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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTATATACATTTTGATTTCCATCATGTTTGTCGTGGAGGTAACTTTGACAATTTGCAAGCTCTCTACAATCAAATTGAGGAAGCTATTCATAAGCAAGGgtaatttttaaatatctaacatttcatgcttactttttttcctaagcacactgctttaagatttatattcataactaaaggtttaactgtggcaagtaatttgcttttgcttattttctgggccagctgagcag

Basic information

species Zea mays
transcript GRMZM2G047894_T01
intron # 13
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G047894_T01 (Zea mays), 5'ss of exon 13
lower sequence: LOC_Os03g18080.2 (Oryza sativa), 5'ss of exon 13
GTATATACATTTTGATTTCCATCATGTTTGTCGTGGAGGTAACTTTGACAATTTGCAAGCTCTCTACAATCAAATTGAGGAAGCTATTCATAAGCAAGGgtaatttttaaatatct----------aacatttcatgctta-ctttttttcctaagcacactgctttaagatttatattcataactaaaggtttaactgtggcaagtaatttgcttttgcttattttctgggccagctgagcag
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GTATGTGCATTTTGATTTCCATCATATCTGTCGTGGAGGGAACTTTGATAATCTGCAAGTTCTATACAATCAAATTGAAGAAGCTATTCAGAAACAAGGgtaatttttaaacacctttaaatagccaacattt-acgcttatctcttgttcctgatgagactactttaagatttatttcaactactgaaggtttaactatggcaagtaatttgctcttgattaatttcggggccagctgagcag
















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|31348859|gb|CD433216.1|CD433216
EST:     AATTTGCAAGCTCTCTACAATCAAATTGAGGAAGCTATTCATAAGCAAGGCTGAGCAG                  
genomic: AATTTGCAAGCTCTCTACAATCAAATTGAGGAAGCTATTCATAAGC-A-----AG--Ggtaattttta ... agc
EST: gi|40335862|gb|CK369932.1|CK369932
EST:     AATTTGCAAGCTCTCTACAATCAAATTGAGGAAGCTATTCATAAGCAAGG                         C
genomic: AATTTGCAAGCTCTCTACAATCAAATTGAGGAAGCTATTCATAAGCAAGGgtaattttta ... agctgagcag-
EST: gi|40335862|gb|CK369932.1|CK369932
EST:     AATTTGCAAGCTCTCTACAATCAAATTGAGGAAGCTATTCATAAGCAAGG                         C
genomic: AATTTGCAAGCTCTCTACAATCAAATTGAGGAAGCTATTCATAAGCAAGGgtaattttta ... agctgagcag-
EST: gi|40335862|gb|CK369932.1|CK369932
EST:     AATTTGCAAGCTCTCTACAATCAAATTGAGGAAGCTATTCATAAGCAAGG                         C
genomic: AATTTGCAAGCTCTCTACAATCAAATTGAGGAAGCTATTCATAAGCAAGGgtaattttta ... agctgagcag-
EST: gi|40335862|gb|CK369932.1|CK369932
EST:     AATTTGCAAGCTCTCTACAATCAAATTGAGGAAGCTATTCATAAGCAAGG                         C
genomic: AATTTGCAAGCTCTCTACAATCAAATTGAGGAAGCTATTCATAAGCAAGGgtaattttta ... agctgagcag-
EST: gi|71311517|gb|DR792122.1|DR792122
EST:     AATTTGCAAGCTCTCTACAATCAAATTGAGGAAGCTATTCATAAGCAAGG                         ATATTTTCTTATGAACACTAAAGGAGAGATTTTGCTGGAGCAAAGTGGTGT
genomic: AATTTGCAAGCTCTCTACAATCAAATTGAGGAAGCTATTCATAAGCAAGGgtaattttta ... agctgagcagATATTTTCTTATGAACACTAAAGGAGAGATTTTGCTGGAGCAAAGTGGTGT
EST: gi|5296286|gb|AI783056.1|AI783056
EST:     AATTTGCAAGCTCTCTACAATCAAATTGAGGAAGCTATTCATAAGCAAGGCTGAGCAG                  
genomic: AATTTGCAAGCTCTCTACAATCAAATTGAGGAAGCTATTCATAAGC-A-----AG--Ggtaattttta ... agc
EST: gi|5846902|gb|AI999985.1|AI999985
EST:     AATTTGCAAGCTCTCTACAATCAAATTGAGGAAGCTATTCATAAGCAAGGCTGAGCAG                  
genomic: AATTTGCAAGCTCTCTACAATCAAATTGAGGAAGCTATTCATAAGC-A-----AG--Ggtaattttta ... agc
EST: gi|60343346|gb|DN210319.1|DN210319
EST:     AATTTGCAAGCTCTCTACAATCAAATTGAGGAAGCTATTCATAAGCAAGGCTGAGCAG                  
genomic: AATTTGCAAGCTCTCTACAATCAAATTGAGGAAGCTATTCATAAGC-A-----AG--Ggtaattttta ... agc

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTATATACATTTTGATTTCCATCATGTTTGTCGTGGAGGTAACTTTGACAATTTGCAAGCTCTCTACAATCAAATTGAGGAAGCTATTCATAAGCAAGGgtaatttttaaatatctaacatttcatgcttactttttttcctaagcacactgctttaagatttatattcataactaaaggtttaactgtggcaagtaatttgcttttgcttattttctgggccagctgagcag

- - - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG