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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtgcatcatactcttcatttaccgttttcttatgctttacgcctaccccaacctgcttgcagctagacttttttttgctcctcctcctcctcctgctgttaattaccactgtaccagttagtcacacatgaactgtctgctgcagATTGCATTTCCAAATGAAGCTGATGGCTTCCACGATCAGCTCCTCAAGGTGCAAGACAACATACCGATCTGCGCCTCCATCATCGGGCAGCGCCTGGCGC

Basic information

species Zea mays
transcript GRMZM2G107639_T02
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G107639_T01 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os01g08270.1 (Oryza sativa), 3'ss of exon 9
gtgagtgcatcatactcttcatttaccgttttcttatgctttacgcctaccccaacctgcttgcagctagacttttttttgctcctcctcctcctcctgctgttaattaccactgtaccagttagtcacacatgaactgtctgctgcagATTGCATTTCCAAATGAAGCTGATGGCTTCCACGATCAGCTCCTCAAGGTGCAAGACAACATACCGATCTGCGCCTCCATCATCGGGCAGCGCCTGGCGC
                                        |||    || | | |      ||||| || |  |   || |   || | |   ||     |||| ||   || ||   |    |   ||  |||| ||| ||||||||||||||    ||||| |||||||| ||  | || |  ||||| ||||| |||||||| |||||||| ||||| || |||||||||||||||||||||||||
----------------------------------------ttaaat-tatcaccatagcaatgcag-tataagtaacttagtggctgcacaatctg----tgttgat---cagtgagtcttacaagaactgatgagctgactgctgcagATTGCCCACCCAAACGAAGCTGACGGTCTTCATGCACAGCTGCTCAAAGTGCAAGATAACATACCTATCTGTGCTTCCATCATCGGGCAGCGCCTGGCGC
















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|148950037|gb|EC895569.2|EC895569
EST:     TCTTCTCGTTCTCAAAGGCTTATGGAATGATGGGGTGGCGTGTAGGATAC                         ATTGCATTTCCAAATGAAGCTGATGGCTTCCACGATCAGCTCCTCAAGGTG
genomic: TCTTCTCGTTCTCAAAGGCTTATGGAATGATGGGGTGGCGTGTAGGATACgtgagtgcat ... tctgctgcagATTGCATTTCCAAATGAAGCTGATGGCTTCCACGATCAGCTCCTCAAGGTG
EST: gi|78027605|gb|DV495992.1|DV495992
EST:     ATGGGGTGGCGTGTAGGATAC                         ATTGCATTTCCAAATGAAGCTGATGGCTTCCACGATCAGCTCCTCAAAGTG
genomic: ATGGGGTGGCGTGTAGGATACgtgagtgcat ... tctgctgcagATTGCATTTCCAAATGAAGCTGATGGCTTCCACGATCAGCTCCTCAAGGTG
EST: gi|76017053|gb|DT944223.1|DT944223
EST:     TCTTCTCGTTCTCAAAGGCTTATGGAATGATGGGGTGGCGTGTAGGATAC                         ATTGCATTTCCAAATGAAGCTGATGGCTTCCACGATCAGCTCCTCAAGGTG
genomic: TCTTCTCGTTCTCAAAGGCTTATGGAATGATGGGGTGGCGTGTAGGATACgtgagtgcat ... tctgctgcagATTGCATTTCCAAATGAAGCTGATGGCTTCCACGATCAGCTCCTCAAGGTG
EST: gi|31357857|gb|CD442214.1|CD442214
EST:     TCTTCTCGTTCTCAAAGGCTTATGGAATGATGGGGTGGCGTGTAGGATAC                         ATTGCATTTCCAAATGAAGCTGATGGCTTCCACGATCAGCTCCTCAAAGTG
genomic: TCTTCTCGTTCTCAAAGGCTTATGGAATGATGGGGTGGCGTGTAGGATACgtgagtgcat ... tctgctgcagATTGCATTTCCAAATGAAGCTGATGGCTTCCACGATCAGCTCCTCAAGGTG
EST: gi|149051688|gb|EE155800.2|EE155800
EST:     TCTTCTCGTTCTCAAAGGCTTATGGAATGATGGGGTGGCGTGTAGGATAC                         ATTGCATTTCCAAATGAAGCTGATGGCTTCCACGATCAGCTCCTCAAGGTG
genomic: TCTTCTCGTTCTCAAAGGCTTATGGAATGATGGGGTGGCGTGTAGGATACgtgagtgcat ... tctgctgcagATTGCATTTCCAAATGAAGCTGATGGCTTCCACGATCAGCTCCTCAAGGTG
EST: gi|67011573|gb|CO440322.1|CO440322
EST:     TCTTCTCGTTCTCAAAGGCTTATGGAATGATGGGGTGGCGTGTAGGATAC                         ATTGCATTTCCAAATGAAGCTGATGGCTTCCACGATCAGCTCCTCAAAGTG
genomic: TCTTCTCGTTCTCAAAGGCTTATGGAATGATGGGGTGGCGTGTAGGATACgtgagtgcat ... tctgctgcagATTGCATTTCCAAATGAAGCTGATGGCTTCCACGATCAGCTCCTCAAGGTG
EST: gi|211043539|gb|FL214489.1|FL214489
EST:     TCTTCTCGTTCTCAAAGGCTTATGGAATGATGGGGTGGCGTGTAGGATAC                         ATTGCATTTCCAAATGAAGCTGATGGCTTCCACGATCAGCTCCTCAAAGTG
genomic: TCTTCTCGTTCTCAAAGGCTTATGGAATGATGGGGTGGCGTGTAGGATACgtgagtgcat ... tctgctgcagATTGCATTTCCAAATGAAGCTGATGGCTTCCACGATCAGCTCCTCAAGGTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcctgctgttaattaccactgtaccagttagtcacacatgaactgtctgctgcagATTGCATTTCCAAATGAAGCTGATGGCTTCCACGATCAGCTCCTCAAGGTGCAAGACAACATACCGATCTGCGCCTCCATCATCGGGCAGCGCCTGGCGC
      tgttaat  putative branch site (score: 3)
      tgttaatta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagtgcatcatactcttcatttaccgttttcttatgctttacgcctaccccaacctgcttgcagctagacttttttttgctcctcctcctcctcctgctgttaattaccactgtaccagttagtcacacatgaactgtctgctgcagATTGCATTTCCAAATGAAGCTGATGGCTTCCACGATCAGCTCCTCAAGGTGCAAGACAACATACCGATCTGCGCCTCCATCATCGGGCAGCGCCTGGCGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA