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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAATGGACCCCATAAACGAGAGGAAAATGTTTCAGCAGCTTGTCAGAGCTGCCAGCCAAATTAACACGCCGCAgttagtgacagtgcactcagcactttgtacctcttgcagatctgcaaacctgacatccgataacctcccctttcttttgcttgcag

Basic information

species Zea mays
transcript GRMZM2G440916_T02
intron # 27
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G440916_T01 (Zea mays), 5'ss of exon 27
lower sequence: LOC_Os05g51790.1 (Oryza sativa), 5'ss of exon 27
GAATGGACCCCATAAACGAGAGGAAAATGTTTCAGCAGCTTGTCAGAGCTGCCAGCCAAATTAACACGCCGCAgttagtgacagtgcactcagcactttgtacctcttgcagatctgcaaacctgacatccgataacctcccc-tttcttttgcttgcag---
||||||| ||||||||||||||||| ||||| ||||||||||| ||||| ||||| || ||||| || ||||| |||||||| | || |||| || | || | || | | |||| ||| || |||||| || ||
GAATGGATCCCATAAACGAGAGGAAGATGTTCCAGCAGCTTGTGAGAGCAGCCAGTCAGCCAAACACTCCACAgtttgtgacagtactcttagcatttcaggaggc------attttcaga--tagcatctaccaactcccatgtttcttaatctggctatag
















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|33097205|gb|CF057165.1|CF057165
EST:     AAAATGTTTCAGCAGCTTGTCAGAGCTGCCAGCCAAATTAACACGCCGCA                         GTGCTTCCTTCTGACGCCCAAGCTCCTACCTGATCTGGAGTACAGCGATGC
genomic: AAAATGTTTCAGCAGCTTGTCAGAGCTGCCAGCCAAATTAACACGCCGCAgttagtgaca ... ttgcttgcagGTGCTTCCTTCTGACGCCCAAGCTCCTACCTGATCTGGAGTACAGCGATGC
EST: gi|211323882|gb|FK953778.1|FK953778
EST:     AAAATGTTTCAGCAGCTTGTCAGAGCTGCCAGCCAAATTAACACGCCGCA                         GTGCTTCCTTCTGACGCCCAAGCTCCTACCTGATCTGGAGTACAGCGATGC
genomic: AAAATGTTTCAGCAGCTTGTCAGAGCTGCCAGCCAAATTAACACGCCGCAgttagtgaca ... ttgcttgcagGTGCTTCCTTCTGACGCCCAAGCTCCTACCTGATCTGGAGTACAGCGATGC
EST: gi|32930688|gb|CF035500.1|CF035500
EST:     AAAATGTTTCAGCAGCTTGTCAGAGCTGCCAGCCAAATTAACACGCCGCA                         GTGCTTCCTTCTGACGCCCAAGCTCCTACCTGATCTGGAGT
genomic: AAAATGTTTCAGCAGCTTGTCAGAGCTGCCAGCCAAATTAACACGCCGCAgttagtgaca ... ttgcttgcagGTGCTTCCTTCTGACGCCCAAGCTCCTACCTGATCTGGAGT
EST: gi|211323885|gb|FK953781.1|FK953781
EST:     AAAATGTTTCAGCAGCTTGTCAGAGCTGSCAGCCAAATTAACACGCCGCA                         GTGCTTCCTTCTGACGCCCAAGCTCCTACCTGATCTGGAGTACAGCGATGC
genomic: AAAATGTTTCAGCAGCTTGTCAGAGCTGCCAGCCAAATTAACACGCCGCAgttagtgaca ... ttgcttgcagGTGCTTCCTTCTGACGCCCAAGCTCCTACCTGATCTGGAGTACAGCGATGC
EST: gi|33092036|gb|CF052030.1|CF052030
EST:     AAAATGTTTCAGCAGCTTGTCAGAGCTGCCAGCCAAATTAACACGCCGCA                         GTGCTTCCTTCTGACGCCCAAGCTCCTACCTGATCTGGAGT
genomic: AAAATGTTTCAGCAGCTTGTCAGAGCTGCCAGCCAAATTAACACGCCGCAgttagtgaca ... ttgcttgcagGTGCTTCCTTCTGACGCCCAAGCTCCTACCTGATCTGGAGT
EST: gi|211323884|gb|FK953780.1|FK953780
EST:     AAAATGTTTCAGCAGCTTGTCAGAGCTGCCAGCCAAATTAACACGCCGCA                         GTGCTTCCTTCTGACGCCCA
genomic: AAAATGTTTCAGCAGCTTGTCAGAGCTGCCAGCCAAATTAACACGCCGCAgttagtgaca ... ttgcttgcagGTGCTTCCTTCTGACGCCCA
EST: gi|9732498|gb|BE511250.1|BE511250
EST:     CCAAATTAACACGCCGCA                         GTGCTTCCTTCTGACGCCCAAGCTCCTACCTGATCTGGAGTACAGCGATGC
genomic: CCAAATTAACACGCCGCAgttagtgaca ... ttgcttgcagGTGCTTCCTTCTGACGCCCAAGCTCCTACCTGATCTGGAGTACAGCGATGC
EST: gi|78075393|gb|DV503827.1|DV503827
EST:     AAAATGTTTCAGCAGCTTGTCAGAGCTGCCAGCCAAATTAACACGCCGCA                         GTGCTTCTTTTTGACGCCCAAGCTCCTACCTGATCTGGAGTACAGCGATGC
genomic: AAAATGTTTCAGCAGCTTGTCAGAGCTGCCAGCCAAATTAACACGCCGCAgttagtgaca ... ttgcttgcagGTGCTTCCTTCTGACGCCCAAGCTCCTACCTGATCTGGAGTACAGCGATGC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAATGGACCCCATAAACGAGAGGAAAATGTTTCAGCAGCTTGTCAGAGCTGCCAGCCAAATTAACACGCCGCAgttagtgacagtgcactcagcactttgtacctcttgcagatctgcaaacctgacatccgataacctcccctttcttttgcttgcag

- - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - AGCTGC