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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttcttttcgccttccctttattcaacctatgtcatagagctctctatcttttttgttgcttacacacacttgaatccttcagGACTTCCAAGAGGGTTGTGGAGCTCCAGTTTTTCTGCTAACCACACAAGTTGGTGGGCTTGGACTTACACTCACCAAGGCAACTCGTGTCATTGTAGTTG

Basic information

species Zea mays
transcript GRMZM2G138125_T02
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G138125_T02 (Zea mays), 3'ss of exon 12
lower sequence: LOC_Os04g59624.3 (Oryza sativa), 3'ss of exon 11
gttcttttc--gccttccctttattcaacctatgtcatag--agctctctatcttttttgttgcttacacacacttgaatcct--tcagGACTTCCAAGAGGGTTGTGGAGCTCCAGTTTTTCTGCTAACCACACAAGTTGGTGGGCTTGGACTTACACTCACCAAGGCAACTCGTGTCATTGTAGTTG
|||||| ||   | ||||||||  |     |||| ||| |  |    | |  ||  | | |||||||||   | |  | |  |  |||||||||||||||||||  |||||||||| | ||| |||| |||||||||||||||||||||||||||||||||||||||||| |||||||||| |||||||
gttcttctctgtctttccctttccttcttttatgccatgggcaaaattgttactgctatattgcttacatggaatgcatttgtgatcagGACTTCCAAGAGGGTCCTGGAGCTCCAATATTTTTGCTGACCACACAAGTTGGTGGGCTTGGACTTACACTCACCAAGGCAGCTCGTGTCATAGTAGTTG
















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|28873896|gb|CB329825.1|CB329825
EST:     TGCGCATTGATGGCACCACCAAGGTTTCTGACCGGGAAAGGATTGTGAAG                         GACTTCCAAGAGGGTTGTGGAGCTCCAGTTTTTCTGCTAACCACACAAGTT
genomic: TGCGCATTGATGGCACCACCAAGGTTTCTGACCGGGAAAGGATTGTGAAGgttcttttcg ... aatccttcagGACTTCCAAGAGGGTTGTGGAGCTCCAGTTTTTCTGCTAACCACACAAGTT
EST: gi|67035224|gb|CO463757.1|CO463757
EST:     CGCATTGATGGCACCACCAAGGTTTNCTGACCGGGAAAGGATTGTGAANG                         GACTTCCNAGAGG-TTGTGGAGCTCCAGTTTTTCTGCTAACCACACAAGT
genomic: CGCATTGATGGCACCACCAAGGTTT-CTGACCGGGAAAGGATTGTGAA-Ggttcttttcg ... aatccttcagGACTTCCAAGAGGGTTGTGGAGCTCCAGTTTTTCTGCTAACCACACAAGT
EST: gi|28987103|gb|CB351465.1|CB351465
EST:     TGCGCATTGATGGCACCACCAAGGTTTCTGACCGGGAAAGGATTGTGAAG                         GACTTCCAAGAGGGTTGTGGAGCTCCAGTTTTTCTGCTAACCACACAAGTT
genomic: TGCGCATTGATGGCACCACCAAGGTTTCTGACCGGGAAAGGATTGTGAAGgttcttttcg ... aatccttcagGACTTCCAAGAGGGTTGTGGAGCTCCAGTTTTTCTGCTAACCACACAAGTT
EST: gi|94475969|gb|EB704927.1|EB704927
EST:     TGCGCATTGATGGCACCACCAAGGTTTCTGACCGGGAAAGGATTGTGAAG                         GACTTCCAAGAGGGTTGTGGAGCTCCAGTTTTTCTGCTAACCACACAAGTT
genomic: TGCGCATTGATGGCACCACCAAGGTTTCTGACCGGGAAAGGATTGTGAAGgttcttttcg ... aatccttcagGACTTCCAAGAGGGTTGTGGAGCTCCAGTTTTTCTGCTAACCACACAAGTT
EST: gi|31909131|gb|CD650765.1|CD650765
EST:     TGCGCATTGATGGCACCACCAAGGTTTCTGACCGGGAAAGGATTGTGAAG                         GACTTCCAAGAGGGTTGTGGAGCTCCAGTTTTTCTGCTAACCACACAAGTT
genomic: TGCGCATTGATGGCACCACCAAGGTTTCTGACCGGGAAAGGATTGTGAAGgttcttttcg ... aatccttcagGACTTCCAAGAGGGTTGTGGAGCTCCAGTTTTTCTGCTAACCACACAAGTT
EST: gi|28930971|gb|CB334332.1|CB334332
EST:     TGCGCATTGATGGCACCACCAAGGTTTCTGACCGGGAAAGGATTGTGAAG                         GACTTCCAAGAGGGTTGTGGAGCTCCAGTTTTTCTGCTAACCACACAAGTT
genomic: TGCGCATTGATGGCACCACCAAGGTTTCTGACCGGGAAAGGATTGTGAAGgttcttttcg ... aatccttcagGACTTCCAAGAGGGTTGTGGAGCTCCAGTTTTTCTGCTAACCACACAAGTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatgtcatagagctctctatcttttttgttgcttacacacacttgaatccttcagGACTTCCAAGAGGGTTGTGGAGCTCCAGTTTTTCTGCTAACCACACAAGTTGGTGGGCTTGGACTTACACTCACCAAGGCAACTCGTGTCATTGTAGTTG
                             tgcttac  putative branch site (score: 2)
                                               tccttc  putative PPT
                 tatctttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttcttttcgccttccctttattcaacctatgtcatagagctctctatcttttttgttgcttacacacacttgaatccttcagGACTTCCAAGAGGGTTGTGGAGCTCCAGTTTTTCTGCTAACCACACAAGTTGGTGGGCTTGGACTTACACTCACCAAGGCAACTCGTGTCATTGTAGTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG