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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGCTCTTGGTGGGAAGACATTTAAAATGAAATTTGGACATCATGGCGGGAATCACCCTGTCTGTGATCTCCGTAGTGGACGTGTAGACATAAGTGCACAGgtttgttcctacctcttacttttttatgcttgatgttggtcatgtctgttaaaaaaaccaacctaggaggaactaggcatctttgaaattaagagagaaa...

Basic information

species Zea mays
transcript GRMZM2G029573_T01
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G029573_T01 (Zea mays), 5'ss of exon 9
lower sequence: LOC_Os02g47850.3 (Oryza sativa), 5'ss of exon 9
GGCTCTTGGTGGGAAGACATTTAAAATGAAATTTGGACATCATGGCGGGAATCACCCTGTCTGTGATCTCCGTAGTGGACGTGTAGACATAAGTGCACAGgtttgttcct------acctcttactttttt-atgcttgatgttggtcatgtctgttaaaaaaaccaacctaggaggaactaggcatc--tttgaaattaagagagaaa
 ||||||||||||||||||||||||||||| ||||| |||||||| || ||||| ||||| ||||| || || ||||||||||| |||||||||||||| ||||||||||      || ||||||| |||| || ||  |||    |||||| | || |          || |  |||| ||| | ||  |||||| || ||    |  
AGCTCTTGGTGGGAAGACATTTAAAATGAAGTTTGGTCATCATGGAGGAAATCATCCTGTTTGTGACCTTCGAAGTGGACGTGTCGACATAAGTGCACAAgtttgttcctgacctgacttcttactgttttgatactgaatgcgattcatgttttttgac--------tctcgagggaaatagccttccgtttgaatttcagtacaat-
















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|6445511|gb|AW179429.1|AW179429
EST:     ATCACCCTGTCTGTGATCTCCGTAGTGGACGTGTAGACATAAGTGCACAG                         AACCATAACTACGCAGTTGACCCAGAATCACTCCCAGAAG
genomic: ATCACCCTGTCTGTGATCTCCGTAGTGGACGTGTAGACATAAGTGCACAGgtttgttcct ... ttccctgtagAACCATAACTACGCAGTTGACCCAGAATCACTCCCAGAAG
EST: gi|31362536|gb|CD446893.1|CD446893
EST:     ATCACCCTGTCTGTGATCTCCGTAGTGGACGTGTAGACATAAGTGCACAG                         ACCCATATCTACGCAGTTGACCCAGAATCACTCCCAGAAGGAGCAAAAGTA
genomic: ATCACCCTGTCTGTGATCTCCGTAGTGGACGTGTAGACATAAGTGCACAGgtttgttcct ... ttccctgtagAACCATAACTACGCAGTTGACCCAGAATCACTCCCAGAAGGAGCAAAAGTA
EST: gi|71760287|gb|DR958224.1|DR958224
EST:     ATCACCCTGTCTGTGATCTCCGTAGTGGACGTGTAGACATAAGTGCACAG                         AACCATAACTACGCAGTTGACCCAGAATCACTCCCAGAAGGAGCAAAAGTA
genomic: ATCACCCTGTCTGTGATCTCCGTAGTGGACGTGTAGACATAAGTGCACAGgtttgttcct ... ttccctgtagAACCATAACTACGCAGTTGACCCAGAATCACTCCCAGAAGGAGCAAAAGTA
EST: gi|32845426|gb|CD985107.1|CD985107
EST:     ATCACCCTGTCTGTGATCTCCGTAGTGGACGTGTAGACATAAGTGCACAG                         AACCATAACTACGCAGTTGACCCAGAATCACTCCCAGAAGGAGCAAAAGTA
genomic: ATCACCCTGTCTGTGATCTCCGTAGTGGACGTGTAGACATAAGTGCACAGgtttgttcct ... ttccctgtagAACCATAACTACGCAGTTGACCCAGAATCACTCCCAGAAGGAGCAAAAGTA
EST: gi|211106984|gb|FL115271.1|FL115271
EST:     ATCACCCTGTCTGTGATCTCCGTAGTGGACGTGTAGACATAAGTGCACAG                         AACCATAACTACGCAGTTGACCCAGAATCACTCCCAGAAGGAGCAAAAGTA
genomic: ATCACCCTGTCTGTGATCTCCGTAGTGGACGTGTAGACATAAGTGCACAGgtttgttcct ... ttccctgtagAACCATAACTACGCAGTTGACCCAGAATCACTCCCAGAAGGAGCAAAAGTA
EST: gi|211518595|gb|FL052563.1|FL052563
EST:     ATCACCCTGTCTGTGATCTCCGTAGTGGACGTGTAGACATAAGTGCACAG                         AACCATAACTACGCAGTTGACCCAGAATCACTCCCAGAAGGAGCAAAAGTW
genomic: ATCACCCTGTCTGTGATCTCCGTAGTGGACGTGTAGACATAAGTGCACAGgtttgttcct ... ttccctgtagAACCATAACTACGCAGTTGACCCAGAATCACTCCCAGAAGGAGCAAAAGTA
EST: gi|33101065|gb|CF061025.1|CF061025
EST:     ATCACCCTGTCTGTGATCTCCGTAGTGGACGTGTAGACATAAGTGCACAG                         AACCATAACTACGCAGTTGACCCAGAATCACTCCCAGAAGGAGCAAAAGTA
genomic: ATCACCCTGTCTGTGATCTCCGTAGTGGACGTGTAGACATAAGTGCACAGgtttgttcct ... ttccctgtagAACCATAACTACGCAGTTGACCCAGAATCACTCCCAGAAGGAGCAAAAGTA
EST: gi|6342748|gb|AW165572.1|AW165572
EST:     ATCACCCTGTCTGTGATCTCCGTAGTGGACGTGTAGACATAAGTGCACAG                         AACCATAACTACGCAGTTGACCCAGAATCACTCCCAGAAGGAGCAAAAGTA
genomic: ATCACCCTGTCTGTGATCTCCGTAGTGGACGTGTAGACATAAGTGCACAGgtttgttcct ... ttccctgtagAACCATAACTACGCAGTTGACCCAGAATCACTCCCAGAAGGAGCAAAAGTA
EST: gi|67018136|gb|CO446885.1|CO446885
EST:     ATCACCCTGTCTGTGATCTCCGTAGTGGACGTGTAGACATAAGTGCACAG                         AACCATAACTACGCAGTTGACCCAGAATCACTCCCAGAAGGAGCAAAAGTA
genomic: ATCACCCTGTCTGTGATCTCCGTAGTGGACGTGTAGACATAAGTGCACAGgtttgttcct ... ttccctgtagAACCATAACTACGCAGTTGACCCAGAATCACTCCCAGAAGGAGCAAAAGTA
EST: gi|211038354|gb|FL445366.1|FL445366
EST:     ATCACCCTGTCTGTGATCTCCGTAGTGGACGTGTAGACATAAGTGCACAG                         AACCATAACTACGCAGTTGACCCAGAATCACTCCCAGAAGGAGCAAAAGTA
genomic: ATCACCCTGTCTGTGATCTCCGTAGTGGACGTGTAGACATAAGTGCACAGgtttgttcct ... ttccctgtagAACCATAACTACGCAGTTGACCCAGAATCACTCCCAGAAGGAGCAAAAGTA
EST: gi|37401297|gb|CF638011.1|CF638011
EST:     ATCACCCTGTCTGTGATCTCCGTAGTGGACGTGTAGACATAAGTGCACAG                         AACCATAACTACGCAGTTGACCCAGAATCACTCCCAGAAGGAGCAAAAGTA
genomic: ATCACCCTGTCTGTGATCTCCGTAGTGGACGTGTAGACATAAGTGCACAGgtttgttcct ... ttccctgtagAACCATAACTACGCAGTTGACCCAGAATCACTCCCAGAAGGAGCAAAAGTA
EST: gi|32844104|gb|CD983785.1|CD983785
EST:     ATCACCCTGTCTGTGATCTCCGTAGTGGACGTGTAGACATAAGTGCACAG                         AACCATAACTACGCAGTTGACCCAGAATCACTCCCAGAAGGAGCAAAAGTA
genomic: ATCACCCTGTCTGTGATCTCCGTAGTGGACGTGTAGACATAAGTGCACAGgtttgttcct ... ttccctgtagAACCATAACTACGCAGTTGACCCAGAATCACTCCCAGAAGGAGCAAAAGTA
EST: gi|60343079|gb|DN210052.1|DN210052
EST:     ATCACCCTGTCTGTGATCTCCGTAGTGGACGTGTAGACATAAGTGCACAG                         AACCATAACTACGCAGTTGACCCAGAATCACTCCCAGAAGGAGCAAAAGTA
genomic: ATCACCCTGTCTGTGATCTCCGTAGTGGACGTGTAGACATAAGTGCACAGgtttgttcct ... ttccctgtagAACCATAACTACGCAGTTGACCCAGAATCACTCCCAGAAGGAGCAAAAGTA
EST: gi|6012497|gb|AW061934.1|AW061934
EST:     ATCACCCTGTCTGTGATCTCCGTAGTGGACGTGTAGACATAAGTGCACAG                         AACCATAACTACGCAGTTGACCCAGAATCACTCCCAGAAGGAGCAAAAGTA
genomic: ATCACCCTGTCTGTGATCTCCGTAGTGGACGTGTAGACATAAGTGCACAGgtttgttcct ... ttccctgtagAACCATAACTACGCAGTTGACCCAGAATCACTCCCAGAAGGAGCAAAAGTA
EST: gi|88751312|gb|DY535453.1|DY535453
EST:     ATCACCCTGTCTGTGATCTCCGTAGTGGACGTGTAGACATAAGTGCACAG                         AACCATAACTACGCAGTTGACCCAGAATCACTCCCAGAAGGAGCAAAAGTA
genomic: ATCACCCTGTCTGTGATCTCCGTAGTGGACGTGTAGACATAAGTGCACAGgtttgttcct ... ttccctgtagAACCATAACTACGCAGTTGACCCAGAATCACTCCCAGAAGGAGCAAAAGTA
EST: gi|211287671|gb|FL254549.1|FL254549
EST:     ATCACCCTGTCTGTGATCTCCGTAGTGGACGTGTAGACATAAGTGCACAG                         AACCATAACTACGCAGTTGACCCAGAATCACTCCCAGAATGAGCAAAAGTA
genomic: ATCACCCTGTCTGTGATCTCCGTAGTGGACGTGTAGACATAAGTGCACAGgtttgttcct ... ttccctgtagAACCATAACTACGCAGTTGACCCAGAATCACTCCCAGAAGGAGCAAAAGTA
EST: gi|71764309|gb|DR962246.1|DR962246
EST:     CATAAGTGCACAG                         AACCATAACTACGCAGTTGACCCAGAATCACTCCCAGAAGGAGCAAAAGTA
genomic: CATAAGTGCACAGgtttgttcct ... ttccctgtagAACCATAACTACGCAGTTGACCCAGAATCACTCCCAGAAGGAGCAAAAGTA
EST: gi|31356811|gb|CD441168.1|CD441168
EST:     ATCACCCTGTCTGTGATCTCCGTAGTGGACGTGTAGACATAAGTGCACAG                         AACCATAACTACGCAGTTGACCCAGAATCACTCCCAGAAGGAGCAAAAGTA
genomic: ATCACCCTGTCTGTGATCTCCGTAGTGGACGTGTAGACATAAGTGCACAGgtttgttcct ... ttccctgtagAACCATAACTACGCAGTTGACCCAGAATCACTCCCAGAAGGAGCAAAAGTA
EST: gi|32844356|gb|CD984037.1|CD984037
EST:     ATCACCCTGTCTGTGATCTCCGTAGTGGACGTGTAGACATAAGTGCACAG                         AACCATAACTACGCAGTTGACCCAGAATCACTCCCAGAAGGAGCAAAAGTA
genomic: ATCACCCTGTCTGTGATCTCCGTAGTGGACGTGTAGACATAAGTGCACAGgtttgttcct ... ttccctgtagAACCATAACTACGCAGTTGACCCAGAATCACTCCCAGAAGGAGCAAAAGTA
EST: gi|37379091|gb|CF626275.1|CF626275
EST:     ATCACCCTGTCTGTGATCTCCGTAGTGGACGTGTAGACTTAAGTGCACAG                         AACCATAACTACGCAGTTGACCCAGAATCACTCCCAGAAGGAGCAATAGTA
genomic: ATCACCCTGTCTGTGATCTCCGTAGTGGACGTGTAGACATAAGTGCACAGgtttgttcct ... ttccctgtagAACCATAACTACGCAGTTGACCCAGAATCACTCCCAGAAGGAGCAAAAGTA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGCTCTTGGTGGGAAGACATTTAAAATGAAATTTGGACATCATGGCGGGAATCACCCTGTCTGTGATCTCCGTAGTGGACGTGTAGACATAAGTGCACAGgtttgttcctacctcttacttttttatgcttgatgttggtcatgtctgttaaaaaaaccaacctaggaggaactaggcatctttgaaattaagagagaaa

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGTGGA