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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagcatatgatgccatactgttgtgccattgtagttatgtgcatgtatttgtttttggccatcatatatttagatgcgagtgtgacatattactttgaaattgccagGCCAATCTCTTCGTCGCAGCAGGCATCAG

Basic information

species Zea mays
transcript GRMZM2G099980_T02
intron # 5
splice site 3'
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|60349637|gb|DN216610.1|DN216610
EST:     ATGAGGAGGGCACCATTATCGTCAGCTGGGAACCTGCCTCCTATGGGGAG                         GCCAATCTCTTCGTCGCAGCAGGCATCAG
genomic: ATGAGGAGGGCACCATTATCGTCAGCTGGGAACCTGCCTCCTATGGGGAGgtaagcatat ... aaattgccagGCCAATCTCTTCGTCGCAGCAGGCATCAG
EST: gi|5895715|gb|AW036961.1|AW036961
EST:     ATGAGGAGGGCACCATTATCGTCAGCTGGGAACCTGCCTCCTATGGGGAG                         GCCAATCTCTTCGTCGCAGCAGGCATCAG
genomic: ATGAGGAGGGCACCATTATCGTCAGCTGGGAACCTGCCTCCTATGGGGAGgtaagcatat ... aaattgccagGCCAATCTCTTCGTCGCAGCAGGCATCAG
EST: gi|5006225|gb|AI712287.1|AI712287
EST:     ATGAGGAGGGCACCATTATCGTCAGCTGGGAACCTCCCTCCTATGGGGAG                         GCCAATCTCTTCGTCGCAGCAGGCATCAG
genomic: ATGAGGAGGGCACCATTATCGTCAGCTGGGAACCTGCCTCCTATGGGGAGgtaagcatat ... aaattgccagGCCAATCTCTTCGTCGCAGCAGGCATCAG
EST: gi|71428991|gb|DR810041.1|DR810041
EST:     ATGAGGAGGGCACCATTATCGTCAGCTGGGAACCTGCCTCCTATGGGGAG                         GCCAATCTCTTCGTCGCAGCAGGCATCAG
genomic: ATGAGGAGGGCACCATTATCGTCAGCTGGGAACCTGCCTCCTATGGGGAGgtaagcatat ... aaattgccagGCCAATCTCTTCGTCGCAGCAGGCATCAG
EST: gi|33770989|gb|CF273283.1|CF273283
EST:     ATGAGGAGGGCACCATTATCGTCAGCTGGGAACCTGCCTCCTATGGGGAG                         GC-AATCTCTTCGTCGCAGCAGGCATCAG
genomic: ATGAGGAGGGCACCATTATCGTCAGCTGGGAACCTGCCTCCTATGGGGAGgtaagcatat ... aaattgccagGCCAATCTCTTCGTCGCAGCAGGCATCAG
EST: gi|60349938|gb|DN216911.1|DN216911
EST:     ATGAGGAGGGCACCATTATCGTCAGCTGGGAACCTGCCTCCTATGGGGAG                         GCCAATCTCTTCGTCGCAGCAGGCATCAG
genomic: ATGAGGAGGGCACCATTATCGTCAGCTGGGAACCTGCCTCCTATGGGGAGgtaagcatat ... aaattgccagGCCAATCTCTTCGTCGCAGCAGGCATCAG
EST: gi|67033833|gb|CO462582.1|CO462582
EST:     ATGAGGAGGGCACCATTATCGTCAGCTGGGAACCTGCCTCCTATGGGGAG                         GCCAATCTCTTCGTCGCAGCAGGCATCAG
genomic: ATGAGGAGGGCACCATTATCGTCAGCTGGGAACCTGCCTCCTATGGGGAGgtaagcatat ... aaattgccagGCCAATCTCTTCGTCGCAGCAGGCATCAG
EST: gi|71428990|gb|DR810040.1|DR810040
EST:     ATGAGGAGGGCACCATTATCGTCAGCTGGGAACCTGCCTCCTATGGGGAG                         GCCAATCTTTTCGTCGCAGCAGGCATCAG
genomic: ATGAGGAGGGCACCATTATCGTCAGCTGGGAACCTGCCTCCTATGGGGAGgtaagcatat ... aaattgccagGCCAATCTCTTCGTCGCAGCAGGCATCAG
EST: gi|76283944|gb|DV023512.1|DV023512
EST:     ATGAGGAGGGCACCATTATCGTCAGCTGGGAACCTGCCTCCTATGGGGAG                         GCCAATCTCTTCGTCGCAGCAGGCATCAG
genomic: ATGAGGAGGGCACCATTATCGTCAGCTGGGAACCTGCCTCCTATGGGGAGgtaagcatat ... aaattgccagGCCAATCTCTTCGTCGCAGCAGGCATCAG
EST: gi|20513022|gb|BQ280208.1|BQ280208
EST:     ATGAGGAGGGCACCATTATCGTCAGCTGGGAACCTCCCTCCTATGGGGAG                         GCCAATCTCTTCGTCGCAGCAGGCATCAG
genomic: ATGAGGAGGGCACCATTATCGTCAGCTGGGAACCTGCCTCCTATGGGGAGgtaagcatat ... aaattgccagGCCAATCTCTTCGTCGCAGCAGGCATCAG
EST: gi|26457465|gb|CA829048.1|CA829048
EST:     ATGAGGAGGGCACCATTATCGTCAGCTGGGAACCTCCCTCCTATGGGGAG                         GCCAATCTCTTCGTCGCAGCAGGCATCAG
genomic: ATGAGGAGGGCACCATTATCGTCAGCTGGGAACCTGCCTCCTATGGGGAGgtaagcatat ... aaattgccagGCCAATCTCTTCGTCGCAGCAGGCATCAG
EST: gi|71427898|gb|DR808948.1|DR808948
EST:     ATGAGGAGGGCACCATTATCGTCAGCTGGGAACCTGCCTCCTATGGGGAG                         GCCAATCTCTTCGTCGCAGCAGGCATCAG
genomic: ATGAGGAGGGCACCATTATCGTCAGCTGGGAACCTGCCTCCTATGGGGAGgtaagcatat ... aaattgccagGCCAATCTCTTCGTCGCAGCAGGCATCAG
EST: gi|71449093|gb|DR830143.1|DR830143
EST:     ATGAGGAGGGCACCATTATCGTCAGCTGGGAACCTGCCTCCTATGGGGAG                         GCCAATCTCTTCGTCGCAGCAGGCATCAG
genomic: ATGAGGAGGGCACCATTATCGTCAGCTGGGAACCTGCCTCCTATGGGGAGgtaagcatat ... aaattgccagGCCAATCTCTTCGTCGCAGCAGGCATCAG
EST: gi|78025444|gb|DV493831.1|DV493831
EST:     ATGAGGAGGGCACCATTATCGTCAGCTGGGAACCTCCCTCCTATGGGGAG                         GCCAATCTTTTCGTCGCAGCAGGCATCAG
genomic: ATGAGGAGGGCACCATTATCGTCAGCTGGGAACCTGCCTCCTATGGGGAGgtaagcatat ... aaattgccagGCCAATCTCTTCGTCGCAGCAGGCATCAG
EST: gi|78544427|gb|DV621925.1|DV621925
EST:     ATGAGGAGGGCACCATTATCGTCAGCTGGGAACCTCCCTCCTATGGGGAG                         GCCAATCTTTTTGTCGCAGCAGGCATCAG
genomic: ATGAGGAGGGCACCATTATCGTCAGCTGGGAACCTGCCTCCTATGGGGAGgtaagcatat ... aaattgccagGCCAATCTCTTCGTCGCAGCAGGCATCAG
EST: gi|32944273|gb|CF049092.1|CF049092
EST:     ATGAGGAGGGCACCATTATCGTCAGCTGGGAACCTCCCTCCTATGGGGAG                         GCCAATCTCTTCGTCGTAGCAGGCATCAG
genomic: ATGAGGAGGGCACCATTATCGTCAGCTGGGAACCTGCCTCCTATGGGGAGgtaagcatat ... aaattgccagGCCAATCTCTTCGTCGCAGCAGGCATCAG
EST: gi|60359114|gb|DN226087.1|DN226087
EST:     ATGAGGAGGGCACCATTATCGTCAGCTGGGAACCTGCCTCCTATGGGGAG                         GCCAATCTCTTCGTCGCAGCAGGCATCAG
genomic: ATGAGGAGGGCACCATTATCGTCAGCTGGGAACCTGCCTCCTATGGGGAGgtaagcatat ... aaattgccagGCCAATCTCTTCGTCGCAGCAGGCATCAG
EST: gi|91048017|gb|EB158435.1|EB158435
EST:     ATGAGGAGGGCACCATTATCGTCAGCTGGGAACCTGCCTCCTATGGGGAG                         GCCAATCTCTTCGTCGCAGCA
genomic: ATGAGGAGGGCACCATTATCGTCAGCTGGGAACCTGCCTCCTATGGGGAGgtaagcatat ... aaattgccagGCCAATCTCTTCGTCGCAGCA
EST: gi|21626078|gb|BQ620999.1|BQ620999
EST:     ATGAGGAGGGCACCATTATCGTCAGCTGGGAACCTCCCTCCTATGGGGAG                         GCCAATCTCTTCGTCGCAGCAGGCATCAG
genomic: ATGAGGAGGGCACCATTATCGTCAGCTGGGAACCTGCCTCCTATGGGGAGgtaagcatat ... aaattgccagGCCAATCTCTTCGTCGCAGCAGGCATCAG
EST: gi|211383597|gb|FL452880.1|FL452880
EST:     ATGAGGAGGGCACCATTATCGTCAGCTGGGAACCTGCCTCCTATGGGGAG                         GCCAATCTCTTCGTCGCAGCAGGCATCAG
genomic: ATGAGGAGGGCACCATTATCGTCAGCTGGGAACCTGCCTCCTATGGGGAGgtaagcatat ... aaattgccagGCCAATCTCTTCGTCGCAGCAGGCATCAG
EST: gi|61118250|gb|DN559211.1|DN559211
EST:     ATGAGGAGGGCACCATTATCGTCAGCTGGGAACCTGCCTCCTATGGGGAG                         GCCAATCTCTTCGTCGCAGCAGGCATCAG
genomic: ATGAGGAGGGCACCATTATCGTCAGCTGGGAACCTGCCTCCTATGGGGAGgtaagcatat ... aaattgccagGCCAATCTCTTCGTCGCAGCAGGCATCAG
EST: gi|31612035|gb|CD568657.1|CD568657
EST:     ATGAGGAGGGCACCATTATCGTCAGCTGGGAACCTGCCTCCTATGGGGAG                         GCCAATCTCTTCGTCGCAGCAGGCATCAG
genomic: ATGAGGAGGGCACCATTATCGTCAGCTGGGAACCTGCCTCCTATGGGGAGgtaagcatat ... aaattgccagGCCAATCTCTTCGTCGCAGCAGGCATCAG
EST: gi|12970923|gb|BG267226.1|BG267226
EST:     ATGAGGAGGGCACCATTATCGTCAGCTGGGAACCTCCCTCCTATGGGGAG                         GCCAATCTTTTCGTCGCAGCAGGCATCAG
genomic: ATGAGGAGGGCACCATTATCGTCAGCTGGGAACCTGCCTCCTATGGGGAGgtaagcatat ... aaattgccagGCCAATCTCTTCGTCGCAGCAGGCATCAG

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), 29 (downstream exon)
Score: 340

GGATGATGAGTTCAGAATCTGATCCATCACTAAATGTTGAACATCGGAGCATGAGGAGGGCACCATTATCGTCAGCTGGGAACCTGCCTCCTATGGGGAGgtaagcatat ... aaattgccagGCCAATCTCTTCGTCGCAGCAGGCATCAG


Block sizes: 43 (upstream exon), 29 (downstream exon)
Score: 99

GGATGATGAGTTCAGAATCTGATCCATCACTAAATGTTGAACATCGGAGCATGAGGAGGGCACCATTATCGTCAGCTGGGAACCTGCCTCCTATGGGGAGgtaagcatat ... aaattgccagGCCAATCTCTTCGTCGCAGCAGGCATCAG


Block sizes: 45 (upstream exon), 29 (downstream exon)
Score: 142

GGATGATGAGTTCAGAATCTGATCCATCACTAAATGTTGAACATCGGAGCATGAGGAGGGCACCATTATCGTCAGCTGGGAACCTGCCTCCTATGGGGAGgtaagcatat ... aaattgccagGCCAATCTCTTCGTCGCAGCAGGCATCAG


Block sizes: 47 (upstream exon), 29 (downstream exon)
Score: 165

GGATGATGAGTTCAGAATCTGATCCATCACTAAATGTTGAACATCGGAGCATGAGGAGGGCACCATTATCGTCAGCTGGGAACCTGCCTCCTATGGGGAGgtaagcatat ... aaattgccagGCCAATCTCTTCGTCGCAGCAGGCATCAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttggccatcatatatttagatgcgagtgtgacatattactttgaaattgccagGCCAATCTCTTCGTCGCAGCAGGCATCAG
                                  atattactttgaaatt  TA-rich tract