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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGCACAAGGGCTGGCTCATATTCTGATGAAGGTTCTCAGAAGAAGCCTGCAGgtatgtctcattgaatttttattttgacttatttatattaatgtggttagcacttgattaattatttgcctattctcctgaacttttgatgaag

Basic information

species Zea mays
transcript GRMZM2G107106_T02
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G107106_T06 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os08g41010.4 (Oryza sativa), 5'ss of exon 6
GGCACAAGGGCTGGCTCATATTCTGATGAAGGTTCTCAGAAGAAGCCTGCAGgtatgtctcattgaatttttattttgacttatttatattaatgtggttagcacttgattaattatttgcctattctcctgaacttttgatgaag
||| | |||||||| |||||||| || ||||| || |||||||||||||||||||| | |  |  |||    |||||||||  |    ||| || | |||  |  ||| ||   |||||     ||||  ||||||||   | |  
GGCGCGAGGGCTGGTTCATATTCCGAGGAAGGATCCCAGAAGAAGCCTGCAGgtatatattttcaaatga--attttgactgttc---attgattttgttgtccattggtt---tattt-----ttcttatgaactttattttag-
















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|32929362|gb|CF034174.1|CF034174
EST:     CACGAGGGCTGGCTCATATTCCGATGAAGGTTCTCAGAAGAAGCCTGCAG                         GAGCTGGCCGTGATAATGATTGGGAGTGCCCAAATTGCCATAACATCAACT
genomic: CACAAGGGCTGGCTCATATTCTGATGAAGGTTCTCAGAAGAAGCCTGCAGgtatgtctca ... tttgatgaagGAGCTGGCCGTGATAATGATTGGGAGTGTCCAAATTGCCATAACATCAACT
EST: gi|71765408|gb|DR963345.1|DR963345
EST:     CACAAGGGCTGGCTCATATTCTGATGAAGGTTCTCAGAAGAAGCCTGCAG                         GAGCTGGCCGTGATAATGATTGGGAGTGTCCAAATTGGCATAACATCAACT
genomic: CACAAGGGCTGGCTCATATTCTGATGAAGGTTCTCAGAAGAAGCCTGCAGgtatgtctca ... tttgatgaagGAGCTGGCCGTGATAATGATTGGGAGTGTCCAAATTGCCATAACATCAACT
EST: gi|71439462|gb|DR820512.1|DR820512
EST:     CACAAGGGCTGGCTCATATTCTGATGAAGGTTCTCAGAAGAAGCCTGCAG                         GAGCTGGCCGTGATAATGATTGGGAGTGTCCAAATTGCCATAACATCAACT
genomic: CACAAGGGCTGGCTCATATTCTGATGAAGGTTCTCAGAAGAAGCCTGCAGgtatgtctca ... tttgatgaagGAGCTGGCCGTGATAATGATTGGGAGTGTCCAAATTGCCATAACATCAACT
EST: gi|74243877|gb|DT651791.1|DT651791
EST:     ACAAGGGCTGGCTCATATTCTGATGAAGGTTCTCAGAAGAAAGC-TGCAG                         GAGCTGGCCGTGATAATGATTGGGAGTGTCCAAATTGCCATAACATCAAC
genomic: ACAAGGGCTGGCTCATATTCTGATGAAGGTTCTCAGAAGAA-GCCTGCAGgtatgtctca ... tttgatgaagGAGCTGGCCGTGATAATGATTGGGAGTGTCCAAATTGCCATAACATCAAC
EST: gi|71439479|gb|DR820529.1|DR820529
EST:     CACAAGGGCTGGCTCATATTCTGATGAAGGTTCTCAGAAGAAGCCTGCAG                         GAGCTGGCCGTGATAATGATTGGGAGTGTCCAAATTGCCATAACATCAACT
genomic: CACAAGGGCTGGCTCATATTCTGATGAAGGTTCTCAGAAGAAGCCTGCAGgtatgtctca ... tttgatgaagGAGCTGGCCGTGATAATGATTGGGAGTGTCCAAATTGCCATAACATCAACT
EST: gi|31353283|gb|CD437640.1|CD437640
EST:     CACAAGGGCTGGCTCATATTCCGATGAAGGTTCTCAGAAGAAGCCTGCAG                         GAGCTGGCCGTGATAATGATTGGGAGTGTCCAAATTGCCATAACATCAACT
genomic: CACAAGGGCTGGCTCATATTCTGATGAAGGTTCTCAGAAGAAGCCTGCAGgtatgtctca ... tttgatgaagGAGCTGGCCGTGATAATGATTGGGAGTGTCCAAATTGCCATAACATCAACT
EST: gi|61119710|gb|DN560671.1|DN560671
EST:     CACAAGGGCTGGCTCATATTCTGATGAAGGTTCTCAGAAGAAGCCTGCAG                         GAGCTGGCCGTGATAATGATTGGGAGTGTCCAAATTGCCATAACATCAACT
genomic: CACAAGGGCTGGCTCATATTCTGATGAAGGTTCTCAGAAGAAGCCTGCAGgtatgtctca ... tttgatgaagGAGCTGGCCGTGATAATGATTGGGAGTGTCCAAATTGCCATAACATCAACT
EST: gi|32929980|gb|CF034792.1|CF034792
EST:     CACAAGGGCTGGCTCATATTCCGATGAAGGTTCTCAGAAGAAGCCTGCAG                         GAGCTGGCCGTGATAATGATTGGGAGTGTCCAAATTGCCATAACATCAACT
genomic: CACAAGGGCTGGCTCATATTCTGATGAAGGTTCTCAGAAGAAGCCTGCAGgtatgtctca ... tttgatgaagGAGCTGGCCGTGATAATGATTGGGAGTGTCCAAATTGCCATAACATCAACT
EST: gi|71313388|gb|DR793244.1|DR793244
EST:     CACAAGGGCTGGCTCATATTCTGATGAAGGTTCTCAGAAGAAGCCTGCAG                         GAGCTGGCCGTGATAATGATTGGGAGTGTCCAAATTGCCATAACATCAACT
genomic: CACAAGGGCTGGCTCATATTCTGATGAAGGTTCTCAGAAGAAGCCTGCAGgtatgtctca ... tttgatgaagGAGCTGGCCGTGATAATGATTGGGAGTGTCCAAATTGCCATAACATCAACT
EST: gi|71313389|gb|DR793245.1|DR793245
EST:     CACAAGGGCTGGCTCATATTCTGATGAAGGTTCTCAGAAGAAGCCTGCAG                         GAGCTGGCCGTGATAATGATTGGGAGTGTCCAAATTGCCATAACATCAACT
genomic: CACAAGGGCTGGCTCATATTCTGATGAAGGTTCTCAGAAGAAGCCTGCAGgtatgtctca ... tttgatgaagGAGCTGGCCGTGATAATGATTGGGAGTGTCCAAATTGCCATAACATCAACT
EST: gi|78115667|gb|DV534055.1|DV534055
EST:     CACAAGGGCTGGCTCATATTCTGATGAAGGTTCTCAGAAGAAGCCTGCAG                         GAGCTGGCCGTGAATA-TGATTGGGAGTG
genomic: CACAAGGGCTGGCTCATATTCTGATGAAGGTTCTCAGAAGAAGCCTGCAGgtatgtctca ... tttgatgaagGAGCTGGCCGTGA-TAATGATTGGGAGTG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGCACAAGGGCTGGCTCATATTCTGATGAAGGTTCTCAGAAGAAGCCTGCAGgtatgtctcattgaatttttattttgacttatttatattaatgtggttagcacttgattaattatttgcctattctcctgaacttttgatgaag

- - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - CTGCAG