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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gcttgtctacacgtaggatagaacatagaaggtcatctagtgtttatgcgcctaaattgatctgttctgataacatttgtccttatttcttgccttgcagGTTTGCTGGACGGCAAATCCATGCGAGCGAAGACGATGGCTCTGTTAACCATGCTCTTATCCGTGATTACGACGCGGAGGTGTCAAGGCTGGATCGATTT

Basic information

species Zea mays
transcript GRMZM2G171660_T01
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G171660_T01 (Zea mays), 3'ss of exon 12
lower sequence: LOC_Os04g41910.1 (Oryza sativa), 3'ss of exon 12
gcttgtctacacgt-aggatagaacatagaaggtcatctag-tgtttatgcgcctaaatt----gatctgttctgataacatttgtcctt-atttcttgccttgcagGTTTGCTGGACGGCAAATCCATGCGAGCGAAGACGATGGCTCTGTTAACCATGCTCTTATCCGTGATTACGACGCGGAGGTGTCAAGGCTGGATCGATTT
       |    ||  | || |  |||    | |  || |  | |  | |      ||||    ||||  |  |  || || |||| ||| |||| || | | ||||||||| |||    |||||||| ||||| ||||| || || ||| | ||||||||||| ||||||||||| || || |||||||||||||| |||||||||
-------tgggtgttggaattgtgcatgcttgcttttcaacctatcgaagaattagaatttgtggatcattcgttttatcaattgttcttgatttgttccttcgcagGTTTGGTGGGAATCAAATCCAGGCGAGTGAAGATGACGGTTCTATCAACCATGCTCTGATCCGTGATTATGATGCAGAGGTGTCAAGGCTTGATCGATTT
















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|50335299|gb|CO530425.1|CO530425
EST:     AAAGACAGGAAAGATGGTGCCAAATGCATAGAGAAGATGAACGGCAGATG                         GTTTGCTGGACGGCAAATCCATGCGAGCGAAGACGATGGCTCTGTTAACCA
genomic: AAAGACAGGAAAGATGGTGCCAAATGCATAGAGAAGATGAACGGCAGATGgtgagtcaac ... tgccttgcagGTTTGCTGGACGGCAAATCCATGCGAGCGAAGACGATGGCTCTGTTAACCA
EST: gi|148994719|gb|EE034216.2|EE034216
EST:     AAAGACAGGAAAGATGGTGCCAAATGCATAGAGAAGATGAACGGCAGATG                         GTTTGCTGGACGGCAAATCCATGCGAGCGAAGACGATGGCTCTGTTAACCA
genomic: AAAGACAGGAAAGATGGTGCCAAATGCATAGAGAAGATGAACGGCAGATGgtgagtcaac ... tgccttgcagGTTTGCTGGACGGCAAATCCATGCGAGCGAAGACGATGGCTCTGTTAACCA
EST: gi|31350522|gb|CD434879.1|CD434879
EST:     AAAGACAGGAAAGATGGTGCCAAATGCATAGAGAAGATGAACGGCAGATG                         GTTTGCTGGACGGCAAATCCATGCGAGCGAAGACGATGGCTCTGTTAACCA
genomic: AAAGACAGGAAAGATGGTGCCAAATGCATAGAGAAGATGAACGGCAGATGgtgagtcaac ... tgccttgcagGTTTGCTGGACGGCAAATCCATGCGAGCGAAGACGATGGCTCTGTTAACCA
EST: gi|211350120|gb|FL467182.1|FL467182
EST:     AAAGACAGGAAAGATGGTGCCAAATGCATAGAGAAGATGAACGGCAGATG                         GTTTGCTGGACGGCAAATCCATGCGAGCGAAGACGATGGCTCTGTTAACCA
genomic: AAAGACAGGAAAGATGGTGCCAAATGCATAGAGAAGATGAACGGCAGATGgtgagtcaac ... tgccttgcagGTTTGCTGGACGGCAAATCCATGCGAGCGAAGACGATGGCTCTGTTAACCA
EST: gi|76909702|gb|DV163492.1|DV163492
EST:     AAAGACAGGAAAGATGGTGCCAAATGCATAGAGAAGATGAACGGCAGATG                         GTTTGCTGGACGGCAAATCCATGCGAGCGAAGACGATGGCTCTGTTAACCA
genomic: AAAGACAGGAAAGATGGTGCCAAATGCATAGAGAAGATGAACGGCAGATGgtgagtcaac ... tgccttgcagGTTTGCTGGACGGCAAATCCATGCGAGCGAAGACGATGGCTCTGTTAACCA
EST: gi|86471788|gb|DY238158.1|DY238158
EST:     AAAGACAGGAAAGATGGTGCCAAATGCATAGAGAAGATGAACGGCAGATG                         GTTTGCTGGACGGCAAATCCATGCGAGCGAAGACGATGGCTCTGTTAACCA
genomic: AAAGACAGGAAAGATGGTGCCAAATGCATAGAGAAGATGAACGGCAGATGgtgagtcaac ... tgccttgcagGTTTGCTGGACGGCAAATCCATGCGAGCGAAGACGATGGCTCTGTTAACCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgcgcctaaattgatctgttctgataacatttgtccttatttcttgccttgcagGTTTGCTGGACGGCAAATCCATGCGAGCGAAGACGATGGCTCTGTTAACCATGCTCTTATCCGTGATTACGACGCGGAGGTGTCAAGGCTGGATCGATTT
                      tgataac  putative branch site (score: 2)
                              tttgtccttatttctt  CT-rich tract
       taaattgat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gcttgtctacacgtaggatagaacatagaaggtcatctagtgtttatgcgcctaaattgatctgttctgataacatttgtccttatttcttgccttgcagGTTTGCTGGACGGCAAATCCATGCGAGCGAAGACGATGGCTCTGTTAACCATGCTCTTATCCGTGATTACGACGCGGAGGTGTCAAGGCTGGATCGATTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA