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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCATTTTCAGTTATTGCGAATTCACCTCTACGTATTGATCTCTCGTGTGTCCTGGATCATGTTGTTTCTGAGCTCACAGCTTTCCTTCGCAAGgtacttgcatagttgcatggatctttgttgccttcatttgatttttattttctctgaaaagcatagcaaagagcaagataatgccttcattttctctctcttatgtaacag

Basic information

species Zea mays
transcript GRMZM2G168629_T05
intron # 18
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G168629_T04 (Zea mays), 5'ss of exon 18
lower sequence: LOC_Os02g07120.1 (Oryza sativa), 5'ss of exon 18
GCATTTTCAGTTATTGCGAATTCACCTCTACGTATTGATCTCTCGTGTGTCCTGGATCATGTTGTTTCTGAGCTCACAGCTTTCCTTCGCAAGgtacttgcatagttgcatggatctttgttgcc-ttcatttgatttttattttctctgaaaagcatagcaaagagcaagataatgccttcattttctctctcttatgt-aacag
|| ||| |||| ||||| || |||||||| || |||||||| ||||||||||| || |||||  ||||||||||||| ||||||||||| ||||||    ||  |||   |   | |||||  |  |||||  ||    | ||||   | | |   ||   ||   |   | ||| |  ||  ||    | |  |||| | |||||
GCGTTTGCAGTGATTGCTAAATCACCTCTTCGCATTGATCTTTCGTGTGTCCTAGACCATGTCATTTCTGAGCTCACGGCTTTCCTTCGAAAGgtatacccagtgtttactttgt-tttgtcacgattcatgggaaaact-ttttaaataacagttatga-aacttgttcgctaa-gttttatttgatgcacatttatttcaacag
















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|18383962|gb|BM417162.1|BM417162
EST:     CGTGTGTCCTGGATCATGTTGNTTCTGAGCTCACAGCTTTCCTTCGCAAG                         GCCAACAGAGCTCTTAGGCAGGCGACGTTGGGAACTCTAAATTCTTTGGTT
genomic: CGTGTGTCCTGGATCATGTTGTTTCTGAGCTCACAGCTTTCCTTCGCAAGgtacttgcat ... tatgtaacagGCCAACAGAGCTCTTAGGCAGGCGACGTTGGGAACTCTAAATTCTTTGGTT
EST: gi|22489194|gb|BU049130.1|BU049130
EST:     CGTGTGTCCTGGATCATGTTGTTTCTGAGCTCACAGCTTTCCTTCGCAAG                         GCCAACAGAGCTCTTAGGCAGGCGACGTTGGGAACTCTAAATTCTTTGGTT
genomic: CGTGTGTCCTGGATCATGTTGTTTCTGAGCTCACAGCTTTCCTTCGCAAGgtacttgcat ... tatgtaacagGCCAACAGAGCTCTTAGGCAGGCGACGTTGGGAACTCTAAATTCTTTGGTT
EST: gi|211432450|gb|FL213954.1|FL213954
EST:     CGTGTGTCCTGGATCATGTTGTTTCTGAGCTCACAGCTTTCCTTCGCAAG                         GCCAACAGAGCTCTTAGGCAGGCGACGTTGGGAACTCTAAATTCTTTGGNT
genomic: CGTGTGTCCTGGATCATGTTGTTTCTGAGCTCACAGCTTTCCTTCGCAAGgtacttgcat ... tatgtaacagGCCAACAGAGCTCTTAGGCAGGCGACGTTGGGAACTCTAAATTCTTTGGTT
EST: gi|32868683|gb|CF008365.1|CF008365
EST:     GTCCTGGATCATGTTGTTTCTGAGCTCACAGCTTTCCTTCGCAAG                         GCCAACAGAGCTCTTAGGCAGGCGACGTTGGGAACTCTAAATTCTTTGGTT
genomic: GTCCTGGATCATGTTGTTTCTGAGCTCACAGCTTTCCTTCGCAAGgtacttgcat ... tatgtaacagGCCAACAGAGCTCTTAGGCAGGCGACGTTGGGAACTCTAAATTCTTTGGTT
EST: gi|87298767|gb|DY470770.1|DY470770
EST:     CGTGTGTCCTGGATCATGTTGTTTCTGAGCTCACAGCTTTCCTTCGCAAG                         GCCAACAGAGCTCTTAGGCAGGCGACGTTGGGAACTCTAAATTCTTTGGTT
genomic: CGTGTGTCCTGGATCATGTTGTTTCTGAGCTCACAGCTTTCCTTCGCAAGgtacttgcat ... tatgtaacagGCCAACAGAGCTCTTAGGCAGGCGACGTTGGGAACTCTAAATTCTTTGGTT
EST: gi|32859371|gb|CD999052.1|CD999052
EST:     CGTGTGTCCTGGATCATGTTGTTTCTGAGCTCACAGCTTTCCTTCGCAAG                         GCCAACAGAGCT
genomic: CGTGTGTCCTGGATCATGTTGTTTCTGAGCTCACAGCTTTCCTTCGCAAGgtacttgcat ... tatgtaacagGCCAACAGAGCT
EST: gi|211432451|gb|FL213955.1|FL213955
EST:     CGTGTGTCCTGGATCATGTTGTTTCTGAGCTCACAGCTTTCCTTCGCAAG                         GCCAACAGAGCTCTTAGGCAGGCGACGTTGGGAACTCTAAATTCTTTGGTT
genomic: CGTGTGTCCTGGATCATGTTGTTTCTGAGCTCACAGCTTTCCTTCGCAAGgtacttgcat ... tatgtaacagGCCAACAGAGCTCTTAGGCAGGCGACGTTGGGAACTCTAAATTCTTTGGTT

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: 48 (upstream exon), 49 (downstream exon)
Score: 377

GCATTTTCAGTTATTGCGAATTCACCTCTACGTATTGATCTCTCGTGTGTCCTGGATCATGTTGTTTCTGAGCTCACAGCTTTCCTTCGCAAGgtacttgcat ... tatgtaacagGCCAACAGAGCTCTTAGGCAGGCGACGTTGGGAACTCTAAATTCTTTGGTTGTCACATATGGTGGTCAGATTGGCTCTTCTTCGTATGAGACAATAATCG


Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 169

GCATTTTCAGTTATTGCGAATTCACCTCTACGTATTGATCTCTCGTGTGTCCTGGATCATGTTGTTTCTGAGCTCACAGCTTTCCTTCGCAAGgtacttgcat ... tatgtaacagGCCAACAGAGCTCTTAGGCAGGCGACGTTGGGAACTCTAAATTCTTTGGTTGTCACATATGGTGGTCAGATTGGCTCTTCTTCGTATGAGACAATAATCG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 180

GCATTTTCAGTTATTGCGAATTCACCTCTACGTATTGATCTCTCGTGTGTCCTGGATCATGTTGTTTCTGAGCTCACAGCTTTCCTTCGCAAGgtacttgcat ... tatgtaacagGCCAACAGAGCTCTTAGGCAGGCGACGTTGGGAACTCTAAATTCTTTGGTTGTCACATATGGTGGTCAGATTGGCTCTTCTTCGTATGAGACAATAATCG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 222

GCATTTTCAGTTATTGCGAATTCACCTCTACGTATTGATCTCTCGTGTGTCCTGGATCATGTTGTTTCTGAGCTCACAGCTTTCCTTCGCAAGgtacttgcat ... tatgtaacagGCCAACAGAGCTCTTAGGCAGGCGACGTTGGGAACTCTAAATTCTTTGGTTGTCACATATGGTGGTCAGATTGGCTCTTCTTCGTATGAGACAATAATCG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCATTTTCAGTTATTGCGAATTCACCTCTACGTATTGATCTCTCGTGTGTCCTGGATCATGTTGTTTCTGAGCTCACAGCTTTCCTTCGCAAGgtacttgcatagttgcatggatctttgttgccttcatttgatttttattttctctgaaaagcatagcaaagagcaagataatgccttcattttctctctcttatgtaacag

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