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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AATGGCTGAACTTGAAGAGGGCTCTGGAACAGAAGCATCTGACGCCGAACTGCTCGAGCAGTTCGATTCCATTCAGCCAGAAGACTACGCGAGgtgggcatatcaatttttttgggcatttttttttctcatcaagagttcttaagttttattttttcttatcttaaattcacatccatgcatggcactacac...

Basic information

species Zea mays
transcript GRMZM2G078458_T04
intron # 15
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G078458_T04 (Zea mays), 5'ss of exon 15
lower sequence: LOC_Os06g03676.1 (Oryza sativa), 5'ss of exon 15
AATGGCTGAACTTGAAGAGGGCTCTGGAACAGAAGCATCTGACGCCGAACTGCTCGAGCAGTTCGATTCCATTCAGCCAGAAGACTACGCGAGgtgggcatatcaatttttttgg-----------gcatttttttttct-cat-caagagttcttaagttttattttttcttatcttaaattcacatccatgcatggcactac-ac-----------------------
|||| ||||||||||||||||| ||||||| ||||||||||||  | |||| || ||| | ||||||  || | |  ||||||||    |||||| || |  |      |||||            | ||  |||||||| |||   ||   | | | | || |  ||| | | | |  |  ||   |   ||  |  ||| |  ||                       
AATGACTGAACTTGAAGAGGGCACTGGAACTGAAGCATCTGACAGCCAACTACTTGAGAAATTCGATCTCAGTGATTCAGAAGACGCAACGAGgtagggacgtagggccttttgacgttgcttaatggatacttttttctgcatattagcactatcatgcttgacatttccatctgtacacctcttgtttttgtgtttcaccattactctcattgtctttttcacagaag
















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|74241323|gb|DT649237.1|DT649237
EST:     GCCGAACTGCTCGAGCAGTTCGATTCCATTCAGCCAGAAGACTACGCGAG                         TGAAAGCGGCGAGAAGCACGAAAGGAAGTCAAAGACAAACTACCGTTCGTG
genomic: GCCGAACTGCTCGAGCAGTTCGATTCCATTCAGCCAGAAGACTACGCGAGgtgggcatat ... tctttctcagTGAAAGCGGCGAGAAGCACGAAAGGAAGTCAAAGACAAACTACCGTTCGTG
EST: gi|110940705|gb|EE160862.1|EE160862
EST:     GCCGAACTGCTCGAGCAGTTCGATTCCATTCAGCCAGAAGACTACGCGAG                         TGAAAGCGGCGAGAAGCACGAAAGGAAGTCAAAGACAAACTACCGTTCGTG
genomic: GCCGAACTGCTCGAGCAGTTCGATTCCATTCAGCCAGAAGACTACGCGAGgtgggcatat ... tctttctcagTGAAAGCGGCGAGAAGCACGAAAGGAAGTCAAAGACAAACTACCGTTCGTG
EST: gi|211219812|gb|FL295368.1|FL295368
EST:     GCCGAACTGCTCGAGCAGTTCGATTCCATTCAGCCAGAAGACTACGCGAG                         TGAAAGCGGCGAGAAGCACGAAAGGAAGTCAAAGACAAACTACCGTTCGTG
genomic: GCCGAACTGCTCGAGCAGTTCGATTCCATTCAGCCAGAAGACTACGCGAGgtgggcatat ... tctttctcagTGAAAGCGGCGAGAAGCACGAAAGGAAGTCAAAGACAAACTACCGTTCGTG
EST: gi|71766034|gb|DR963971.1|DR963971
EST:     GCCGAACTGCTCGAGCAGTTCGATTCCATTCAGCCAGAAGACTACGCGAG                         TGAAAGCGGCGAGAAGCACGAAAGGAAGTCAAAGACAAACTACCGTTCGTG
genomic: GCCGAACTGCTCGAGCAGTTCGATTCCATTCAGCCAGAAGACTACGCGAGgtgggcatat ... tctttctcagTGAAAGCGGCGAGAAGCACGAAAGGAAGTCAAAGACAAACTACCGTTCGTG
EST: gi|148953146|gb|EE152627.2|EE152627
EST:     GCCGAACTGCTCGAGCAGTTCGATTCCATTCAGCCAGAAGACTACGCGAG                         TGAAAGCGGCGAGAAGCACGAAAGGAAGTCAAAGACAAACTCCCGTTCGTG
genomic: GCCGAACTGCTCGAGCAGTTCGATTCCATTCAGCCAGAAGACTACGCGAGgtgggcatat ... tctttctcagTGAAAGCGGCGAGAAGCACGAAAGGAAGTCAAAGACAAACTACCGTTCGTG
EST: gi|71761805|gb|DR959742.1|DR959742
EST:     GCCGAACTGCTCGAGCAGTTCGATTCCATTCAGCCAGAAGACTACGCGAG                         TGAAAGCGGCGAGAAGCACGAAAGGAAGTCAAAGACAAACTACCGTTCGTG
genomic: GCCGAACTGCTCGAGCAGTTCGATTCCATTCAGCCAGAAGACTACGCGAGgtgggcatat ... tctttctcagTGAAAGCGGCGAGAAGCACGAAAGGAAGTCAAAGACAAACTACCGTTCGTG
EST: gi|86473471|gb|DY239841.1|DY239841
EST:     GCCGAACTGCTCGAGCAGTTCGATTCCATTCAGCCAGAAGACTACGCGAG                         TGAAAGCGGCGAGAAGCACGAAAGGAAGTCAAAGACAAACTCCCGTTCGTG
genomic: GCCGAACTGCTCGAGCAGTTCGATTCCATTCAGCCAGAAGACTACGCGAGgtgggcatat ... tctttctcagTGAAAGCGGCGAGAAGCACGAAAGGAAGTCAAAGACAAACTACCGTTCGTG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AATGGCTGAACTTGAAGAGGGCTCTGGAACAGAAGCATCTGACGCCGAACTGCTCGAGCAGTTCGATTCCATTCAGCCAGAAGACTACGCGAGgtgggcatatcaatttttttgggcatttttttttctcatcaagagttcttaagttttattttttcttatcttaaattcacatccatgcatggcactacac

- - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCAG