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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gcatattgataagcctttaattattttgcaaacataactttattatgcgcagactgagtgacaaatatcgttcatggttaacctggtatattttgtgcagGCATGCTGTGCTGTTCTTCAAAGTTGGGTCTCAAGAAAATTTATGACTGGATG

Basic information

species Zea mays
transcript GRMZM2G046098_T02
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G046098_T02 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os01g64780.2 (Oryza sativa), 3'ss of exon 1
gcatattgataagcctttaattattttgcaaacataactttattatgcgcagactgag---tgacaaatatcgttcatggttaacctggtatattttgtgcagGCATGCTGTGCTGTTCTTCAAAGTTGGGTCTCAAGAAAATTTATGACTGGATG
  | |||   ||         | ||    |   || | |||  ||||| |    | |    | |   || |  |||||  |||   |||| | |||||||||||||||||| |||||||||||||||||||| |||||||||||||||||||||||
-taaatttgcaaaaacagttgtgttcaataggaatgagttt--tatgcacttcttaaaatttcatgtatttatttcattcttagtttggtgtgttttgtgcagGCATGCTGCGCTGTTCTTCAAAGTTGGGTGTCAAGAAAATTTATGACTGGATG

upper sequence: GRMZM2G046098_T02 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os01g64780.1 (Oryza sativa), 3'ss of exon 1
gcatattgataagcctttaattattttgcaaacataactttattatgcgcagactgag---tgacaaatatcgttcatggttaacctggtatattttgtgcagGCATGCTGTGCTGTTCTTCAAAGTTGGGTCTCAAGAAAATTTATGACTGGATG-----------------------------------------------
  | |||   ||         | ||    |   || | |||  ||||| |    | |    | |   || |  |||||  |||   |||| | |||||||||||||||||| |||||||||||||||||||| |||||||||||||||||||||||                                               
-taaatttgcaaaaacagttgtgttcaataggaatgagttt--tatgcacttcttaaaatttcatgtatttatttcattcttagtttggtgtgttttgtgcagGCATGCTGCGCTGTTCTTCAAAGTTGGGTGTCAAGAAAATTTATGACTGGATGGTACATCTTTGACAGGAACCAAGTTAAGCATGTTACCAAACAAAAAG
















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|51871157|gb|CV126041.1|CV126041
EST:     CAGCCAAGTCGCCGCCGCGACCCAGCTCGCCCACCACCTCCACACGCAAG                         GCATGCTGTGCTGTTCTTCAAAGTTGGGTCTCAAGAAAATTTATGACTGGA
genomic: CAGCCAAGTCGCCGCCGCGACCCAGCTCGCCCACCACCTCCACACGCAAGgtccggatct ... ttttgtgcagGCATGCTGTGCTGTTCTTCAAAGTTGGGTCTCAAGAAAATTTATGACTGGA
EST: gi|40287177|gb|CK327569.1|CK327569
EST:     CAGCCAAGTCGCCGCCGCGACCCAGCTCGCCCACCACCTCCACACGCAAG                         GNATGCTGTGCTGTTCTTCAAAGTTGGGTCTCAAGAAAATTTATGACTGGA
genomic: CAGCCAAGTCGCCGCCGCGACCCAGCTCGCCCACCACCTCCACACGCAAGgtccggatct ... ttttgtgcagGCATGCTGTGCTGTTCTTCAAAGTTGGGTCTCAAGAAAATTTATGACTGGA
