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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGCAGCCGCAGATGTTGGAATAGCCATGCGAACTCATTCAAAAGAGAACGCTGCCTCTGATGCAGCTTCAGTTGTTCTACTAGGCAACAGACTTTCTCAGgtaaggttctttcctgtaatgtttctttctctgagtaactcaactcaagtgccattaacggggatcaaacaatctcctgtgcag

Basic information

species Zea mays
transcript GRMZM5G855347_T03
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G855347_T03 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os03g08070.1 (Oryza sativa), 5'ss of exon 14
AGCAGCCGCAGATGTTGGAATAGCCATGCGAACTCATTCAAAAGAGAACGCTGCCTCTGATGCAGCTTCAGTTGTTCTACTAGGCAACAGACTTTCTCAGgtaaggttctttcctgtaatgtttctttctctgagtaactcaactcaagtgc-cattaacggggatcaaacaatctcctgtgcag
|||||| || ||||| ||| |||| ||||||||  | ||||||||||  ||||||||||| || ||||||||||||||| |||| |||||||||||||||||| | |||| | || || || |  | |  |||  ||  |||| |    | |    |||     |  || ||  || | |   ||
AGCAGCTGCTGATGTGGGAGTAGCTATGCGAACAAACTCAAAAGAGAGTGCTGCCTCTGACGCGGCTTCAGTTGTTCTATTAGGAAACAGACTTTCTCAGgtaggattctgttctcta-tgatattgtaactgcatagttcaagtggcattcgtgctaataaacaagaaccaccctacggcttag
















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|60353203|gb|DN220176.1|DN220176
EST:     CTGCCTCTGATGCAGCTTCAGTTGTTCTACTAGGCAACAGACTTTCTCAG                         GTGGTAGATGCGCTATCCCTGTCGAAGGCAACGATGGCAAAAGTTCACCAA
genomic: CTGCCTCTGATGCAGCTTCAGTTGTTCTACTAGGCAACAGACTTTCTCAGgtaaggttct ... tcctgtgcagGTGGTAGATGCGCTATCCCTGTCGAAGGCAACGATGGCAAAAGTTCACCAA
EST: gi|32835068|gb|CD974746.1|CD974746
EST:     CTGCCTCTGATGCAGCTTCAGTTGTTCTACTAGGCAACAGACTTTCTCAG                         GTGGTAGATGCGCTATCCCTGTCGAAGGCAACGATGGCAAAAGTTCACCAA
genomic: CTGCCTCTGATGCAGCTTCAGTTGTTCTACTAGGCAACAGACTTTCTCAGgtaaggttct ... tcctgtgcagGTGGTAGATGCGCTATCCCTGTCGAAGGCAACGATGGCAAAAGTTCACCAA
EST: gi|211367137|gb|FL432362.1|FL432362
EST:     TGCAGCTTCAGTTGTTCTACTAGGCAACAGACTTTCTCAG                         GTGGGTAGATGCGCTATCCCTGTCGAAGGCAACGATGGCAAAAGTTCACCA
genomic: TGCAGCTTCAGTTGTTCTACTAGGCAACAGACTTTCTCAGgtaaggttct ... tcctgtgcagGT-GGTAGATGCGCTATCCCTGTCGAAGGCAACGATGGCAAAAGTTCACCA
EST: gi|5525756|gb|AI861649.1|AI861649
EST:     CTG-CTCTGATGCAGCTTCAGTTGTTCTNCTAGGCANCAGNCTTTCTCAG                         GTGGTAGATGCGCTATCCCTGTCGAAGGCAACGATGGCAAAAGTTCNCCAA
genomic: CTGCCTCTGATGCAGCTTCAGTTGTTCTACTAGGCAACAGACTTTCTCAGgtaaggttct ... tcctgtgcagGTGGTAGATGCGCTATCCCTGTCGAAGGCAACGATGGCAAAAGTTCACCAA
EST: gi|5847391|gb|AW000470.1|AW000470
EST:     CTGCCTCTGATGCAGCTTCAGTTGTTCTACTAGGCAACAGACTTTCTCAG                         GTGGTAGATGCGCTATCCCTGTCGAAGGCAACGATGGCAAA
genomic: CTGCCTCTGATGCAGCTTCAGTTGTTCTACTAGGCAACAGACTTTCTCAGgtaaggttct ... tcctgtgcagGTGGTAGATGCGCTATCCCTGTCGAAGGCAACGATGGCAAA
EST: gi|60358034|gb|DN225007.1|DN225007
EST:     CTGCCTCTGATGCAGCTTCAGTTGTTCTACTAGGCAACAGACTTTCTCAG                         GTGGTAGATGCGCTATCCCTGTCGAAGGCAACGATGGCAAAAGTTCACCAA
genomic: CTGCCTCTGATGCAGCTTCAGTTGTTCTACTAGGCAACAGACTTTCTCAGgtaaggttct ... tcctgtgcagGTGGTAGATGCGCTATCCCTGTCGAAGGCAACGATGGCAAAAGTTCACCAA
EST: gi|32832471|gb|CD972149.1|CD972149
EST:     CTGCCTCTGATGCAGCTTCAGTTGTTCTACTAGGCAACAGACTTTCTCAG                         GTGGTAGATGCGCTATCCCTGTCGAAGGCAACGATGGCAAAAGTTCACCAA
genomic: CTGCCTCTGATGCAGCTTCAGTTGTTCTACTAGGCAACAGACTTTCTCAGgtaaggttct ... tcctgtgcagGTGGTAGATGCGCTATCCCTGTCGAAGGCAACGATGGCAAAAGTTCACCAA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGCAGCCGCAGATGTTGGAATAGCCATGCGAACTCATTCAAAAGAGAACGCTGCCTCTGATGCAGCTTCAGTTGTTCTACTAGGCAACAGACTTTCTCAGgtaaggttctttcctgtaatgtttctttctctgagtaactcaactcaagtgccattaacggggatcaaacaatctcctgtgcag

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