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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCGGCCATCTGAAGATAGAACTATTCCATTAAGTGTTATTGCTGAGCGGACTAAGCTTTCAATCAGTGACGTGGAATGTCTTCTTATGAAGAGCCTCTCGgtaacttgattaacattctttttagcacaagatattgttgtcatgaactcacttttcacttgtgctgttccttgtgggccatcatattttttatggaaac...

Basic information

species Zea mays
transcript GRMZM5G868757_T07
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G868757_T04 (Zea mays), 5'ss of exon 6
lower sequence: LOC_Os01g32800.1 (Oryza sativa), 5'ss of exon 5
TCGGCCATCTGAAGATAGAACTATTCCATTAAGTGTTATTGCTGAGCGGACTAAGCTTTCAATCAGTGACGTGGAATGTCTTCTTATGAAGAGCCTCTCGgtaacttgatta---acattctttttagcacaagatattgttgtcatgaactcacttttcacttgtgctgttccttgtgggccatcatattttttatggaaac-
 |||||||| ||||| |||||||| |||||||||||||| |||||||| ||||||||||| |||||||| ||||||| ||||||||||||||||||||||||||||  |||    || |||| | |  || |||||||| ||  |||   |       |   ||||  ||||     |        || ||     ||| |   
CCGGCCATCAGAAGACAGAACTATCCCATTAAGTGTTATAGCTGAGCGCACTAAGCTTTCTATCAGTGATGTGGAATATCTTCTTATGAAGAGCCTCTCGgtaactgcatttcctactttctatcttccataagatattatttgcattttcatggaaattcattgt--tgttatgcataaattg--attttaagcttgggagtt

upper sequence: GRMZM5G868757_T04 (Zea mays), 5'ss of exon 6
lower sequence: LOC_Os03g11570.1 (Oryza sativa), 5'ss of exon 5
TCGGCCATCTGAAGATAGAACTATTCCATTAAGTGTTATTGCTGAGCGGACTAAGCTTTCAATCAGTGACGTGGAATGTCTTCTTATGAAGAGCCTCTCGgtaacttgatta---acattctttttagcacaagatattgttgtcatgaactcacttttcacttgtgctgttccttg--tgggccat-catattttttatggaaac
 ||| | || ||||| |||||||| |||||||||||||| || ||||| ||||||||||| |||||||| ||||||| |||||||||||||||||||||||||| |  |||    ||||||  | |  || |||||||| ||  ||  |   || | |    ||      ||  | |  | | | || |||   |   ||      
CCGGGCGTCAGAAGACAGAACTATCCCATTAAGTGTTATAGCCGAGCGCACTAAGCTTTCTATCAGTGATGTGGAATATCTTCTTATGAAGAGCCTCTCGgtaattgcatttcttacattcgatctttcataagatattatttgcaatatgccaatatcatgttaattcattgttgggatagacaatgcatgaatgccat------
















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|148948406|gb|EC893923.2|EC893923
EST:     CTAAGCTTTCAATCAGTGACGTGGAATGTCTTCTTATGAAGAGCCTCTCG                         GTTCATCTTATTGAGGGAATAATTGATGAAGTGGACAGTACAGTTCACGTA
genomic: CTAAGCTTTCAATCAGTGACGTGGAATGTCTTCTTATGAAGAGCCTCTCGgtaacttgat ... tcaaatgcagGTTCATCTTATTGAGGGAATAATTGATGAAGTGGACAGTACAGTTCACGTA
EST: gi|211275924|gb|FL440062.1|FL440062
EST:     CTAAGCTTTCAATCAGTGACGTGGAATGTCTTCTTATGAAGAGCCTCTCG                         GTTCATCTTATTGAGGGAATAATTGATGAAGTGGACAGTACAGTTCACGTA
genomic: CTAAGCTTTCAATCAGTGACGTGGAATGTCTTCTTATGAAGAGCCTCTCGgtaacttgat ... tcaaatgcagGTTCATCTTATTGAGGGAATAATTGATGAAGTGGACAGTACAGTTCACGTA
EST: gi|6563772|gb|AW231304.1|AW231304
EST:     CTAAGCTTTCAATCAGTGACGTGGAATGTCTTCTTATGAAGAGCCTCTCG                         GTTCATCTTATTGAGGGAATAATTGATGAAGTGGACAGTACAGTTCACGTA
genomic: CTAAGCTTTCAATCAGTGACGTGGAATGTCTTCTTATGAAGAGCCTCTCGgtaacttgat ... tcaaatgcagGTTCATCTTATTGAGGGAATAATTGATGAAGTGGACAGTACAGTTCACGTA
EST: gi|60395185|gb|DN228054.1|DN228054
EST:     CTAAGCTTTCAATCAGTGACGTGGAATGTCTTCTTATGAAGAGCCTCTCG                         GTTCATCTTATTGAGGGAATAATTGATGAAGTGGACAGTACAGTTCACGTA
genomic: CTAAGCTTTCAATCAGTGACGTGGAATGTCTTCTTATGAAGAGCCTCTCGgtaacttgat ... tcaaatgcagGTTCATCTTATTGAGGGAATAATTGATGAAGTGGACAGTACAGTTCACGTA
EST: gi|149078128|gb|EE166877.2|EE166877
EST:     CTAAGCTTTCAATCAGTGACGTGGAATGTTTTCTTATGAAGAGCCTCTCG                         GTTCATCTTATTGAGGGAATAATTGATGAAGTGGACAGTACAGTTCACGTA
genomic: CTAAGCTTTCAATCAGTGACGTGGAATGTCTTCTTATGAAGAGCCTCTCGgtaacttgat ... tcaaatgcagGTTCATCTTATTGAGGGAATAATTGATGAAGTGGACAGTACAGTTCACGTA
EST: gi|194716906|gb|FK934065.1|FK934065
EST:     CTAAGCTTTCAATCAGTGACGTGGAATGTCTTCTTATGAAGAGCCTCTCG                         GTTCATCTTATTGAGGGAATAATTGATGAAGTGGACAGTAC
genomic: CTAAGCTTTCAATCAGTGACGTGGAATGTCTTCTTATGAAGAGCCTCTCGgtaacttgat ... tcaaatgcagGTTCATCTTATTGAGGGAATAATTGATGAAGTGGACAGTAC
EST: gi|37385820|gb|CF630071.1|CF630071
EST:     CTAAGCTTTCAATCAGTGACGTGGAATGTCTTCTTATGAAGAGCCTCTCG                         GTTCATCTTATTGAGGGAATAATTGATGAAGTGGACAGTACAGTTCACGTA
genomic: CTAAGCTTTCAATCAGTGACGTGGAATGTCTTCTTATGAAGAGCCTCTCGgtaacttgat ... tcaaatgcagGTTCATCTTATTGAGGGAATAATTGATGAAGTGGACAGTACAGTTCACGTA
EST: gi|211082970|gb|FL307146.1|FL307146
EST:     CTAAGCTTTCAATCAGTGACGTGAAATGTCTTCTTATGAAGAGCCTCTCG                         GTTCATCTTATTGAGGGAATAATTGATGAAGTGGACAGTACAGTTCACGTA
genomic: CTAAGCTTTCAATCAGTGACGTGGAATGTCTTCTTATGAAGAGCCTCTCGgtaacttgat ... tcaaatgcagGTTCATCTTATTGAGGGAATAATTGATGAAGTGGACAGTACAGTTCACGTA
EST: gi|28987392|gb|CB351612.1|CB351612
EST:     CTAAGCTTTCAATCAGTGACGTGGAATGTCTTCTTATGAAGAGCCTCTCG                         GTTCATCTTATTGAGGGAATAATTGATGAAGTGGACAGTACAGTTCACGTA
genomic: CTAAGCTTTCAATCAGTGACGTGGAATGTCTTCTTATGAAGAGCCTCTCGgtaacttgat ... tcaaatgcagGTTCATCTTATTGAGGGAATAATTGATGAAGTGGACAGTACAGTTCACGTA
EST: gi|211096437|gb|FL454798.1|FL454798
EST:     CTAAGCTTTCAATCAGTGACGTGGAATGTCTTCTTATGAAGAGCCTCTCG                         GTTCATCTTATTGAGGGAATAATTGATGAAGTGGACAGTACAGTTCACGTA
genomic: CTAAGCTTTCAATCAGTGACGTGGAATGTCTTCTTATGAAGAGCCTCTCGgtaacttgat ... tcaaatgcagGTTCATCTTATTGAGGGAATAATTGATGAAGTGGACAGTACAGTTCACGTA
EST: gi|5847513|gb|AW000592.1|AW000592
EST:     CTAAGCTTTCAATCAGTGACGTGGAATGTCTTCTTATGAAGAGCCTCTCG                         GTTCATCTTATTGAGGGAATAATTGATGAAGTGGACAGTACAGTTCACGTA
genomic: CTAAGCTTTCAATCAGTGACGTGGAATGTCTTCTTATGAAGAGCCTCTCGgtaacttgat ... tcaaatgcagGTTCATCTTATTGAGGGAATAATTGATGAAGTGGACAGTACAGTTCACGTA
EST: gi|6020410|gb|AW065338.1|AW065338
EST:     CTAAGCTTTCAATCAGTGACGTGGAATGTCTTCTTATGAAGAGCCTCTCG                         GTTCATCTTATTGAGGGAATAATTGATGAAGTGGACAGTACAGTTCACGTA
genomic: CTAAGCTTTCAATCAGTGACGTGGAATGTCTTCTTATGAAGAGCCTCTCGgtaacttgat ... tcaaatgcagGTTCATCTTATTGAGGGAATAATTGATGAAGTGGACAGTACAGTTCACGTA
EST: gi|148928048|gb|EC872430.2|EC872430
EST:     CTAAGCTTTCAATCAGTGACGTGGAATGTCTTCTTATGAAGAGCCTCTCG                         GTTCATCTTATTGAGGGAATAATTGATGAAGTGGACAGTACAGTTCACGTA
genomic: CTAAGCTTTCAATCAGTGACGTGGAATGTCTTCTTATGAAGAGCCTCTCGgtaacttgat ... tcaaatgcagGTTCATCTTATTGAGGGAATAATTGATGAAGTGGACAGTACAGTTCACGTA
EST: gi|32862654|gb|CF002336.1|CF002336
EST:     CTAAGCTTTCAATCAGTGACGTGGAATGTCTTCTTATGAAGAGCCTCTCG                         GTTCATCTTATTGAGGGAATAATTGATGAAGTGGACAGTACAGTTCACGTA
genomic: CTAAGCTTTCAATCAGTGACGTGGAATGTCTTCTTATGAAGAGCCTCTCGgtaacttgat ... tcaaatgcagGTTCATCTTATTGAGGGAATAATTGATGAAGTGGACAGTACAGTTCACGTA
EST: gi|24765659|gb|CA400818.1|CA400818
EST:     CTAACCTTTCAATCAGTGACGTGGAATGTCTTCTTATGAAGAGCCTCTCG                         GTTCATCTTATTGAGGGAATAATTGATGAAGTGGACAGTACAGTTCACGTA
genomic: CTAAGCTTTCAATCAGTGACGTGGAATGTCTTCTTATGAAGAGCCTCTCGgtaacttgat ... tcaaatgcagGTTCATCTTATTGAGGGAATAATTGATGAAGTGGACAGTACAGTTCACGTA
EST: gi|149081819|gb|EE170978.2|EE170978
EST:     CTAAGCTTTCAATCAGTGACGTGGAATGTCTTCTTATGAAGAGCCTCTCG                         GTTCATCTTATTGAGGGAATAATTGATGAAGTGGACAGTACAGTTCACGTA
genomic: CTAAGCTTTCAATCAGTGACGTGGAATGTCTTCTTATGAAGAGCCTCTCGgtaacttgat ... tcaaatgcagGTTCATCTTATTGAGGGAATAATTGATGAAGTGGACAGTACAGTTCACGTA
EST: gi|211013700|gb|FL252294.1|FL252294
EST:     CTAAGCTTTCAATCAGTGACGTGGAATGTCTTCTTATGAAGAGCCTCTCG                         GTTCATCTTATTGAGGGAATAATTGATGAAGTGGACAGTACAGTTCACGTA
genomic: CTAAGCTTTCAATCAGTGACGTGGAATGTCTTCTTATGAAGAGCCTCTCGgtaacttgat ... tcaaatgcagGTTCATCTTATTGAGGGAATAATTGATGAAGTGGACAGTACAGTTCACGTA
EST: gi|148982850|gb|EE028700.2|EE028700
EST:     CTAAGCTTTCAATCAGTGACGTGGAATGTCTTCTTATGAAGAGCCTCTCG                         GTTCATCTTATTGAGGGAATAATTGATGAAGTGGACAGTACAGTTCACGTA
genomic: CTAAGCTTTCAATCAGTGACGTGGAATGTCTTCTTATGAAGAGCCTCTCGgtaacttgat ... tcaaatgcagGTTCATCTTATTGAGGGAATAATTGATGAAGTGGACAGTACAGTTCACGTA
EST: gi|211117255|gb|FL447738.1|FL447738
EST:     CTAAGCTTTCAATCAGTGACGTGGAATGTCTTCTTATGAAGAGCCTCTCG                         GTTCATCTTATTGAGGGAATAATTGATGAAGTGGACAGTACAGTTCACGTA
genomic: CTAAGCTTTCAATCAGTGACGTGGAATGTCTTCTTATGAAGAGCCTCTCGgtaacttgat ... tcaaatgcagGTTCATCTTATTGAGGGAATAATTGATGAAGTGGACAGTACAGTTCACGTA
EST: gi|211013699|gb|FL252293.1|FL252293
EST:     CTAAGCTTTCAATCAGTGACGTGGAATGTCTTCTTATGAAGAGCCTCTCG                         GTTCATCTTATTGAGGGAATAATTGATGAAGTGGACAGTACAGTTCACGTA
genomic: CTAAGCTTTCAATCAGTGACGTGGAATGTCTTCTTATGAAGAGCCTCTCGgtaacttgat ... tcaaatgcagGTTCATCTTATTGAGGGAATAATTGATGAAGTGGACAGTACAGTTCACGTA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCGGCCATCTGAAGATAGAACTATTCCATTAAGTGTTATTGCTGAGCGGACTAAGCTTTCAATCAGTGACGTGGAATGTCTTCTTATGAAGAGCCTCTCGgtaacttgattaacattctttttagcacaagatattgttgtcatgaactcacttttcacttgtgctgttccttgtgggccatcatattttttatggaaac

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA