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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCCTGCTTCTCCGACCTCGAGGAGCGCCAGGTCGTGCGCGTCCAGGGCACCGATCGGGCCCGCCGAACCATCGTCCGTGTCGTCGGCAAGTTCTTCCCGGgtgcgcgaatcggccacgtatttgctccccttacagctgcagttgctcggtcaggcgtggattgctatgaaaaaaaaaaatgaatagaatgagatttaat...

Basic information

species Zea mays
transcript GRMZM2G129108_T01
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G129108_T01 (Zea mays), 5'ss of exon 1
lower sequence: LOC_Os01g71980.2 (Oryza sativa), 5'ss of exon 1
GCCTGCTTCTCCGACCTCGAGGAGCGCCAGGTCGTGCGCGTCCAGGGCACCGATCGGGCCCGCCGAACCATCGTCCGTGTCGTCGGCAAGTTCTTCCCGGgtgcgcgaatcggccacgtatttgctccccttacagctgcagttgctcggtcagg------cgtggattgctatgaaaaaaaaaaatgaatagaatgagatttaat
|    ||||||||||||||| |||| ||||||||| |||||||||||||||||  ||||| |  |   ||||||||| |||||||||| ||||||||| ||||||| || || || | | |   | || ||     |    || |||   ||||       ||||| |  ||     |   |   || |      || |       
GAGGACTTCTCCGACCTCGAAGAGCTCCAGGTCGTCCGCGTCCAGGGCACCGACAGGGCCGGGAGGCGCATCGTCCGCGTCGTCGGCAGGTTCTTCCCTGgtgcgccaaacgccctcttctccccacctctcctttcctttgtggctttatcagattggatcgtggttcccttctggatgtatctatcatctatgtgggt------
















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|78089554|gb|DV517928.1|DV517928
EST:     CGATCGGGCCCGCCGAACCATCGTCCGTGTCGTCGGCAAGTTCTTCCCGG                         CTCCAGCAATTGACGGTGAACGTCTGAAAAAGTATGTGTTCTACAAACTCC
genomic: CGATCGGGCCCGCCGAACCATCGTCCGTGTCGTCGGCAAGTTCTTCCCGGgtgcgcgaat ... tggtttccagCTCCAGCAATTGACGGTGAACGTCTGAAAAAGTATGTGTTCTACAAACTCC
EST: gi|211401308|gb|FL085284.1|FL085284
EST:     GATTCGGGCCCGCCGAACCATCGTCCGCGTCGTCGGCAAGTTCTTCCCGG                         CTCCAGCAATTGACGGTGAACGTCTGAAAAAGTATGTGTTCTACAAACTCC
genomic: GA-TCGGGCCCGCCGAACCATCGTCCGTGTCGTCGGCAAGTTCTTCCCGGgtgcgcgaat ... tggtttccagCTCCAGCAATTGACGGTGAACGTCTGAAAAAGTATGTGTTCTACAAACTCC
EST: gi|148987287|gb|EE031124.2|EE031124
EST:     CGATCGGGCCCGCCGAACCATCGTCCGTGTCGTCGGCAAGTTCTTCCCGG                         CTCCAGCAATTGACGGTGAACGTCTGAAAAAGTATGTGTTCTACAAACTCC
genomic: CGATCGGGCCCGCCGAACCATCGTCCGTGTCGTCGGCAAGTTCTTCCCGGgtgcgcgaat ... tggtttccagCTCCAGCAATTGACGGTGAACGTCTGAAAAAGTATGTGTTCTACAAACTCC
EST: gi|14242939|gb|BG840278.2|BG840278
EST:     CGGGCCCGCCGAA-CATCGTCCGTGTCGTCGGCAAGTTCTTCCCGG                         CTCCAGCAATTGACGGTGAACGTCTGAAAAAGTATGTGTTCTACAAACTCC
genomic: CGGGCCCGCCGAACCATCGTCCGTGTCGTCGGCAAGTTCTTCCCGGgtgcgcgaat ... tggtttccagCTCCAGCAATTGACGGTGAACGTCTGAAAAAGTATGTGTTCTACAAACTCC
EST: gi|149088239|gb|EE177344.2|EE177344
EST:     CGATCGGGCCCGCCGAACCATCGTCCGTGTCGTCGGCAAGTTCTTCCCGG                         CTCCAGCAATTGACGGTGAACGTCTGAAAAAGTATGTGTTCTACAAACTCC
genomic: CGATCGGGCCCGCCGAACCATCGTCCGTGTCGTCGGCAAGTTCTTCCCGGgtgcgcgaat ... tggtttccagCTCCAGCAATTGACGGTGAACGTCTGAAAAAGTATGTGTTCTACAAACTCC
EST: gi|148987286|gb|EE031123.2|EE031123
EST:     CGATCGGGCCCGCCGAACCATCGTCCGTGTCGTCGGCAAGTTCTTCCCGG                         CTCCAGCAATTGACGGTGAACGTCTGAAAAAGTATGTGTTCTACAAACTCC
genomic: CGATCGGGCCCGCCGAACCATCGTCCGTGTCGTCGGCAAGTTCTTCCCGGgtgcgcgaat ... tggtttccagCTCCAGCAATTGACGGTGAACGTCTGAAAAAGTATGTGTTCTACAAACTCC
EST: gi|71772295|gb|DR970231.1|DR970231
EST:     CGATCGGGCCCGCCGAACCATCGTCCGTGTCGTCGGCAAGTTCTTCCCGG                         CTCCAGCAATTGACGGTGAACGTCTGAAAAAGTATGTGTTCTACAAACTCC
genomic: CGATCGGGCCCGCCGAACCATCGTCCGTGTCGTCGGCAAGTTCTTCCCGGgtgcgcgaat ... tggtttccagCTCCAGCAATTGACGGTGAACGTCTGAAAAAGTATGTGTTCTACAAACTCC

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
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---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCCTGCTTCTCCGACCTCGAGGAGCGCCAGGTCGTGCGCGTCCAGGGCACCGATCGGGCCCGCCGAACCATCGTCCGTGTCGTCGGCAAGTTCTTCCCGGgtgcgcgaatcggccacgtatttgctccccttacagctgcagttgctcggtcaggcgtggattgctatgaaaaaaaaaaatgaatagaatgagatttaat

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- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gaatagaa