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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGAGGTGGGAGGTCGTCGGGCAGAGAAACCGTTGGAAGGGTGGCTGCAGGGGCCCTCGCCAAGAAAATTCTTAAGCTCAAATGTGGATTAGAGgtgcggttctattctatcggtaatcccttgccctacatgttagccatggtagttattggccttggccaatgtgtaacagaagagcaccaccatgtacttgcag

Basic information

species Zea mays
transcript GRMZM2G036861_T01
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G036861_T01 (Zea mays), 5'ss of exon 6
lower sequence: LOC_Os03g14990.1 (Oryza sativa), 5'ss of exon 6
GGAGGTGGGAGGTCGTCGGGCAGAGAAACCGTTGGAAGGGTGGCTGCAGGGGCCCTCGCCAAGAAAATTCTTAAGCTCAAATGTGGATTAGAGgtgcggttctattctatcggtaatcccttgccctacatgttagccatggtagttattggccttggccaatgtgtaacagaagagcaccaccatgtacttgcag-------
|||||||| || || || |  ||||| ||| ||||||||||||||||||| || || || |||||||||||||||||||||| |||| |||||||| | | ||| |     || || |  || | ||  |   |   || | |   |||    | | || | ||    |||      |    ||||| ||     |       
GGAGGTGGAAGATCATCAGCAAGAGAGACCATTGGAAGGGTGGCTGCAGGAGCTCTTGCAAAGAAAATTCTTAAGCTCAAATCTGGAGTAGAGgtgtgatcctactt----ggcaaccttttactcttaac--tgatcaagatttgtatcaagcatcgcaattg----acatgtttacttatccatgaacaattggacgctga
















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|148950436|gb|EC896004.2|EC896004
EST:     CTGCAGGGGCCCTCGCCAAGAAAATTCTTAAGCTCAAATGTGGATTAGAG                         ATCTTGTCGTTTGTTTCCAAAGTGCATTANGTTGTGCTCCCAGAAGACGCG
genomic: CTGCAGGGGCCCTCGCCAAGAAAATTCTTAAGCTCAAATGTGGATTAGAGgtgcggttct ... gtacttgcagATCTTGTCGTTTGTTTCCAAAGTGCATCAGGTTGTGCTCCCAGAAGACGCG
EST: gi|149096924|gb|EE182722.2|EE182722
EST:     CTGCAGGGGCCCTCGCCAAGAAAATTCTTAAGCTCAAATGTGGATTAGAG                         ATCTTGTCGTTTGTTTCCAAAGTGCATCAGGTTGTGCTCCCAGAAGACGCG
genomic: CTGCAGGGGCCCTCGCCAAGAAAATTCTTAAGCTCAAATGTGGATTAGAGgtgcggttct ... gtacttgcagATCTTGTCGTTTGTTTCCAAAGTGCATCAGGTTGTGCTCCCAGAAGACGCG
EST: gi|149088025|gb|EE177228.2|EE177228
EST:     CTGCAGGGGCCCTCGCCAAGAAAATTCTTAAGCTCAAATGTGGATTAGAG                         ATCTTGTCGTTTGTTTTCAAAGTGCATCAGGTTGTGCTCCCAGAAGACGCG
genomic: CTGCAGGGGCCCTCGCCAAGAAAATTCTTAAGCTCAAATGTGGATTAGAGgtgcggttct ... gtacttgcagATCTTGTCGTTTGTTTCCAAAGTGCATCAGGTTGTGCTCCCAGAAGACGCG
EST: gi|149089246|gb|EE178450.2|EE178450
EST:     CTGCAGGGGCCCTCGCCAAGAAAATTCTTAAGCTCAAATGTGGATTAGAG                         ATCTTGTCGTTTGTTTCCAAAGTGCATCAGGTTGTGCTCCCAGAAGACGCG
genomic: CTGCAGGGGCCCTCGCCAAGAAAATTCTTAAGCTCAAATGTGGATTAGAGgtgcggttct ... gtacttgcagATCTTGTCGTTTGTTTCCAAAGTGCATCAGGTTGTGCTCCCAGAAGACGCG
EST: gi|149106625|gb|EE188518.2|EE188518
EST:     CTGCAGGGGCCCTCGCCAAGAAAATTCTTAAGCTCAAATGTGGATTAGAG                         ATCTTGTCGTTTGTTTCCAAAGTGCATCAGGTTGTGCTCCCAGAAGACGCG
genomic: CTGCAGGGGCCCTCGCCAAGAAAATTCTTAAGCTCAAATGTGGATTAGAGgtgcggttct ... gtacttgcagATCTTGTCGTTTGTTTCCAAAGTGCATCAGGTTGTGCTCCCAGAAGACGCG
EST: gi|148951094|gb|EC896759.2|EC896759
EST:     CTGCAGGGGCCCTCGCCAAGAAAATTCTTAAGCTCAAATGTGGATTAGAG                         ATCTTGTCGTTTGTTTCCAAAGTGCATCAGGTTGTGCTCCCAGAAGACGCG
genomic: CTGCAGGGGCCCTCGCCAAGAAAATTCTTAAGCTCAAATGTGGATTAGAGgtgcggttct ... gtacttgcagATCTTGTCGTTTGTTTCCAAAGTGCATCAGGTTGTGCTCCCAGAAGACGCG
EST: gi|211106358|gb|FL258167.1|FL258167
EST:     TGCAGGGGCCCTCGCCAAAGAAA-TTCTTAAGCTCAAATGTGGAT-AGAG                         ATCTTGTCGTTTGTTTCCAAAGGGCATCAAGTTTGGGCTCCCA
genomic: TGCAGGGGCCCTCGCCAA-GAAAATTCTTAAGCTCAAATGTGGATTAGAGgtgcggttct ... gtacttgcagATCTTGTCGTTTGTTTCCAAAGTGCATCAGGTT-GTGCTCCCA
EST: gi|76281790|gb|DV021358.1|DV021358
EST:     CTGCAGGGGCCCTCGCCAAGAAAATTCTTAAGCTCAAATGGGGATTAGAG                         ATCCTGTCGTTTGTTTCCAA-GTGCAT
genomic: CTGCAGGGGCCCTCGCCAAGAAAATTCTTAAGCTCAAATGTGGATTAGAGgtgcggttct ... gtacttgcagATCTTGTCGTTTGTTTCCAAAGTGCAT
EST: gi|149067437|gb|EE287007.2|EE287007
EST:     CTGCAGGGGCCCTCGCCAAGAAAATTCTTAAGCTCAAATGTGGATTAGAG                         ATCTTGTCGTTTGTTTCCAAAGTGCATCAGGTTGTGCTCCCAGAAGACGCG
genomic: CTGCAGGGGCCCTCGCCAAGAAAATTCTTAAGCTCAAATGTGGATTAGAGgtgcggttct ... gtacttgcagATCTTGTCGTTTGTTTCCAAAGTGCATCAGGTTGTGCTCCCAGAAGACGCG
EST: gi|149098825|gb|EE184838.2|EE184838
EST:     CTGCAGGGGCCCTCGCCAAGAAAATTCTTAAGCTCAAATGTGGATTAGAG                         ATCTTGTCGTTTGTTTCCAAAGTGCATCAGGTTGTGCTCCCAGAAGACGCG
genomic: CTGCAGGGGCCCTCGCCAAGAAAATTCTTAAGCTCAAATGTGGATTAGAGgtgcggttct ... gtacttgcagATCTTGTCGTTTGTTTCCAAAGTGCATCAGGTTGTGCTCCCAGAAGACGCG
EST: gi|149071022|gb|EE159425.2|EE159425
EST:     CTGCAGGGGCCCTCGCCAAGAAAATTCTTAAGCTCAAATGTGGATTAGAG                         ATCTTGTCGTTTGTTTCCAAAGTGCATCAGGTTGTGCTCCCAGAAGACGCG
genomic: CTGCAGGGGCCCTCGCCAAGAAAATTCTTAAGCTCAAATGTGGATTAGAGgtgcggttct ... gtacttgcagATCTTGTCGTTTGTTTCCAAAGTGCATCAGGTTGTGCTCCCAGAAGACGCG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGAGGTGGGAGGTCGTCGGGCAGAGAAACCGTTGGAAGGGTGGCTGCAGGGGCCCTCGCCAAGAAAATTCTTAAGCTCAAATGTGGATTAGAGgtgcggttctattctatcggtaatcccttgccctacatgttagccatggtagttattggccttggccaatgtgtaacagaagagcaccaccatgtacttgcag

- - - - - - - - - - - - - - - - - - - - -  CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA