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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCGTGTCGGTAACATAGTTTGGATTCGAGAGAATGAAGAAGTACCATGTGATCTTGTTTTGTTGGGAACTTCTGAACCACAAGGCATCTGTCATGTTGAGgtaaataaatgctgtaaccccgccacaccttctgtctgtttgtattgtgcttggtttgctcaggaaataactttgctgtattggccatgtggggcatttc...

Basic information

species Zea mays
transcript GRMZM2G411940_T01
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G411940_T01 (Zea mays), 5'ss of exon 6
lower sequence: LOC_Os11g25980.1 (Oryza sativa), 5'ss of exon 4
CCGTGTCGGTAACATAGTTTGGATTCGAGAGAATGAAGAAGTACCATGTGATCTTGTTTTGTTGGGAACTTCTGAACCACAAGGCATCTGTCATGTTGAGgtaaataaatgctgtaaccccgccacaccttctgtctgtttgtattgtgcttggtttgc-tcaggaaataactttgctgtattggccatgtggggcatttc-
 ||||| ||||| ||||| ||||||||||| ||||| |||||||||||||| |||||| || | |||||||| ||  | |||||||| || |||||||||||||   |    || |    |   | |  ||    |  |   | |  ||| ||  |    ||| |  |  || |   | | ||  | |  |  |   |||| 
TCGTGTTGGTAATATAGTATGGATTCGAGAAAATGAGGAAGTACCATGTGACCTTGTTCTGATAGGAACTTCCGACTCGCAAGGCATTTGCCATGTTGAGgtaagacatgaatgaatagactaaaaatgtttaacccctacatttgttgcatgactgatatcaagtgaacacctatttttctt--caaactaagaattttct
















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|91057078|gb|EB167496.1|EB167496
EST:     ATCTTGTTTTGTTGGGAACTTCTGAACCACAAGGCATCTGTCATGTTGAG                         ACAGCTGCTCTTGATGGGGAAATTGATTTGAAGACAAGAGCAAGCCCACCA
genomic: ATCTTGTTTTGTTGGGAACTTCTGAACCACAAGGCATCTGTCATGTTGAGgtaaataaat ... atgtttgtagACAGCTGCTCTTGATGGGGAAATTGATTTGAAGACAAGAGCAAGCCCACCA




















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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---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CCGTGTCGGTAACATAGTTTGGATTCGAGAGAATGAAGAAGTACCATGTGATCTTGTTTTGTTGGGAACTTCTGAACCACAAGGCATCTGTCATGTTGAGgtaaataaatgctgtaaccccgccacaccttctgtctgtttgtattgtgcttggtttgctcaggaaataactttgctgtattggccatgtggggcatttc

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ccccgcc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ggaaataa