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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gttcatgcatgcatcgaaaaaacctcgctcatatatagctataattaatactgacactgagaatgttgaattatttattcactcatgcatgcatggacagATAATGAGCAACTCCGTGTACAAGAGCGTGGAGCACCGGGTGGTCGTGAACGCCGAGGAGGAGCGCATATCCCTCGCCATCTTCTACAACCCCAAGGGCG

Basic information

species Zea mays
transcript GRMZM2G122280_T02
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G122280_T02 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os01g61610.3 (Oryza sativa), 3'ss of exon 2
gttcatgcatgcatcgaaaaaacctc--gctcatatatagctataattaatactgacactgagaatgt-tgaattatttattcactcatgcatgcatggacagATAATGAGCAACTCCGTGTACAAGAGCGTGGAGCACCGGGTGGTCGTGAACGCCGAGGAGGAGCGCATATCCCTCGCCATCTTCTACAACCCCAAGGGCG
  |||   |||  || |      ||     |   || |  |   || |||||    |    |   ||  || ||     |||||   | | | | | | ||||||  ||||||||||  |||||||||||||||||||||| ||| ||||||||||||||||||||||||| || |||||  ||||||||||||| |  ||||
catcaataatgtttcaagctgttcttctattttaatttctcaggaactaatatcttcttgtactgtgcatggatgga--attcatggacggacg-acgtacagATCTTGAGCAACTCGATGTACAAGAGCGTGGAGCACCGCGTGATCGTGAACGCCGAGGAGGAGCGCATCTCGCTCGCACTCTTCTACAACCCGAGAGGCG
















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|94472610|gb|EB701568.1|EB701568
EST:     TGCGCCCCGTCCGCGACGCCTTCATCGTCAACGTCGGCGACCAAGTCCAG                         ATAATGAGCAACTCCGTGTACAAGAGCGTGGAGCACCGGGTGGTCGTGAAC
genomic: TGCGCCCCGTCCGCGACGCCTTCATCGTCAACGTCGGCGACCAAGTCCAGgtaatatagc ... gcatggacagATAATGAGCAACTCCGTGTACAAGAGCGTGGAGCACCGGGTGGTCGTGAAC
EST: gi|71312883|gb|DR792967.1|DR792967
EST:     TGCGCCCCGTCCGCGACGCCTTCATCGTCAACGTCGGCGACCAAGTCCAG                         ATAATGAGCAACTCCGTGTACAAGAGCGTGGAGCACCGGGTGGTCGTGAAC
genomic: TGCGCCCCGTCCGCGACGCCTTCATCGTCAACGTCGGCGACCAAGTCCAGgtaatatagc ... gcatggacagATAATGAGCAACTCCGTGTACAAGAGCGTGGAGCACCGGGTGGTCGTGAAC
EST: gi|71312885|gb|DR792968.1|DR792968
EST:     TGCGCCCCGTCCGCGACGCCTTCATCGTCAACGTCGGCGACCAAGTCCAG                         ATAATGAGCAACTCCGTGTACAAGAGCGTGGAGCACCGGGTGGTCGTGAAC
genomic: TGCGCCCCGTCCGCGACGCCTTCATCGTCAACGTCGGCGACCAAGTCCAGgtaatatagc ... gcatggacagATAATGAGCAACTCCGTGTACAAGAGCGTGGAGCACCGGGTGGTCGTGAAC
EST: gi|78077395|gb|DV505829.1|DV505829
EST:     TGCGCCCCGTCCGCGACGCCTTCATCGTCAACGTCGGGGACCAAGTCCAG                         ATAATGAGCAACTCCGTGTACAAGAGCGTGGAGCACCGGGTGGTCGTGAAC
genomic: TGCGCCCCGTCCGCGACGCCTTCATCGTCAACGTCGGCGACCAAGTCCAGgtaatatagc ... gcatggacagATAATGAGCAACTCCGTGTACAAGAGCGTGGAGCACCGGGTGGTCGTGAAC
EST: gi|71429688|gb|DR810738.1|DR810738
EST:     TGCGCCCCGTCCGCGACGCCTTCATCGTCAACGTCGGCGACCAAGTCCAG                         ATAATGAGCAACTCCGTGTACAAGAGCGTGGAGCACCGGGTGGTCGTGAAC
genomic: TGCGCCCCGTCCGCGACGCCTTCATCGTCAACGTCGGCGACCAAGTCCAGgtaatatagc ... gcatggacagATAATGAGCAACTCCGTGTACAAGAGCGTGGAGCACCGGGTGGTCGTGAAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taatactgacactgagaatgttgaattatttattcactcatgcatgcatggacagATAATGAGCAACTCCGTGTACAAGAGCGTGGAGCACCGGGTGGTCGTGAACGCCGAGGAGGAGCGCATATCCCTCGCCATCTTCTACAACCCCAAGGGCG
   tactgac  putative branch site (score: 1)
                aatgttgaattattta  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttcatgcatgcatcgaaaaaacctcgctcatatatagctataattaatactgacactgagaatgttgaattatttattcactcatgcatgcatggacagATAATGAGCAACTCCGTGTACAAGAGCGTGGAGCACCGGGTGGTCGTGAACGCCGAGGAGGAGCGCATATCCCTCGCCATCTTCTACAACCCCAAGGGCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG