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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ggggttttatgtcatggttgtatttttataccacacatcactacatcagttcaagcactcttgtgtgctttttgttacccctgatttttgtattatgcagTGGGACAAAGCAATCTGCACACAGGTTAAAAATAATATTTGGTCTCTCTGGCATGAAAGCAGCTGAACTTCATGGCAACCTTACACAGGCCCAGCGGCTT

Basic information

species Zea mays
transcript GRMZM2G420865_T02
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G420865_T02 (Zea mays), 3'ss of exon 9
lower sequence: LOC_Os12g29660.1 (Oryza sativa), 3'ss of exon 8
ggggttttatgtcatggttgtatttttataccacacatcactacatcagttcaagcactcttgtgtgctttttgttacccctgatttttgtat---tatgcagTGGGACAAAGCAATCTGCACACAGGTTAAAAATAATATTTGGTCTCTCTGGCATGAAAGCAGCTGAACTTCATGGCAACCTTACACAGGCCCAGCGGCTT
    |||  |||| |   || || ||| |       || | |  |  | || || |||   | | |  | | |  ||    |||| ||  | |   | |||||||| |||||||| ||||| ||||| || |||||||||||||||||||| || |||||||| ||||||||||||||||||||||| |||||||||||||||
cctatttactgtccta-ctgcatgtttgtgtactggatgattctagtactt-aatcacatgtatattttgtataatatgt-tgatattcatgtccctttgcagTGGCACAAAGCATTCTGCTCACAGATTGAAAATAATATTTGGTCTCTCCGGGATGAAAGCTGCTGAACTTCATGGCAACCTTACGCAGGCCCAGCGGCTT
















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|78027541|gb|DV495928.1|DV495928
EST:     GTTTGAAGACTTTCAAGCGAAGTGTTATCATTTTTAG                         TGGGACAAAGCAATCTGCACACAGGTTAAAAATAATATTTGGTCTCTCTGG
genomic: GTTTGAAGACTTTCAAGCGAAGTGTTATCATTTTTAGgtttgtgttc ... tattatgcagTGGGACAAAGCAATCTGCACACAGGTTAAAAATAATATTTGGTCTCTCTGG
EST: gi|67031210|gb|CO459959.1|CO459959
EST:     CTTCTTGCACTCTGTTTGAAGACTTTCAAGCGAAGTGTTATCATTTTTAG                         TGGGACAAAGCAATCTGCACACAGGTTAAAAATAATATTTGGTCTCTCTGG
genomic: CTTCTTGCACTCTGTTTGAAGACTTTCAAGCGAAGTGTTATCATTTTTAGgtttgtgttc ... tattatgcagTGGGACAAAGCAATCTGCACACAGGTTAAAAATAATATTTGGTCTCTCTGG
EST: gi|31349040|gb|CD433397.1|CD433397
EST:     CTTCTTGCACTCTGTTTGAAGACTTTCAATCCAAGTGTTATCATTTTTAG                         TGGGACAAAGCAATCTGCACACAGGTTAAAAATAATATTTGGTCTCTCTGG
genomic: CTTCTTGCACTCTGTTTGAAGACTTTCAAGCGAAGTGTTATCATTTTTAGgtttgtgttc ... tattatgcagTGGGACAAAGCAATCTGCACACAGGTTAAAAATAATATTTGGTCTCTCTGG
EST: gi|78090029|gb|DV518403.1|DV518403
EST:     CTTCTTGCACTCTGTTTGAAGACTTTCAAGCGAAGTGTTATCATTTTTAG                         TGGGACAAAGCAATCTGCACACAGGTTAAAAATAATATTTGGTCTCTCTGG
genomic: CTTCTTGCACTCTGTTTGAAGACTTTCAAGCGAAGTGTTATCATTTTTAGgtttgtgttc ... tattatgcagTGGGACAAAGCAATCTGCACACAGGTTAAAAATAATATTTGGTCTCTCTGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcagttcaagcactcttgtgtgctttttgttacccctgatttttgtattatgcagTGGGACAAAGCAATCTGCACACAGGTTAAAAATAATATTTGGTCTCTCTGGCATGAAAGCAGCTGAACTTCATGGCAACCTTACACAGGCCCAGCGGCTT
                                 ccctgat  putative branch site (score: 4)
                                       tttttgt  CT-rich tract
                                    tgatttttgtattat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ggggttttatgtcatggttgtatttttataccacacatcactacatcagttcaagcactcttgtgtgctttttgttacccctgatttttgtattatgcagTGGGACAAAGCAATCTGCACACAGGTTAAAAATAATATTTGGTCTCTCTGGCATGAAAGCAGCTGAACTTCATGGCAACCTTACACAGGCCCAGCGGCTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - -tgtcatg
- - - - - - - - - tgtattt
- - - - - - - - - - - - - - - ccacaca
- - - - - - - - - - - - - - - - - - - - ctacatc
- - - - - - - - - - - - - - - - - - - - - - - - - -caagcac