EST: gi|51871146|gb|CV126030.1|CV126030
EST:     CAGCCAAGTCGCCGCCGCGACCCAGCTCGCCCACCACCTCCACACGCAAG                         GCATGCTGTGCTGTTCTTCAAAGTTGGGTCTCAAGAAAATTTATGACTGGA
genomic: CAGCCAAGTCGCCGCCGCGACCCAGCTCGCCCACCACCTCCACACGCAAGgtccggatct ... ttttgtgcagGCATGCTGTGCTGTTCTTCAAAGTTGGGTCTCAAGAAAATTTATGACTGGA
EST: gi|211391866|gb|FL013594.1|FL013594
EST:     CAGCCAAGTCGCCGCCGCGACCCAGCTCGCCCACCACCTCCACACGCAAG                         GCATGCTGTGCTGTTCTTCAAAGTTGGGTCTCAAGAAAATTTATGACTGGA
genomic: CAGCCAAGTCGCCGCCGCGACCCAGCTCGCCCACCACCTCCACACGCAAGgtccggatct ... ttttgtgcagGCATGCTGTGCTGTTCTTCAAAGTTGGGTCTCAAGAAAATTTATGACTGGA
EST: gi|50336995|gb|CO532121.1|CO532121
EST:     CAGCCAAGTCGCCGCCGCGACCCAGCTCGCCCACCACCTCCACACGCAAG                         GCATGCTGTGCTGTTCTTCAAAGTTGGGTCTCAAGAAAATTTATGACTGGA
genomic: CAGCCAAGTCGCCGCCGCGACCCAGCTCGCCCACCACCTCCACACGCAAGgtccggatct ... ttttgtgcagGCATGCTGTGCTGTTCTTCAAAGTTGGGTCTCAAGAAAATTTATGACTGGA
EST: gi|50323815|gb|CO518941.1|CO518941
EST:     CAGCCAAGTCGCCGCCGCGACCCAGCTCGCCCACCACCTCCACACGCAAG                         GCATGCTGTGCTGTTCTTCAAAGTTGGGTCTCAAGAAAATTTATGACTGGA
genomic: CAGCCAAGTCGCCGCCGCGACCCAGCTCGCCCACCACCTCCACACGCAAGgtccggatct ... ttttgtgcagGCATGCTGTGCTGTTCTTCAAAGTTGGGTCTCAAGAAAATTTATGACTGGA
EST: gi|88755429|gb|DY539570.1|DY539570
EST:     CAGCCAAGTCGCCGCCGCGACCCAGCTCGCCCACCACCTCCACACGCAAG                         GCATGCTGTGCTGTTCTTCAAAGTTGGGTCTCAAGAAAATTTATGACTGGA
genomic: CAGCCAAGTCGCCGCCGCGACCCAGCTCGCCCACCACCTCCACACGCAAGgtccggatct ... ttttgtgcagGCATGCTGTGCTGTTCTTCAAAGTTGGGTCTCAAGAAAATTTATGACTGGA
EST: gi|42491828|gb|CK700874.1|CK700874
EST:     CAGCCAAGTCGCCGCCGCGACCCAGCTCGCCCACCACCTCCACACGCAAG                         GCATGCTGTGCTGTTCTTCAAAGTTGGGTCTCAAGAAAATTTATGACTGGA
genomic: CAGCCAAGTCGCCGCCGCGACCCAGCTCGCCCACCACCTCCACACGCAAGgtccggatct ... ttttgtgcagGCATGCTGTGCTGTTCTTCAAAGTTGGGTCTCAAGAAAATTTATGACTGGA
EST: gi|91053372|gb|EB163790.1|EB163790
EST:     CAGCCAAGTCGCCGCCGCGACCCAGCTCGCCCACCACCTCCACACGCAAG                         GCATGCTGTGCTGTTCTTCAAAGTTGGGTCTCAAGAAAATTTATGACTGGA
genomic: CAGCCAAGTCGCCGCCGCGACCCAGCTCGCCCACCACCTCCACACGCAAGgtccggatct ... ttttgtgcagGCATGCTGTGCTGTTCTTCAAAGTTGGGTCTCAAGAAAATTTATGACTGGA
EST: gi|28910665|gb|CB331552.1|CB331552
EST:     CAGCCAAGTCGCCGCCGCGACCCAGCTCGCCCACCACCTCCACACGCAAG                         GCATGCTGTGCTGTTCTTCAAAGTTGGGTCTCAAGAAAATTTATGACTGGA
genomic: CAGCCAAGTCGCCGCCGCGACCCAGCTCGCCCACCACCTCCACACGCAAGgtccggatct ... ttttgtgcagGCATGCTGTGCTGTTCTTCAAAGTTGGGTCTCAAGAAAATTTATGACTGGA
EST: gi|76293651|gb|DV033219.1|DV033219
EST:     CAGCCAAGTCGCCGCCGCGACCCAGCTCGCCCACCACCTCCACACGCAAG                         GCATGCTGTGCTGTTCTTCAAAGTTGGGTCTCAAGAAAATTTATGACTGGA
genomic: CAGCCAAGTCGCCGCCGCGACCCAGCTCGCCCACCACCTCCACACGCAAGgtccggatct ... ttttgtgcagGCATGCTGTGCTGTTCTTCAAAGTTGGGTCTCAAGAAAATTTATGACTGGA
EST: gi|42491878|gb|CK700924.1|CK700924
EST:     CAGCCAAGTCGCCGCCGCGACCCAGCTCGCCCACCACCTCCACACGCAAG                         GCATGCTGTGCTGTTCTTCAAAGTTGGGTCTCAAGAAAATTTATGACTGGA
genomic: CAGCCAAGTCGCCGCCGCGACCCAGCTCGCCCACCACCTCCACACGCAAGgtccggatct ... ttttgtgcagGCATGCTGTGCTGTTCTTCAAAGTTGGGTCTCAAGAAAATTTATGACTGGA
EST: gi|40287192|gb|CK327584.1|CK327584
EST:     CAGCCAAGTCGCCGCCGCGACCCAGCTCGCCCACCACCTCCACACGCAAG                         GCATGCTGTGCTGTTCTTCAAAGNTGGGTCNNAAGAAAATTTATGACTGGA
genomic: CAGCCAAGTCGCCGCCGCGACCCAGCTCGCCCACCACCTCCACACGCAAGgtccggatct ... ttttgtgcagGCATGCTGTGCTGTTCTTCAAAGTTGGGTCTCAAGAAAATTTATGACTGGA
EST: gi|74239462|gb|DT647376.1|DT647376
EST:     CAGCCAAGTCGCCGCCGCGACCCAGCTCGCCCACCACCTCCACACGCAAG                         GCATGCTGTGCTGTTCTTCAAAGTTGGGTCTCAAGAAAATTTATGACTGGA
genomic: CAGCCAAGTCGCCGCCGCGACCCAGCTCGCCCACCACCTCCACACGCAAGgtccggatct ... ttttgtgcagGCATGCTGTGCTGTTCTTCAAAGTTGGGTCTCAAGAAAATTTATGACTGGA
EST: gi|148949550|gb|EC895017.2|EC895017
EST:     CAGCCAAGTCGCCGCCGCGACCCAGCTCGCCCACCACCTCCACACGCAAG                         GCATGCTGTGCTGTTCTTCAAAGTTGGGTCTCAAGAAAATTTATGACTGGA
genomic: CAGCCAAGTCGCCGCCGCGACCCAGCTCGCCCACCACCTCCACACGCAAGgtccggatct ... ttttgtgcagGCATGCTGTGCTGTTCTTCAAAGTTGGGTCTCAAGAAAATTTATGACTGGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgcgcagactgagtgacaaatatcgttcatggttaacctggtatattttgtgcagGCATGCTGTGCTGTTCTTCAAAGTTGGGTCTCAAGAAAATTTATGACTGGATG
                              ggttaac  putative branch site (score: 3)
                                         tatattttgt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gcatattgataagcctttaattattttgcaaacataactttattatgcgcagactgagtgacaaatatcgttcatggttaacctggtatattttgtgcagGCATGCTGTGCTGTTCTTCAAAGTTGGGTCTCAAGAAAATTTATGACTGGATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA