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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CACAACTGCAGCAGTCATGACAATAGTCCCAAAACTTGGCATGAATGATGTTTATCTGGCTTACCTTCCATTGGCTCATGTCTTTGAACTAGCAGGAGAGgtgatgtatattttaactcataaacatgtagttttacaagagttgtcgctatctttaatgatatgatgttgacatgttgtcaatccag

Basic information

species Zea mays
transcript GRMZM2G079236_T02
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G079236_T01 (Zea mays), 5'ss of exon 6
lower sequence: LOC_Os05g25310.2 (Oryza sativa), 5'ss of exon 5
CACAACTGCAGCAGTCATGACAATAGTCCCAAAACTTGGCATGAATGATGTTTATCTGGCTTACCTTCCATTGGCTCATGTCTTTGAACTAGCAGGAGAGgtgatgtatattttaactcataaacatgtagttttacaagagttgtcgctatctttaatgatatgatgttgacatgttgtcaatccag
|||||||||||| |||||||||||  | |||||||||||||     |||||||||||||| ||||||||  |||||||||||||||||||||||| ||||||||  | | ||  || | | | | |||   || |  ||||  |||   ||| | || ||| ||  |||||   | ||||    ||||
CACAACTGCAGCTGTCATGACAATCATACCAAAACTTGGCACAGGGGATGTTTATCTGGCATACCTTCCGCTGGCTCATGTCTTTGAACTAGCAGCAGAGgtgacatcttttgcaattgagagagatgccattat-taagaactgtgaatatttcta-tgacatattgttg---ttttgtttggccag
















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|211254876|gb|FL311210.1|FL311210
EST:     TTTATCTGGCTTACCTTCCATTGGCTCATGTCTTTGAACTAGCAGGAGAG                         ACTGTCATGCTAGCTTCTGGTACTGCCATTGGATATGGTTCAACATTGACT
genomic: TTTATCTGGCTTACCTTCCATTGGCTCATGTCTTTGAACTAGCAGGAGAGgtgatgtata ... gtcaatccagACTGTCATGCTAGCTTCTGGTACTGCCATTGGATATGGTTCAACATTGACT
EST: gi|211295641|gb|FL337574.1|FL337574
EST:     TTTATCTGGCTTACCTTCCATTGGCTCATGTCTTTGAACTAGCAGGAGAG                         ACTGTCATGCTAGCTTCTGGTACTGCCATTGGATATGGTTCAACATTGACT
genomic: TTTATCTGGCTTACCTTCCATTGGCTCATGTCTTTGAACTAGCAGGAGAGgtgatgtata ... gtcaatccagACTGTCATGCTAGCTTCTGGTACTGCCATTGGATATGGTTCAACATTGACT
EST: gi|211103068|gb|FL309408.1|FL309408
EST:     TTTATCTGGCTTACCTTCCATTGGCTCATGTCTTTGAACTAGCAGGAGAG                         ACTGTCATGCTAGCTTCTGGTACTGCCATTGGATATGGTTCAACATTGACT
genomic: TTTATCTGGCTTACCTTCCATTGGCTCATGTCTTTGAACTAGCAGGAGAGgtgatgtata ... gtcaatccagACTGTCATGCTAGCTTCTGGTACTGCCATTGGATATGGTTCAACATTGACT
EST: gi|211440066|gb|FL316513.1|FL316513
EST:     TTTATCTGGCTTACCTTCCATTGGCTCATGNCTTTGAACTAGCAGGAGAG                         ACTGTCATGCTAGCTTCTGGTACTGCCATTGGATATGGTTCAACATTGACT
genomic: TTTATCTGGCTTACCTTCCATTGGCTCATGTCTTTGAACTAGCAGGAGAGgtgatgtata ... gtcaatccagACTGTCATGCTAGCTTCTGGTACTGCCATTGGATATGGTTCAACATTGACT
EST: gi|211485905|gb|FL317496.1|FL317496
EST:     TTTATCTGGCTTACCTTCCATTGGCTCATNTCTTTGAACTAGCAGGAGAG                         ACTGTCATGCTAGCTTCTGGTACTGCCATTGGATATGGTTCAACATTGACT
genomic: TTTATCTGGCTTACCTTCCATTGGCTCATGTCTTTGAACTAGCAGGAGAGgtgatgtata ... gtcaatccagACTGTCATGCTAGCTTCTGGTACTGCCATTGGATATGGTTCAACATTGACT
EST: gi|32846288|gb|CD985969.1|CD985969
EST:     TTTATCTGGCTTACCTTCCATTGGCTCATGTCTTTGAACTAGCAGGAGAG                         ACTGTCATGCTAGCTTCTGGT
genomic: TTTATCTGGCTTACCTTCCATTGGCTCATGTCTTTGAACTAGCAGGAGAGgtgatgtata ... gtcaatccagACTGTCATGCTAGCTTCTGGT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CACAACTGCAGCAGTCATGACAATAGTCCCAAAACTTGGCATGAATGATGTTTATCTGGCTTACCTTCCATTGGCTCATGTCTTTGAACTAGCAGGAGAGgtgatgtatattttaactcataaacatgtagttttacaagagttgtcgctatctttaatgatatgatgttgacatgttgtcaatccag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA