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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgcattgttttgagagagtcttataccattctagcgaactgttgtttctgaatgcttttgacgttgctcgccagCCTGCTCATGAAAAGATTGGAGTTGTCGATTCGCAGTGGATCGTTCACCAAGTGGTTCCTTCTCTGGGGAACCAG

Basic information

species Zea mays
transcript GRMZM5G846339_T02
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G846339_T01 (Zea mays), 3'ss of exon 12
lower sequence: LOC_Os05g01760.1 (Oryza sativa), 3'ss of exon 12
gtatgcattgttttgagagagtc---ttataccattctagcgaactgttgtttctga-atgcttttgacgt------tgctcgccagCCTGCTCATGAAAAGATTGGAGTTGTCGATTCGCAGTGGATCGTTCACCAAGTGGTTCCTTCTCTGGGGAACCAG
||||   ||   ||  |   ||    ||  |||   || |   |   |  ||    | |||||    |  |      |||    ||||||||||| ||||||||||| ||||| ||||| |||||||| ||||||||||||||||| ||||| |||||||||
gtataggttaccttttggctgttaaatttcaccggcctggtagaacttcattatgaatatgctcaccaaatgctttgtgcatttcagCCTGCTCACGAAAAGATTGGGGTTGTTGATTCACAGTGGATTGTTCACCAAGTGGTTCCATCTCTCGGGAACCAG

upper sequence: GRMZM5G846339_T01 (Zea mays), 3'ss of exon 12
lower sequence: AT2G28310.3 (Arabidopsis thaliana), 3'ss of exon 12
---------gtatgcattgttttgagagagtcttataccattctagcgaactg-ttgtttctgaatgcttttg-acgttgctcgc-cagCCTGCTCATGAAAAGATTGGAGTTGTCGATTCGCAGTGGATCGTTCACCAAGTGGTTCCTTCTCTGGGGAACCAG-------------------------
          | |||       |     |   | ||| ||   ||      ||  || |  ||||   || ||    |||||    |||||||||||||| |||||||| ||||| |||||||| |||||  | ||  ||||| | ||||| || || |  ||                          
gtaagttgtttttgccccccccttgcttaccttaataacacaatattctcttgactgatgatgaaaatttgtgtgttttgcttttgcagCCTGCTCATGAGAAGATTGGTGTTGTGGATTCGCAATGGATAATACATAAAGTGATACCTTCACTTGGAAGTCAAGGAAAGTCAGAGAATGGGAAAGCTC

upper sequence: GRMZM5G846339_T01 (Zea mays), 3'ss of exon 12
lower sequence: AT1G08040.2 (Arabidopsis thaliana), 3'ss of exon 12
-------------------------gtatgca-ttgttttgagagagtc-ttataccattctagcgaac--tgtt--gtttctgaatgcttttgacgttgctcgc---cagCCTGCTCATGAAAAGATTGGAGTTGTCGATTCGCAGTGGATCGTTCACCAAGTGGTTCCTTCTCTGGGGAACCAG
                          | || | ||  |||| |||  |  ||||| |     | |   |  ||||  || ||    ||  | ||   |    |     |||||||||||||| |||||||| || || ||||| ||||||||  | || |||||| ||||||| || || |  |||
gttatttaccactaccctctgcttcttgtgtaattcctttgggagctttgttatatctcatgaactctccttgttaagtctccatctgtatgtggtctcctccatttgcagCCTGCTCATGAGAAGATTGGTGTGGTAGATTCACAGTGGATTATCCATCAAGTGATTCCTTCCCTTGGAAGTCAG

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|148929009|gb|EC874209.2|EC874209
EST:     ACTTGGTTCATGGTTGGGGCTTGGATTTTGCGCTCAGGAAATGTGTGGAG                         CCTGCTCATGAAAAGATTGGAGTTGTCGATTCGCAGTGGATCGTTCACCAA
genomic: ACTTGGTTCATGGTTGGGGCTTGGATTTTGCGCTCAGGAAATGTGTGGAGgtatgcattg ... tgctcgccagCCTGCTCATGAAAAGATTGGAGTTGTCGATTCGCAGTGGATCGTTCACCAA
EST: gi|148950257|gb|EC895809.2|EC895809
EST:     CATGGTTGGGGCTTGGATTTTGCGCTCAGGAAATGTGTGGAG                         CCTGCTCATGAAAAGATTGGAGTTGTCGATTCGCAGTGGATCGTTCACCAA
genomic: CATGGTTGGGGCTTGGATTTTGCGCTCAGGAAATGTGTGGAGgtatgcattg ... tgctcgccagCCTGCTCATGAAAAGATTGGAGTTGTCGATTCGCAGTGGATCGTTCACCAA
EST: gi|148945517|gb|EC890762.2|EC890762
EST:     ACTTGGTTCATGGTTGGGGCTTGGATTTTGCGCTCAGGAAATGTGTGGAG                         CCTGCTCATGAAAAGATTGGGAGTTGTCGATTCGCAGTGGATCGTTCACCA
genomic: ACTTGGTTCATGGTTGGGGCTTGGATTTTGCGCTCAGGAAATGTGTGGAGgtatgcattg ... tgctcgccagCCTGCTCATGAAAAGATT-GGAGTTGTCGATTCGCAGTGGATCGTTCACCA
EST: gi|211435723|gb|FL461646.1|FL461646
EST:     ACTTGGTTCATGGTTGGGGCTTGGATTTTGCGCTCAGGAAATGTGTGGAG                         CCTGCTCATGAAAAGATTGGAGTTGTCGATTCGCAGTGGATCGTTCACCAA
genomic: ACTTGGTTCATGGTTGGGGCTTGGATTTTGCGCTCAGGAAATGTGTGGAGgtatgcattg ... tgctcgccagCCTGCTCATGAAAAGATTGGAGTTGTCGATTCGCAGTGGATCGTTCACCAA
EST: gi|211015300|gb|FL437092.1|FL437092
EST:     ACTTGGTTCATGGTTGGGGCTTGGATTTTGCGCTCAGGAAATGTGTGGAG                         CCTGCTCATGAAAAGATTGGAGTTGTCGATTCGCAGTGGATCGTTCACCAA
genomic: ACTTGGTTCATGGTTGGGGCTTGGATTTTGCGCTCAGGAAATGTGTGGAGgtatgcattg ... tgctcgccagCCTGCTCATGAAAAGATTGGAGTTGTCGATTCGCAGTGGATCGTTCACCAA
EST: gi|12046797|gb|BF728936.1|BF728936
EST:     TTGGGGCTTGGATTTTGCGCTCAGGAAATGTGTGGAG                         CCTGCTCATGAAAAGATTGGAGTTGTCGATTCGCAGTGGATCGTTCACCAA
genomic: TTGGGGCTTGGATTTTGCGCTCAGGAAATGTGTGGAGgtatgcattg ... tgctcgccagCCTGCTCATGAAAAGATTGGAGTTGTCGATTCGCAGTGGATCGTTCACCAA
EST: gi|211501409|gb|FL138835.1|FL138835
EST:     ACTTGGTTCATGGTTGGGGCTTGGATTTTGCGCTCAGGAAATGTGTGGAG                         CCTGCTCATGAAAAGATTGGAGTTGTCGATTCGCAGTGGATCGKTCACCAA
genomic: ACTTGGTTCATGGTTGGGGCTTGGATTTTGCGCTCAGGAAATGTGTGGAGgtatgcattg ... tgctcgccagCCTGCTCATGAAAAGATTGGAGTTGTCGATTCGCAGTGGATCGTTCACCAA
EST: gi|44682283|gb|CK787331.1|CK787331
EST:     ACTTGGTTCATGGTTGGGGCTTGGATTTTGCGCTCAGGAAATGTGTGGAG                         CCTGCTCATGAAAAGATTGGAGTTGTCGATTC
genomic: ACTTGGTTCATGGTTGGGGCTTGGATTTTGCGCTCAGGAAATGTGTGGAGgtatgcattg ... tgctcgccagCCTGCTCATGAAAAGATTGGAGTTGTCGATTC
EST: gi|149070556|gb|EE158958.2|EE158958
EST:     ACTTGGTTCATGGTTGGGGCTTGGATTTTGCGCTCAGGAAATGTGTGGAG                         CCTGCTCATGAAAAGATTGGAGTTGTCGATTCGCAGTGGATCGTTCACCAA
genomic: ACTTGGTTCATGGTTGGGGCTTGGATTTTGCGCTCAGGAAATGTGTGGAGgtatgcattg ... tgctcgccagCCTGCTCATGAAAAGATTGGAGTTGTCGATTCGCAGTGGATCGTTCACCAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttataccattctagcgaactgttgtttctgaatgcttttgacgttgctcgccagCCTGCTCATGAAAAGATTGGAGTTGTCGATTCGCAGTGGATCGTTCACCAAGTGGTTCCTTCTCTGGGGAACCAG
                                    ttttgac  putative branch site (score: 3)
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgcattgttttgagagagtcttataccattctagcgaactgttgtttctgaatgcttttgacgttgctcgccagCCTGCTCATGAAAAGATTGGAGTTGTCGATTCGCAGTGGATCGTTCACCAAGTGGTTCCTTCTCTGGGGAACCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGTGGA