCAGGAATTGATTCCGGAACAACAG
genomic: CCACGCTGGGGGGTGTGAGGTGGCTGCAGATGCAGAGCGCGTCCGATCTCgtaagacagt ... gcaaatgcagGATCTTAAGTCCCAGTTGCAGGAATTGATTCCGGAACAACAG
EST: gi|211510237|gb|FL228184.1|FL228184
EST:     CCACGCTGGGGGGTGTGAGGTGGCTGCAGATGCAGAGCGCGTCCGATCTC                         GATCTTAAGTCCCAGTTGCAGGAATTGATTCCGGAACAACAG
genomic: CCACGCTGGGGGGTGTGAGGTGGCTGCAGATGCAGAGCGCGTCCGATCTCgtaagacagt ... gcaaatgcagGATCTTAAGTCCCAGTTGCAGGAATTGATTCCGGAACAACAG
EST: gi|149014218|gb|EE043773.2|EE043773
EST:     CCACGCTGGGGGGTGTGAGGTGGCTGCAGATGCAGAGCGCGTCCGATCTC                         GATCTTAAGTCCCAGTTGCAGGAATTGATTCCGGAACAACAG
genomic: CCACGCTGGGGGGTGTGAGGTGGCTGCAGATGCAGAGCGCGTCCGATCTCgtaagacagt ... gcaaatgcagGATCTTAAGTCCCAGTTGCAGGAATTGATTCCGGAACAACAG
EST: gi|211510240|gb|FL228187.1|FL228187
EST:     CCACGCTGGGGGGTGTGAGGTGGCTGCAGATGCAGAGCGCGTCCGATCTC                         GATCTTAAGTCCCAGTTGCAGGAATTGATTCCGGAACAACAG
genomic: CCACGCTGGGGGGTGTGAGGTGGCTGCAGATGCAGAGCGCGTCCGATCTCgtaagacagt ... gcaaatgcagGATCTTAAGTCCCAGTTGCAGGAATTGATTCCGGAACAACAG
EST: gi|149105261|gb|EE290752.2|EE290752
EST:     CCACGCTGGGGGGTGTGAGGTGGCTGCAGATGCAGAGCGCGTCCGATCTC                         GATCTTAAGTCCCAGTTGCAGGAATTGATTCCGGAACAACAG
genomic: CCACGCTGGGGGGTGTGAGGTGGCTGCAGATGCAGAGCGCGTCCGATCTCgtaagacagt ... gcaaatgcagGATCTTAAGTCCCAGTTGCAGGAATTGATTCCGGAACAACAG
EST: gi|93284646|gb|EB676910.1|EB676910
EST:     CCACGCTGGGGGGTGTGAGGTGGCTGCAGATGCAGAGCGCGTCCGATCTC                         GATCTTAAGTCCCAGTTGCAGGAATTGATTCCGGAACAACAG
genomic: CCACGCTGGGGGGTGTGAGGTGGCTGCAGATGCAGAGCGCGTCCGATCTCgtaagacagt ... gcaaatgcagGATCTTAAGTCCCAGTTGCAGGAATTGATTCCGGAACAACAG
EST: gi|148991806|gb|EE033387.2|EE033387
EST:     CCACGCTGGGGGGTGTGAGGTGGCTGCAGATGCAGAGCGCGTCCGATCTC                         GATCTTAAGTCCCAGTTGCAGGAATTGATTCCGGAACAACAG
genomic: CCACGCTGGGGGGTGTGAGGTGGCTGCAGATGCAGAGCGCGTCCGATCTCgtaagacagt ... gcaaatgcagGATCTTAAGTCCCAGTTGCAGGAATTGATTCCGGAACAACAG
EST: gi|148931316|gb|EC874179.2|EC874179
EST:     CCACGCTGGGGGGTGTGAGGTGGCTGCAGATGCAGAGCGCGTCCGATCTC                         GATCTTAAGTCCCAGTTGCAGGAATTGATTCCGGAACAACAG
genomic: CCACGCTGGGGGGTGTGAGGTGGCTGCAGATGCAGAGCGCGTCCGATCTCgtaagacagt ... gcaaatgcagGATCTTAAGTCCCAGTTGCAGGAATTGATTCCGGAACAACAG
EST: gi|211510249|gb|FL228196.1|FL228196
EST:     CCACGCTGGGGGGTGTGAGGTGGCTGCAGATGCAGAGCGCGTCCGATCTC                         GATCTTAAGTCCCAGTTGCAGGAATTGATTCCGGAACAACAG
genomic: CCACGCTGGGGGGTGTGAGGTGGCTGCAGATGCAGAGCGCGTCCGATCTCgtaagacagt ... gcaaatgcagGATCTTAAGTCCCAGTTGCAGGAATTGATTCCGGAACAACAG
EST: gi|211510239|gb|FL228186.1|FL228186
EST:     CCACGCTGGGGGGTGTGAGGTGGCTGCAGATGCAGAGCGCGTCCGATCTC                         GATCTTAAGTCCCAGTTGCAGGAATTGATTCCGGAACAACAG
genomic: CCACGCTGGGGGGTGTGAGGTGGCTGCAGATGCAGAGCGCGTCCGATCTCgtaagacagt ... gcaaatgcagGATCTTAAGTCCCAGTTGCAGGAATTGATTCCGGAACAACAG
EST: gi|78087725|gb|DV516118.1|DV516118
EST:     CCACGCTGGGGGGTGTGAGGTGGCTGCAGATGCAGAGCGCGTCCGATCTC                         GATCTTAAGTCCCAGTTGCAGGAATTGATTCCGGAACAACAG
genomic: CCACGCTGGGGGGTGTGAGGTGGCTGCAGATGCAGAGCGCGTCCGATCTCgtaagacagt ... gcaaatgcagGATCTTAAGTCCCAGTTGCAGGAATTGATTCCGGAACAACAG
EST: gi|211510246|gb|FL228193.1|FL228193
EST:     CCACGCTGGGGGGTGTGAGGTGGCTGCAGATGCAGAGCGCGTCCGATCTC                         GATCTTAAGTCCCAGTTGCAGGAATTGATTCCGGAACAACAG
genomic: CCACGCTGGGGGGTGTGAGGTGGCTGCAGATGCAGAGCGCGTCCGATCTCgtaagacagt ... gcaaatgcagGATCTTAAGTCCCAGTTGCAGGAATTGATTCCGGAACAACAG
EST: gi|211507880|gb|FL228175.1|FL228175
EST:     CCACGCTGGGGGGTGTGAGGTGGCTGCAGATGCAGAGCGCGTCCGATCTC                         GATCTTAAGTCCCAGTTGCAGGAATTGATTCCGGAACAACAG
genomic: CCACGCTGGGGGGTGTGAGGTGGCTGCAGATGCAGAGCGCGTCCGATCTCgtaagacagt ... gcaaatgcagGATCTTAAGTCCCAGTTGCAGGAATTGATTCCGGAACAACAG
EST: gi|148990704|gb|EE032108.2|EE032108
EST:     CCACGCTGGGGGGTGTGAGGTGGCTGCAGATGCAGAGCGCGTCCGATCTC                         GATCTTAAGTCCCAGTTGCAGGAATTGATTCCGGAACAACAG
genomic: CCACGCTGGGGGGTGTGAGGTGGCTGCAGATGCAGAGCGCGTCCGATCTCgtaagacagt ... gcaaatgcagGATCTTAAGTCCCAGTTGCAGGAATTGATTCCGGAACAACAG
EST: gi|211507878|gb|FL228173.1|FL228173
EST:     CCACGCTGGGGGGTGTGAGGTGGCTGCAGATGCAGAGCGCGTCCGATCTC                         GATCTTAAGTCCCCAGTTGCAGGAATTGATTCCCGGAACAACAG
genomic: CCACGCTGGGGGGTGTGAGGTGGCTGCAGATGCAGAGCGCGTCCGATCTCgtaagacagt ... gcaaatgcagGATCTTAAGTCCC-AGTTGCAGGAATTGATTCC-GGAACAACAG
EST: gi|71771089|gb|DR969026.1|DR969026
EST:     CCACGCTGGGGGGTGTGAGGTGGCTGCAGATGCAGAGCGCGTCCGATCTC                         GATCTTAAGTCCCAGTTGCAGGAATTGATTCCGGAACAACAG
genomic: CCACGCTGGGGGGTGTGAGGTGGCTGCAGATGCAGAGCGCGTCCGATCTCgtaagacagt ... gcaaatgcagGATCTTAAGTCCCAGTTGCAGGAATTGATTCCGGAACAACAG
EST: gi|211507873|gb|FL228168.1|FL228168
EST:     CCACGCTGGGGGGTGTGAGGTGGCTGCAGATGCAGAGCGCGTCCGATCTC                         GATCTTAAGTCCCAGTTGCAGGAATTGATTCCGGAACAACAG
genomic: CCACGCTGGGGGGTGTGAGGTGGCTGCAGATGCAGAGCGCGTCCGATCTCgtaagacagt ... gcaaatgcagGATCTTAAGTCCCAGTTGCAGGAATTGATTCCGGAACAACAG
EST: gi|211507884|gb|FL228179.1|FL228179
EST:     CCACGCTGGGGGGTGTGAGGTGGCTGCAGATGCAGAGCGCGTCCGATCTC                         GATCTTAAGTCCCAGTTGCAGGAATTGATTCCGGAACAACAG
genomic: CCACGCTGGGGGGTGTGAGGTGGCTGCAGATGCAGAGCGCGTCCGATCTCgtaagacagt ... gcaaatgcagGATCTTAAGTCCCAGTTGCAGGAATTGATTCCGGAACAACAG
EST: gi|211507875|gb|FL228170.1|FL228170
EST:     CCACGCTGGGGGGTGTGAGGTGGCTGCAGATGCAGAGCGCGTCCGATCTC                         GATCTTAAGTCCCAGTTGCAGGAATTGATTCCGGAACAACAG
genomic: CCACGCTGGGGGGTGTGAGGTGGCTGCAGATGCAGAGCGCGTCCGATCTCgtaagacagt ... gcaaatgcagGATCTTAAGTCCCAGTTGCAGGAATTGATTCCGGAACAACAG
EST: gi|148939431|gb|EC883987.2|EC883987
EST:     CCACGCTGGGGGGTGTGAGGTGGCTGCAGATGCAGAGCGCGTCCGATCTC                         GATCTTAAGTCCCAGTTGCAGGAATTGATTCCGGAACAACAG
genomic: CCACGCTGGGGGGTGTGAGGTGGCTGCAGATGCAGAGCGCGTCCGATCTCgtaagacagt ... gcaaatgcagGATCTTAAGTCCCAGTTGCAGGAATTGATTCCGGAACAACAG
EST: gi|89758059|gb|DY687401.1|DY687401
EST:     CCACGCTGGGGGGTGTGAGGTGGCTGCAGATGCAGAGCGCGTCCGATCTC                         GATCTTAAGTCCCAGTTGCAGGAATTGATTCCGGAACAACAG
genomic: CCACGCTGGGGGGTGTGAGGTGGCTGCAGATGCAGAGCGCGTCCGATCTCgtaagacagt ... gcaaatgcagGATCTTAAGTCCCAGTTGCAGGAATTGATTCCGGAACAACAG
EST: gi|149082974|gb|EE172211.2|EE172211
EST:     CCACGCTGGGGGGTGTGAGGTGGCTGCAGATGCAGAGCGCGTCCGATCTC                         GATCTTAAGTCCCAGTTGCAGGAATTGATTCCGGAACAACAG
genomic: CCACGCTGGGGGGTGTGAGGTGGCTGCAGATGCAGAGCGCGTCCGATCTCgtaagacagt ... gcaaatgcagGATCTTAAGTCCCAGTTGCAGGAATTGATTCCGGAACAACAG
EST: gi|211505527|gb|FL228166.1|FL228166
EST:     CCACGCTGGGGGGTGTGAGGTGGCTGCAGATGCAGAGCGCGTCCGATCTC                         GATCTTAAGTCCCAGTTGCAGGAATTGATTCCGGAACAACAG
genomic: CCACGCTGGGGGGTGTGAGGTGGCTGCAGATGCAGAGCGCGTCCGATCTCgtaagacagt ... gcaaatgcagGATCTTAAGTCCCAGTTGCAGGAATTGATTCCGGAACAACAG
EST: gi|211510238|gb|FL228185.1|FL228185
EST:     CCACGCTGGGGGGTGTGAGGTGGCTGCAGATGCAGAGCGCGTCCGATCTC                         GATCTTAAGTCCCAGTTGCAGGAATTGATTCCGGAACAACAG
genomic: CCACGCTGGGGGGTGTGAGGTGGCTGCAGATGCAGAGCGCGTCCGATCTCgtaagacagt ... gcaaatgcagGATCTTAAGTCCCAGTTGCAGGAATTGATTCCGGAACAACAG
EST: gi|74035022|gb|DT535512.1|DT535512
EST:     CCACGCTGGGGGGTGTGAGGTGGCTGCAGATGCAGAGCGCGTCCGATCTC                         GATCTTAAGTCCCAGTTGCAGGAATTGATTCCGGAACAACAG
genomic: CCACGCTGGGGGGTGTGAGGTGGCTGCAGATGCAGAGCGCGTCCGATCTCgtaagacagt ... gcaaatgcagGATCTTAAGTCCCAGTTGCAGGAATTGATTCCGGAACAACAG

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), 47 (downstream exon)
Score: 327

GCGCAGGAGGCCACCACGCTGGGGGGTGTGAGGTGGCTGCAGATGCAGAGCGCGTCCGATCTCgtaagacagt ... gcaaatgcagGATCTTAAGTCCCAGTTGCAGGAATTGATTCCGGAACAACAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 1619

GCGCAGGAGGCCACCACGCTGGGGGGTGTGAGGTGGCTGCAGATGCAGAGCGCGTCCGATCTCgtaagacagt ... gcaaatgcagGATCTTAAGTCCCAGTTGCAGGAATTGATTCCGGAACAACAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 1215

GCGCAGGAGGCCACCACGCTGGGGGGTGTGAGGTGGCTGCAGATGCAGAGCGCGTCCGATCTCgtaagacagt ... gcaaatgcagGATCTTAAGTCCCAGTTGCAGGAATTGATTCCGGAACAACAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 914

GCGCAGGAGGCCACCACGCTGGGGGGTGTGAGGTGGCTGCAGATGCAGAGCGCGTCCGATCTCgtaagacagt ... gcaaatgcagGATCTTAAGTCCCAGTTGCAGGAATTGATTCCGGAACAACAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCGCAGGAGGCCACCACGCTGGGGGGTGTGAGGTGGCTGCAGATGCAGAGCGCGTCCGATCTCgtaagacagttcgtcttcctgttatgccttgtggtagagttttgtgtactctggatagcatgctgattgtgtttctgcaaatgcag

- - - - - - - - - - - - - - - - - - CTGCAG
- - - - - - - - - - - - - - - - - - - GCAGAT
- - - - - - - - - - - - - - - - - - -  CAGATG