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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTCATCCATTTCAAGCTCTGATCTTTTTGGCCGTACCAATGTGGACGATTCTAACCTGGACCTAAGCGCTGCAGATCTCATCAACAGAATATCTTTCCAGgtaacttgttggcataacctgttgtttcttggaattttagcgtgtagcaccatagtttgcatacgttttaagccacaattgaactatgagttagcggaaacgtgctaaggaaaaaccaataccatgcagagacgtcgtgtgaaagttgcataaagtcaacagtctcatttcctgtcatggttttgtag

Basic information

species Zea mays
transcript GRMZM2G083546_T01
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G083546_T01 (Zea mays), 5'ss of exon 6
lower sequence: LOC_Os03g63710.2 (Oryza sativa), 5'ss of exon 5
TTCATCCATTTCAAGCTCTGATCTTTTTGGCCGTACCAATGTGGACGATTCTAACCTGGACCTAAGCGCTGCAGATCTCATCAACAGAATATCTTTCCAGgtaacttgttggcataacctgttgtttcttggaattttagcgtgtagcaccatagtttgcatacgttttaagccacaattgaac-tatgagttagcggaaacgtgctaaggaaaaaccaataccatgcagagacgtcgtgtgaaagttgcataaagtcaacagtctcatttcctgtcatggttttgtag
||| |||||||||||  ||||||||||||||||   | |  |||| || || || |||||  |||| ||||| |||||||||||||||||||| |||||||||  |  |  | | |      |  ||    |  ||||  |        |  | |  |   ||  ||||||||   ||  || | |   | | |     |     || ||  |  ||  | |  || |||  ||   |  |||   ||| |       || | ||| |  | |||  || ||| || ||
TTCGTCCATTTCAAGTGCTGATCTTTTTGGCCGCCGCGACATGGATGACTCGAATCTGGATTTAAGTGCTGCGGATCTCATCAACAGAATATCATTCCAGgtagttattctgtaaa------taattgccagccttttgtcac------ctcttgcatatttagtttttaagc---aaccgagcatgcaaatcatt---actacactgagttactactga-attattcagt-acaaagattgatccttgaaacgcacaaata-tcttacctgctgggattgttgtgcag
















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|148994701|gb|EE034198.2|EE034198
EST:     TTAACCTGGACCTAAGCGCTGCAGATTTCATCAACAGAATATCTTTCCAG                         GCGTCACAGGATCTGTCTTCACTCAAGGACATAGCTGGAGAGACTGGAAAG
genomic: CTAACCTGGACCTAAGCGCTGCAGATCTCATCAACAGAATATCTTTCCAGgtaacttgtt ... ggttttgtagGCGTCACAGGATCTGTCTTCACTCAAGGACATAGCTGGAGAGACTGGAAAG
EST: gi|32939942|gb|CF044761.1|CF044761
EST:     CTAACCTGGACCTAAGCGCTGCAGATCTCATCAACAGAATATCTTTCCAG                         GCGTCACAGGATCTGTCTTCACTCAAGGACATAGCTGGAGAGACTGGAAAG
genomic: CTAACCTGGACCTAAGCGCTGCAGATCTCATCAACAGAATATCTTTCCAGgtaacttgtt ... ggttttgtagGCGTCACAGGATCTGTCTTCACTCAAGGACATAGCTGGAGAGACTGGAAAG
EST: gi|18162325|gb|BM332164.1|BM332164
EST:     CTAACCTGGACCTAAGCGCTGCAGATCTCATCAACAGAATATCTTTCCAG                         GCGTCACAGGATCTGTCTTCACTCAAGGACATAGCTGGAGAGACTGGAAAG
genomic: CTAACCTGGACCTAAGCGCTGCAGATCTCATCAACAGAATATCTTTCCAGgtaacttgtt ... ggttttgtagGCGTCACAGGATCTGTCTTCACTCAAGGACATAGCTGGAGAGACTGGAAAG
EST: gi|37379430|gb|CF626459.1|CF626459
EST:     CTAACCTGGACCTAAGCGCTGCAGATCTCATCAACAGAATATCTTTCCAG                         GCGTCACAGGATCTGTCTTCACTCAAGGACATAGCTGGAGAGACTGGAAAG
genomic: CTAACCTGGACCTAAGCGCTGCAGATCTCATCAACAGAATATCTTTCCAGgtaacttgtt ... ggttttgtagGCGTCACAGGATCTGTCTTCACTCAAGGACATAGCTGGAGAGACTGGAAAG
EST: gi|78092043|gb|DV520417.1|DV520417
EST:     CTAACCTGGACCTAAGCGCTGCAGATCTCATCAACAGAATATCTTTCCAG                         GCGTCACAGGATCTGTCTTCACTCAAGGACATAGCTGGAGAGACTGGAAAG
genomic: CTAACCTGGACCTAAGCGCTGCAGATCTCATCAACAGAATATCTTTCCAGgtaacttgtt ... ggttttgtagGCGTCACAGGATCTGTCTTCACTCAAGGACATAGCTGGAGAGACTGGAAAG
EST: gi|110209090|gb|EC890987.1|EC890987
EST:     CTAACCTGGACCTAAGCGCTGCAGATCTCATCAACAGAATATCTTTCCAG                         GCGTCACAGGATCTGTCTTCACTCAAGGACATAGCTGGAGAGACTGGAAAG
genomic: CTAACCTGGACCTAAGCGCTGCAGATCTCATCAACAGAATATCTTTCCAGgtaacttgtt ... ggttttgtagGCGTCACAGGATCTGTCTTCACTCAAGGACATAGCTGGAGAGACTGGAAAG
EST: gi|88746794|gb|DY530935.1|DY530935
EST:     CTAACCTGGACCTAAGCGCTGCAGATCTCATCAACAGAATATCTTTCCAG                         GCGTCACAGGATCTGTCTTCACTCAAGGACATAGCTGGAGAGACTGGAAAG
genomic: CTAACCTGGACCTAAGCGCTGCAGATCTCATCAACAGAATATCTTTCCAGgtaacttgtt ... ggttttgtagGCGTCACAGGATCTGTCTTCACTCAAGGACATAGCTGGAGAGACTGGAAAG
EST: gi|76924552|gb|DV170001.1|DV170001
EST:     CTAACCTGGACCTAAGCGCTGCAGATCTCATCAACAGAATATCTTTCCAG                         GCGTCACAGGATCTGTCTTCACTCAAGGACATAGCTGGAGAGACTGGAAAG
genomic: CTAACCTGGACCTAAGCGCTGCAGATCTCATCAACAGAATATCTTTCCAGgtaacttgtt ... ggttttgtagGCGTCACAGGATCTGTCTTCACTCAAGGACATAGCTGGAGAGACTGGAAAG
EST: gi|149086706|gb|EE176245.2|EE176245
EST:     CTAACCTGGACCTAAGCGCTGCAGATCTCATCAACAGAATATCTTTCCAG                         GCGTCACAGGATCTGTCTTCACTCAAGGACATAGCTGGAGAGACTGGAAAG
genomic: CTAACCTGGACCTAAGCGCTGCAGATCTCATCAACAGAATATCTTTCCAGgtaacttgtt ... ggttttgtagGCGTCACAGGATCTGTCTTCACTCAAGGACATAGCTGGAGAGACTGGAAAG
EST: gi|60358412|gb|DN225385.1|DN225385
EST:     CTAACCTGGACCTAAGCGCTGCAGATCTCATCAACAGAATATCTTTCCAG                         GCGTCACAGGATCTGTCTTCACTCAAGGACATAGCTGGAGAGACTGGAAAG
genomic: CTAACCTGGACCTAAGCGCTGCAGATCTCATCAACAGAATATCTTTCCAGgtaacttgtt ... ggttttgtagGCGTCACAGGATCTGTCTTCACTCAAGGACATAGCTGGAGAGACTGGAAAG
EST: gi|6022125|gb|AW067053.1|AW067053
EST:     CTAACCTGGACCTAAGCGCTGCAGATCTCATCAACAGAATATCTTTCCAG                         GCGTCACAGGATCTGTCTTCACTCAAGGACATAGCTGGAGAGACTGGAAAG
genomic: CTAACCTGGACCTAAGCGCTGCAGATCTCATCAACAGAATATCTTTCCAGgtaacttgtt ... ggttttgtagGCGTCACAGGATCTGTCTTCACTCAAGGACATAGCTGGAGAGACTGGAAAG
EST: gi|109179344|gb|EC379938.1|EC379938
EST:     CTAACCTGGACCTAAGCGCTGCAGATCTCATCAACAGAATATCTTTCCAG                         GCGTCACAGGATCTGTCTTCACTCAAGGACATAGCTGGAGAGACTGGAAAG
genomic: CTAACCTGGACCTAAGCGCTGCAGATCTCATCAACAGAATATCTTTCCAGgtaacttgtt ... ggttttgtagGCGTCACAGGATCTGTCTTCACTCAAGGACATAGCTGGAGAGACTGGAAAG
EST: gi|37381689|gb|CF627745.1|CF627745
EST:     CTAACCTGGACCTAAGCGCTGCAGATCTCATCAACAGAATATCTTTCCAG                         GCGTCACAGGATCTGTCTTCACTCAAGGACATAGCTGGAGAGACTGGAAAG
genomic: CTAACCTGGACCTAAGCGCTGCAGATCTCATCAACAGAATATCTTTCCAGgtaacttgtt ... ggttttgtagGCGTCACAGGATCTGTCTTCACTCAAGGACATAGCTGGAGAGACTGGAAAG
EST: gi|60358232|gb|DN225205.1|DN225205
EST:     CTAACCTGGACCTAAGCGCTGCAGATCTCATCAACAGAATATCTTTCCAG                         GCGTCACAGGATCTGTCTTCACTCAAGGACATAGCTGGAGAGACTGGAAAG
genomic: CTAACCTGGACCTAAGCGCTGCAGATCTCATCAACAGAATATCTTTCCAGgtaacttgtt ... ggttttgtagGCGTCACAGGATCTGTCTTCACTCAAGGACATAGCTGGAGAGACTGGAAAG
EST: gi|74237116|gb|DT645030.1|DT645030
EST:     CTAACCTGGACCTAAGCGCTGCAGATCTCATCAACAGAATATCTTTCCAG                         GCGTCACAGGATCTGTCTTCACTCAAGGACATAGCTGGAGAGACTGGAAAG
genomic: CTAACCTGGACCTAAGCGCTGCAGATCTCATCAACAGAATATCTTTCCAGgtaacttgtt ... ggttttgtagGCGTCACAGGATCTGTCTTCACTCAAGGACATAGCTGGAGAGACTGGAAAG
EST: gi|89757145|gb|DY686866.1|DY686866
EST:     CTAACCTGGACCTAAGCGCTGCAGATCTCATCAACAGAATATCTTTCCAG                         GCGTCACAGGATCTGTCTTCACTCAAGGACATAGCTGGAGAGACTGGAAAG
genomic: CTAACCTGGACCTAAGCGCTGCAGATCTCATCAACAGAATATCTTTCCAGgtaacttgtt ... ggttttgtagGCGTCACAGGATCTGTCTTCACTCAAGGACATAGCTGGAGAGACTGGAAAG
EST: gi|60342316|gb|DN209289.1|DN209289
EST:     CTAACCTGGACCTAAGCGCTGCAGATCTCATCAACAGAATATCTTTCCAG                         GCGTCACAGGATCTGTCTTCACTCAAGGACATAGCTGGAGAGACTGGAAAG
genomic: CTAACCTGGACCTAAGCGCTGCAGATCTCATCAACAGAATATCTTTCCAGgtaacttgtt ... ggttttgtagGCGTCACAGGATCTGTCTTCACTCAAGGACATAGCTGGAGAGACTGGAAAG
EST: gi|60348664|gb|DN215637.1|DN215637
EST:     CTAACCTGGACCTAAGCGCTGCAGATCTCATCAACAGAATATCTTTCCAG                         GCGTCACAGGATCTGTCTTCACTCAAGGACATAGCTGGAGAGACTGGAAAG
genomic: CTAACCTGGACCTAAGCGCTGCAGATCTCATCAACAGAATATCTTTCCAGgtaacttgtt ... ggttttgtagGCGTCACAGGATCTGTCTTCACTCAAGGACATAGCTGGAGAGACTGGAAAG
EST: gi|148940300|gb|EC885085.2|EC885085
EST:     CTAACCTGGACCTAAGCGCTGCAGATCTCATCAACAGAATATCTTTCCAG                         GCGTCACAGGATCTGTCTTCACTCAAGGACATAGCTGGAGAGACTGGAAAG
genomic: CTAACCTGGACCTAAGCGCTGCAGATCTCATCAACAGAATATCTTTCCAGgtaacttgtt ... ggttttgtagGCGTCACAGGATCTGTCTTCACTCAAGGACATAGCTGGAGAGACTGGAAAG
EST: gi|78024255|gb|DV492642.1|DV492642
EST:     CTAACCTGGACCTAAGCGCTGCAGATCTCATCAACAGAATATCTTTCCAG                         GCGTCACAGGATCTGTCTTCACTCAAGGACATAGCTGGAGAGACTGGAAAG
genomic: CTAACCTGGACCTAAGCGCTGCAGATCTCATCAACAGAATATCTTTCCAGgtaacttgtt ... ggttttgtagGCGTCACAGGATCTGTCTTCACTCAAGGACATAGCTGGAGAGACTGGAAAG
EST: gi|60355340|gb|DN222313.1|DN222313
EST:     CTAACCTGGACCTAAGCGCTGCAGATCTCATCAACAGAATATCTTTCCAG                         GCGTCACAGGATCTGTCTTCACTCAAGGACATAGCTGGAGAGACTGGAAAG
genomic: CTAACCTGGACCTAAGCGCTGCAGATCTCATCAACAGAATATCTTTCCAGgtaacttgtt ... ggttttgtagGCGTCACAGGATCTGTCTTCACTCAAGGACATAGCTGGAGAGACTGGAAAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTCATCCATTTCAAGCTCTGATCTTTTTGGCCGTACCAATGTGGACGATTCTAACCTGGACCTAAGCGCTGCAGATCTCATCAACAGAATATCTTTCCAGgtaacttgttggcataacctgttgtttcttggaattttagcgtgtagcaccatagtttgcatacgttttaagccacaattgaactatgagttagcggaaacgtgctaaggaaaaaccaataccatgcagagacgtcgtgtgaaagttgcataaagtcaacagtctcatttcctgtcatggttttgtag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT