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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTTCAATTCATGAACCCTGGCATGGAGGATGATCCAACTTGTGGTCCTATCCTAGACAACGTTGCCGTCAAGAAGCTCTTCACCCCAGACAAACCAAAGGgtatgagacttattagaagttaacacaaaattgcaatttcattccagctgtgtgttatggttgatttcagcaaagtcttgcacaatctgaagtgttctagctcatttcttaggctatgagatgttgtttctgttgtcaacag

Basic information

species Zea mays
transcript GRMZM2G324705_T01
intron # 3
splice site 5'
intron type U2

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|211517288|gb|FL110063.1|FL110063
EST:     CCTAGACAACGTTGCAGTCAAGAAGCTCTTCACCCCAGACAAACCAAAGG                         ATAACGTGGTGCTGAATGGAGACTTTGAGGAGGGTCCATGGATGTTCCCGA
genomic: CCTAGACAACGTTGCCGTCAAGAAGCTCTTCACCCCAGACAAACCAAAGGgtatgagact ... ttgtcaacagATAACGTGGTGCTGAATGGAGACTTTGAGGAGGGTCCATGGATGTTCCCCA
EST: gi|211517289|gb|FL110064.1|FL110064
EST:     CCTAGACAACGTTGCAGTCAAGAAGCTCTTCACCCCAGACAAACCAAAGG                         ATAACGTGGTGCTGAATGGAGACTTTGAGGAGGGTCCATGGATGTTCCCGA
genomic: CCTAGACAACGTTGCCGTCAAGAAGCTCTTCACCCCAGACAAACCAAAGGgtatgagact ... ttgtcaacagATAACGTGGTGCTGAATGGAGACTTTGAGGAGGGTCCATGGATGTTCCCCA
EST: gi|31612031|gb|CD568653.1|CD568653
EST:     CCTAGACAACGTTGCCGTCAAGAAGCTCTTCACCCCAGACAAACCAAAGG                         ATAACGTGGTGCTGAATGGAGACTTTGAGGAGGGTCCATGGATGTTCCCCA
genomic: CCTAGACAACGTTGCCGTCAAGAAGCTCTTCACCCCAGACAAACCAAAGGgtatgagact ... ttgtcaacagATAACGTGGTGCTGAATGGAGACTTTGAGGAGGGTCCATGGATGTTCCCCA
EST: gi|211517286|gb|FL110061.1|FL110061
EST:     CCTAGACAACGTTGCAGTCAAGAAGCTCTTCACCCCAGACAAACCAAAGG                         ATAACGTGGTGCTGAATGGAGACTTTGAGGAGGGTCCATGGATGTTCCCGA
genomic: CCTAGACAACGTTGCCGTCAAGAAGCTCTTCACCCCAGACAAACCAAAGGgtatgagact ... ttgtcaacagATAACGTGGTGCTGAATGGAGACTTTGAGGAGGGTCCATGGATGTTCCCCA
EST: gi|9953009|gb|BE639592.1|BE639592
EST:     CCTAGACAACGTTGCCGTCAAGAAGCTCTTCACCCCAGACAAACCAAAGG                         ATAACGTGGTGCTGAATGGAGACTTTGAGGAGGGTCCATGGATGTTCCCCA
genomic: CCTAGACAACGTTGCCGTCAAGAAGCTCTTCACCCCAGACAAACCAAAGGgtatgagact ... ttgtcaacagATAACGTGGTGCTGAATGGAGACTTTGAGGAGGGTCCATGGATGTTCCCCA
EST: gi|26456647|gb|CA828230.1|CA828230
EST:     CCTAGACAACGTTGCCGTCAAGAAGCTCTTCACCCCAGACAAACCAAAGG                         ATAACGTGGTGCTGAATGGAGACTTTGAGGAGGGTCCATGGATGTTCCCCA
genomic: CCTAGACAACGTTGCCGTCAAGAAGCTCTTCACCCCAGACAAACCAAAGGgtatgagact ... ttgtcaacagATAACGTGGTGCTGAATGGAGACTTTGAGGAGGGTCCATGGATGTTCCCCA
EST: gi|22936026|gb|BU572301.1|BU572301
EST:     CCTAGACAACGTTGCCGTCAAGAAGCTCTTCACCCCAGACAAACCAAAGG                         ATAACGTGGTGCTGAATGGAGACTTTGAGGAGGGTCCATGGATGTTCCCCA
genomic: CCTAGACAACGTTGCCGTCAAGAAGCTCTTCACCCCAGACAAACCAAAGGgtatgagact ... ttgtcaacagATAACGTGGTGCTGAATGGAGACTTTGAGGAGGGTCCATGGATGTTCCCCA
EST: gi|211517279|gb|FL110054.1|FL110054
EST:     CCTAGACAACGTTGCAGTCAAGAAGCTCTTCACCCCAGACAAACCAAAGG                         ATAACGTGGTGCTGAATGGAGACTTTGAGGAGGGTCCATGGATGTTCCCGA
genomic: CCTAGACAACGTTGCCGTCAAGAAGCTCTTCACCCCAGACAAACCAAAGGgtatgagact ... ttgtcaacagATAACGTGGTGCTGAATGGAGACTTTGAGGAGGGTCCATGGATGTTCCCCA
EST: gi|32929381|gb|CF034193.1|CF034193
EST:     CCTAGACAACGTTGCCGTCAAGAAGCTCTTCACCCCAGACAAACCAAAGG                         ATAACGTGGTGCTGAATGGAGACTTTGAGGAGGGTCCATGGATGTTCCCCA
genomic: CCTAGACAACGTTGCCGTCAAGAAGCTCTTCACCCCAGACAAACCAAAGGgtatgagact ... ttgtcaacagATAACGTGGTGCTGAATGGAGACTTTGAGGAGGGTCCATGGATGTTCCCCA
EST: gi|9953202|gb|BE639785.1|BE639785
EST:     CCTAGACAACGTTGCCGTCAAGAAGCTCTTCACCCCAGACAAACCAAAGG                         ATAACGTGGTGCTGAATGGAGACTTTGAGGAGGGTCCATGGATGTTCCCCA
genomic: CCTAGACAACGTTGCCGTCAAGAAGCTCTTCACCCCAGACAAACCAAAGGgtatgagact ... ttgtcaacagATAACGTGGTGCTGAATGGAGACTTTGAGGAGGGTCCATGGATGTTCCCCA
EST: gi|211517285|gb|FL110060.1|FL110060
EST:     CCTAGACAACGTTGCAGTCAAGAAGCTCTTCACCCCAGACAAACCAAAGG                         ATAACGTGGTGCTGAATGGAGACTTTGAGGAGGGTCCATGGATGTTCCCGA
genomic: CCTAGACAACGTTGCCGTCAAGAAGCTCTTCACCCCAGACAAACCAAAGGgtatgagact ... ttgtcaacagATAACGTGGTGCTGAATGGAGACTTTGAGGAGGGTCCATGGATGTTCCCCA
EST: gi|20508161|gb|BQ279917.1|BQ279917
EST:     CCTAGACAACGTTGCCGTCAAGAAGCTCTTCACCCCAGACAAACCAAAGG                         ATAACGTGGTGCTGAATGGAGACTTTGAGGAGGGTCCATGGATGTTCCCCA
genomic: CCTAGACAACGTTGCCGTCAAGAAGCTCTTCACCCCAGACAAACCAAAGGgtatgagact ... ttgtcaacagATAACGTGGTGCTGAATGGAGACTTTGAGGAGGGTCCATGGATGTTCCCCA
EST: gi|211517282|gb|FL110057.1|FL110057
EST:     CCTAGACAACGTTGCAGTCAAGAAGCTCTTCACCCCAGACAAACCAAAGG                         ATAACGTGGTGCTGAATGGAGACTTTGAGGAGGGTCCATGGATGTTCCCGA
genomic: CCTAGACAACGTTGCCGTCAAGAAGCTCTTCACCCCAGACAAACCAAAGGgtatgagact ... ttgtcaacagATAACGTGGTGCTGAATGGAGACTTTGAGGAGGGTCCATGGATGTTCCCCA
EST: gi|211517278|gb|FL110053.1|FL110053
EST:     CCTAGACAACGTTGCAGTCAAGAAGCTCTTCACCCCAGACAAACCAAAGG                         ATAACGTGGTGCTGAATGGAGACTTTGAGGAGGGTCCATGGATGTTCCCGA
genomic: CCTAGACAACGTTGCCGTCAAGAAGCTCTTCACCCCAGACAAACCAAAGGgtatgagact ... ttgtcaacagATAACGTGGTGCTGAATGGAGACTTTGAGGAGGGTCCATGGATGTTCCCCA
EST: gi|211517287|gb|FL110062.1|FL110062
EST:     CCTAGACAACGTTGCAGTCAAGAAGCTCTTCACCCCAGACAAACCAAAGG                         ATAACGTGGTGCTGAATGGAGACTTTGAGGAGGGTCCATGGATGTTCCCGA
genomic: CCTAGACAACGTTGCCGTCAAGAAGCTCTTCACCCCAGACAAACCAAAGGgtatgagact ... ttgtcaacagATAACGTGGTGCTGAATGGAGACTTTGAGGAGGGTCCATGGATGTTCCCCA
EST: gi|211517284|gb|FL110059.1|FL110059
EST:     CCTAGACAACGTTGCAGTCAAGAAGCTCTTCACCCCAGACAAACCAAAGG                         ATAACGTGGTGCTGAATGGAGACTTTGAGGAGGGTCCATGGATGTTCCCGA
genomic: CCTAGACAACGTTGCCGTCAAGAAGCTCTTCACCCCAGACAAACCAAAGGgtatgagact ... ttgtcaacagATAACGTGGTGCTGAATGGAGACTTTGAGGAGGGTCCATGGATGTTCCCCA
EST: gi|211517283|gb|FL110058.1|FL110058
EST:     CCTAGACAACGTTGCAGTCAAGAAGCTCTTCACCCCAGACAAACCAAAGG                         ATAACGTGGTGCTGAATGGAGACTTTGAGGAGGGTCCATGGATGTTCCCGA
genomic: CCTAGACAACGTTGCCGTCAAGAAGCTCTTCACCCCAGACAAACCAAAGGgtatgagact ... ttgtcaacagATAACGTGGTGCTGAATGGAGACTTTGAGGAGGGTCCATGGATGTTCCCCA

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 4 RNA-Seq libraries.


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 33

CTTCAATTCATGAACCCTGGCATGGAGGATGATCCAACTTGTGGTCCTATCCTAGACAACGTTGCCGTCAAGAAGCTCTTCACCCCAGACAAACCAAAGGgtatgagact ... ttgtcaacagATAACGTGGTGCTGAATGGAGACTTTGAGGAGGGTCCATGGATGTTCCCCAACACGAGCTTCGGCGTGCTGCTCCCAACTAACCTTGACGAGCAAACGTC


Block sizes: 49 (upstream exon), 8 (downstream exon)
Score: 10

CTTCAATTCATGAACCCTGGCATGGAGGATGATCCAACTTGTGGTCCTATCCTAGACAACGTTGCCGTCAAGAAGCTCTTCACCCCAGACAAACCAAAGGgtatgagact ... ttgtcaacagATAACGTGGTGCTGAATGGAGACTTTGAGGAGGGTCCATGGATGTTCCCCAACACGAGCTTCGGCGTGCTGCTCCCAACTAACCTTGACGAGCAAACGTC


Block sizes: 42 (upstream exon), 8 (downstream exon)
Score: 1

CTTCAATTCATGAACCCTGGCATGGAGGATGATCCAACTTGTGGTCCTATCCTAGACAACGTTGCCGTCAAGAAGCTCTTCACCCCAGACAAACCAAAGGgtatgagact ... ttgtcaacagATAACGTGGTGCTGAATGGAGACTTTGAGGAGGGTCCATGGATGTTCCCCAACACGAGCTTCGGCGTGCTGCTCCCAACTAACCTTGACGAGCAAACGTC


Block sizes: 47 (upstream exon), 9 (downstream exon)
Score: 17

CTTCAATTCATGAACCCTGGCATGGAGGATGATCCAACTTGTGGTCCTATCCTAGACAACGTTGCCGTCAAGAAGCTCTTCACCCCAGACAAACCAAAGGgtatgagact ... ttgtcaacagATAACGTGGTGCTGAATGGAGACTTTGAGGAGGGTCCATGGATGTTCCCCAACACGAGCTTCGGCGTGCTGCTCCCAACTAACCTTGACGAGCAAACGTC


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTTCAATTCATGAACCCTGGCATGGAGGATGATCCAACTTGTGGTCCTATCCTAGACAACGTTGCCGTCAAGAAGCTCTTCACCCCAGACAAACCAAAGGgtatgagacttattagaagttaacacaaaattgcaatttcattccagctgtgtgttatggttgatttcagcaaagtcttgcacaatctgaagtgttctagctcatttcttaggctatgagatgttgtttctgttgtcaacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC