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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTGAAGACCCATGGTCCTCACCCATCACCTCGAGCTGGTTGCAGCGGAACTCTCTGTGGAACTAAGTGGTACATAGCTGGCGGCGCAAGCAAGAAAAAACgtaagtctcaagctctctctcaatttggaagatgagttggtgatttatttcttaatgaagaatacatgtattgctaatgatgaccatctagcttcttttgcaatttctaacaagaaatcaaattctcag

Basic information

species Zea mays
transcript GRMZM2G174830_T01
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G174830_T01 (Zea mays), 5'ss of exon 11
lower sequence: LOC_Os12g35350.1 (Oryza sativa), 5'ss of exon 11
GTGAAGACCCATGGTCCTCACCCATCACCTCGAGCTGGTTGCAGCGGAACTCTCTGTGGAACTAAGTGGTACATAGCTGGCGGCGCAAGCAAGAAAAAACgtaagtctcaagctctctctcaatttggaagatgagttggtgat-----ttatttcttaatg-----aagaatacatgtattgctaatgatgacc-atctagcttcttttgcaatttctaacaagaaa--tcaaattctcag
||||| | |||||||||||| ||| |||||||||| |||||||| |||  ||| |||||||||||||||||||| |||||||| | ||||||||||||||||| || ||||||||||     ||  ||||   || ||||  ||      ||||||    ||      ||||  ||    ||   ||  |||    |||| | || |   ||| ||| |||||| |||  || |||||||||
GTGAAAATCCATGGTCCTCATCCAACACCTCGAGCCGGTTGCAGTGGAGTTCTATGTGGAACTAAGTGGTACATTGCTGGCGGTGGAAGCAAGAAAAAACgtatgtttcaagctctcaacttat--ggaaatagaattggaaatgaggtctatttcagtttgtctctgagaaatcacactttcacaagaatggtttatcttgattata--gcagtttgtaacaaaaaatatcgaattctcag
















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|60340595|gb|DN207568.1|DN207568
EST:     TCTCTGTGGAACTAAGTGGTACATAGCTGGCGGCGCAAGCAAGAAAAAAC                         GACATGCTGAAACTTGGGTTTTTGATGTTCTACAATGTAAATGGTCTGTTT
genomic: TCTCTGTGGAACTAAGTGGTACATAGCTGGCGGCGCAAGCAAGAAAAAACgtaagtctca ... aaattctcagGACATGCTGAAACTTGGGTTTTTGATGTTCTACAATGTAAATGGTCTGTTT
EST: gi|91873012|gb|EB402969.1|EB402969
EST:     TCTCTGTGGAACTAAGTGGTACATAGCTGGCGGCGCAAGCAAGAAAAAAC                         GACATGCTGAAACTTGGGTTTTTGATGTTCTACAATGTAAATGGTCTGTTT
genomic: TCTCTGTGGAACTAAGTGGTACATAGCTGGCGGCGCAAGCAAGAAAAAACgtaagtctca ... aaattctcagGACATGCTGAAACTTGGGTTTTTGATGTTCTACAATGTAAATGGTCTGTTT
EST: gi|211020705|gb|FL318029.1|FL318029
EST:     TCTCTGTGGAACTAAGTGGTACATAGCTGGCGGCGCAAGCAAGAAAAAAC                         GACATGCTGAAACTTGGGTTTTTGATGTTCTACAATGTAAATGGTCTGTTT
genomic: TCTCTGTGGAACTAAGTGGTACATAGCTGGCGGCGCAAGCAAGAAAAAACgtaagtctca ... aaattctcagGACATGCTGAAACTTGGGTTTTTGATGTTCTACAATGTAAATGGTCTGTTT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTGAAGACCCATGGTCCTCACCCATCACCTCGAGCTGGTTGCAGCGGAACTCTCTGTGGAACTAAGTGGTACATAGCTGGCGGCGCAAGCAAGAAAAAACgtaagtctcaagctctctctcaatttggaagatgagttggtgatttatttcttaatgaagaatacatgtattgctaatgatgaccatctagcttcttttgcaatttctaacaagaaatcaaattctcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA