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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATATGTCTGTTGCGCTGGCTACATGCCATGCAGTGGAAAGTGTGGCGAGAGCCGGTGCCCAGAGTTCTGTCTTGCAACTGAGgtacaaggacaaggctcactcaagtttcattttaccttggtgtctatttgcactatacttagtatatggttatgtgcttgaattccatgtatagcatgtc...

Basic information

species Zea mays
transcript GRMZM2G060564_T04
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G060564_T02 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os03g03180.1 (Oryza sativa), 5'ss of exon 4
ATATGTCTGTTGCGCTGGCTACATGCCATGCAGTGGAAAGTGTGGCGAGAGCCGGTGCCCAGAGTTCTGTCTTGCAACTGAGgtacaaggacaaggctcactcaagtttcattttaccttggtgtctatttgcactatactta---gtatatggttatgtgcttgaattc-catgtatagcatgtc
||||||||| || ||||| ||||||||||||||||| |||||||| || ||||| |||||||||||||||||||| |||||||||||||  | |  | |  |   | |  ||      ||| || ||  ||   ||  | |||   | |    || |  ||    | ||| |||||     |||  
ATATGTCTGCTGTGCTGGGTACATGCCATGCAGTGGGAAGTGTGGTGAAAGCCGATGCCCAGAGTTCTGTCTTGCTACTGAGgtacaagatccattcccttttttgctg-ataaccttttgatgactgattaggctgaatttataggcagcatgtcacatgtaacagttctcatgtg-gctatg--
















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|71768983|gb|DR966920.1|DR966920
EST:     GTGGAAAGTGTGGCGAGAGCCGGTGCCCAGAGTTCTGTCTTGCAACTGAG                         GTGTTCCTTTGCTTTGGCAATTCAGTTGCATCAACCCGCTTCTTGCTGCAA
genomic: GTGGAAAGTGTGGCGAGAGCCGGTGCCCAGAGTTCTGTCTTGCAACTGAGgtacaaggac ... ttcttttcagGTGTTCCTTTGCTTTGGCAATTCAGTTGCATCAACCCGCTTCTTGCTGCAA
EST: gi|211520834|gb|FL034041.1|FL034041
EST:     GTGGAAAGTGTGGCGAGAGC-GGTGCCCAGAGTTCTGTCTTGCAACTGAG                         GTGTTCCTTTGCTTTGGCAATTCAGTTGCATCAACCCGCTTCTTGC
genomic: GTGGAAAGTGTGGCGAGAGCCGGTGCCCAGAGTTCTGTCTTGCAACTGAGgtacaaggac ... ttcttttcagGTGTTCCTTTGCTTTGGCAATTCAGTTGCATCAACCCGCTTCTTGC
EST: gi|211397639|gb|FL034039.1|FL034039
EST:     GTGGAAAGTGTGGCGAGASC-GGTGCCCAGAGTTCTGTCTTGCAACTGAG                         GTGTTCCTTTGCTTTGGCCAATTC
genomic: GTGGAAAGTGTGGCGAGAGCCGGTGCCCAGAGTTCTGTCTTGCAACTGAGgtacaaggac ... ttcttttcagGTGTTCCTTTGCTTTGGC-AATTC
EST: gi|211520835|gb|FL034042.1|FL034042
EST:     GTGGAAAGTGTGGCGAGAGC-GGTGCCCAGAGTTCTGTCTTGCAACTGAG                         GTGTTCCTTTGCTTTGGCAATTCAGTTGCATCAACCCGCTTCTTGCTGCAA
genomic: GTGGAAAGTGTGGCGAGAGCCGGTGCCCAGAGTTCTGTCTTGCAACTGAGgtacaaggac ... ttcttttcagGTGTTCCTTTGCTTTGGCAATTCAGTTGCATCAACCCGCTTCTTGCTGCAA
EST: gi|78090964|gb|DV519338.1|DV519338
EST:     GTGCAAAGTGTGGCCAGAGCCGGTGCCCAGAGTTCTGTCTTGCAACTGAG                         GTGTTCCTTTGCTTTGGCAATTCAGTTGCCTCAACCCGCTTCTTGCTGCAA
genomic: GTGGAAAGTGTGGCGAGAGCCGGTGCCCAGAGTTCTGTCTTGCAACTGAGgtacaaggac ... ttcttttcagGTGTTCCTTTGCTTTGGCAATTCAGTTGCATCAACCCGCTTCTTGCTGCAA
EST: gi|211520839|gb|FL034046.1|FL034046
EST:     GTGGAAAGTGTGGCGAGAGC-GGTGCCCAGAGTTCTGTCTTGCAACTGAG                         GTGTTCCTTTGCTTTGGCAATTCAGTTGCATCAACCCGCTTCTTGCTGCAA
genomic: GTGGAAAGTGTGGCGAGAGCCGGTGCCCAGAGTTCTGTCTTGCAACTGAGgtacaaggac ... ttcttttcagGTGTTCCTTTGCTTTGGCAATTCAGTTGCATCAACCCGCTTCTTGCTGCAA
EST: gi|211520837|gb|FL034044.1|FL034044
EST:     GTGGAAAGTGTGGCGAGAGC-GGTGCCCAGAGTTCTGTCTTGCAACTGAG                         GTGTTCCTTTGCTTTGGCAATTTCAGTTGCATCAACCCGCTTCTTGCTGCA
genomic: GTGGAAAGTGTGGCGAGAGCCGGTGCCCAGAGTTCTGTCTTGCAACTGAGgtacaaggac ... ttcttttcagGTGTTCCTTTGCTTTGGCAATT-CAGTTGCATCAACCCGCTTCTTGCTGCA
EST: gi|211520836|gb|FL034043.1|FL034043
EST:     GTGGAAAGTGTGGCGAGAGCCGGTGCCCAGAGTTCTGTCTTGCAACTGAG                         GTGTTCCTTTGCTTTGGCAATTCAGTTGCATCAACCCGCTTCTTGCTGCAA
genomic: GTGGAAAGTGTGGCGAGAGCCGGTGCCCAGAGTTCTGTCTTGCAACTGAGgtacaaggac ... ttcttttcagGTGTTCCTTTGCTTTGGCAATTCAGTTGCATCAACCCGCTTCTTGCTGCAA
EST: gi|211520838|gb|FL034045.1|FL034045
EST:     GTGGAAAGTGTGGCGAGAGCCGGTGCCCAGAGTTCTGTCTTGCAACTGAG                         GTGTTCCTTTGCTTTGGCAATTCAGTTGCATCAACCCGCTTCTTGCTGCAA
genomic: GTGGAAAGTGTGGCGAGAGCCGGTGCCCAGAGTTCTGTCTTGCAACTGAGgtacaaggac ... ttcttttcagGTGTTCCTTTGCTTTGGCAATTCAGTTGCATCAACCCGCTTCTTGCTGCAA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATATGTCTGTTGCGCTGGCTACATGCCATGCAGTGGAAAGTGTGGCGAGAGCCGGTGCCCAGAGTTCTGTCTTGCAACTGAGgtacaaggacaaggctcactcaagtttcattttaccttggtgtctatttgcactatacttagtatatggttatgtgcttgaattccatgtatagcatgtc

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