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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GACAGCTGGTTTCACTACCTTTCCTGATTACCTTGTGCTGCACATGCGTAAGTTTGTAATGGAAACAGGATGGGTGCCAAAGAAACTCGgtaataccctccttgccatttatttgagcataaatgctgcatattgaaataaaggtattcaaatccattagagactgctttcatagagcttcgggcatgc...

Basic information

species Zea mays
transcript GRMZM2G107696_T02
intron # 18
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G107696_T02 (Zea mays), 5'ss of exon 18
lower sequence: LOC_Os01g08200.1 (Oryza sativa), 5'ss of exon 14
GACAGCTGGTTTCACTACCTTTCCTGATTACCTTGTGCTGCACATGCGTAAGTTTGTAATGGAAACAGGATGGGTGCCAAAGAAACTCGgtaataccctcct----tgccatttatttgagcataaatgctg----catattgaaataaaggtattcaaatccattagagactgctttcatagagcttcgggcatgc
||| ||||| || |  || |||||||||||||| ||| |||| ||||| ||||||||||||||| |||||||||||||||||||||| ||||||  ||   |    || || || | |   |||   |||||     | |||  ||||   |     || |  ||    ||||| |||| |  |    |        
GACTGCTGGCTTTAAAACATTTCCTGATTACCTGGTGTTGCAGATGCGCAAGTTTGTAATGGAAGCAGGATGGGTGCCAAAGAAACTAGgtaatgtccctatcaagtgtcagttgtctct-catgtgtgctgactctagattcgaatagttgccccaaactgtatggcggactgatttcctgaaagaact-------
















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|116817395|gb|EC860237.1|EC860237
EST:     CAAAGAAACTCG                         ATGTGTATATAGATGTGCCAGATACAATTGATATCACACATATGCGCAGC-
genomic: CAAAGAAACTCGgtaataccct ... tttttcacagATGTTTATATAGATGTGCCAGATACAATTGATATCACACATATGCGCAGCA
EST: gi|211494928|gb|FL217185.1|FL217185
EST:     GCACATGCGTAAGTTTGTAATGGAAACAGGATGGGTGCCAAAGAAACTCG                         ATGTGTATATAGATGTGCCAGATACAATTGATATCACACATATGCGCAGCA
genomic: GCACATGCGTAAGTTTGTAATGGAAACAGGATGGGTGCCAAAGAAACTCGgtaataccct ... tttttcacagATGTTTATATAGATGTGCCAGATACAATTGATATCACACATATGCGCAGCA
EST: gi|71330491|gb|DR802012.1|DR802012
EST:     GCACATGCGTAAGTTTGTAATGGAAACAGGATGGGTGCCAAAGAAACTCG                         ATGTTTATATAGATGTGCCAGATATCA-TTGATATCACACATA
genomic: GCACATGCGTAAGTTTGTAATGGAAACAGGATGGGTGCCAAAGAAACTCGgtaataccct ... tttttcacagATGTTTATATAGATGTGCCAGATA-CAATTGATATCACACATA
EST: gi|31361116|gb|CD445473.1|CD445473
EST:     GCACATGCGTAAGTTTGTAATGGAAACAGGATGGGTGCCAAAGAAACTCG                         ATGTTTATATAGATGTGCCAGATACAATTGATATCACACATATGCGCAGCA
genomic: GCACATGCGTAAGTTTGTAATGGAAACAGGATGGGTGCCAAAGAAACTCGgtaataccct ... tttttcacagATGTTTATATAGATGTGCCAGATACAATTGATATCACACATATGCGCAGCA
EST: gi|149014867|gb|EE044578.2|EE044578
EST:     GGTGCCAAAAGAAACTCG                         ATGTTTATATAGATGTGCCAGATACAATTGATATCACACATATGCGCAGCA
genomic: GGTGCC-AAAGAAACTCGgtaataccct ... tttttcacagATGTTTATATAGATGTGCCAGATACAATTGATATCACACATATGCGCAGCA
EST: gi|71595705|gb|DR906456.1|DR906456
EST:     GCACATGCGTAAGTTTGTAATGGAAACAGGATGGGTGCCAAAGAAACTCG                         ATGTTTATATAGATGTGCCAGATACAATTGATATCACACATATGCGCAGCA
genomic: GCACATGCGTAAGTTTGTAATGGAAACAGGATGGGTGCCAAAGAAACTCGgtaataccct ... tttttcacagATGTTTATATAGATGTGCCAGATACAATTGATATCACACATATGCGCAGCA
EST: gi|20300736|gb|BQ163679.1|BQ163679
EST:     GCACATGCGTAAGTTTGTAATGGAAACAGGATGGGTGCCAAAGAAACTCG                         ATGGTTATATAGATGTGCCAGATACAATTGATATCACACATATGCGCAGCA
genomic: GCACATGCGTAAGTTTGTAATGGAAACAGGATGGGTGCCAAAGAAACTCGgtaataccct ... tttttcacagATGTTTATATAGATGTGCCAGATACAATTGATATCACACATATGCGCAGCA
EST: gi|44682206|gb|CK787254.1|CK787254
EST:     GCACATGCGTAAGTTTGTAATGGAAACAGGATGGGTGCCAAAGAAACTCG                         ATGTTTATATAGATGTGCCAGATACAATTGATATCACACATATGCGCAGCA
genomic: GCACATGCGTAAGTTTGTAATGGAAACAGGATGGGTGCCAAAGAAACTCGgtaataccct ... tttttcacagATGTTTATATAGATGTGCCAGATACAATTGATATCACACATATGCGCAGCA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GACAGCTGGTTTCACTACCTTTCCTGATTACCTTGTGCTGCACATGCGTAAGTTTGTAATGGAAACAGGATGGGTGCCAAAGAAACTCGgtaataccctccttgccatttatttgagcataaatgctgcatattgaaataaaggtattcaaatccattagagactgctttcatagagcttcgggcatgc

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA