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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagtgtcgccattatttaaaccctttgtgcattgttgccatgaacttttggagctgctgtttcatctcgttatgtcattattccttaacagGATGCTCAAAGTGCGATAAATGACTTGAATG

Basic information

species Zea mays
transcript GRMZM5G835213_T01
intron # 8
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|24934275|gb|CA452493.1|CA452493
EST:     AAACAGGACGATCCAGAGGGTTTGGTTTTGTTTCTTTCAGGAACCAGCAG                         GATGCTCAAAGTGCGATAAATGACTTGAATG
genomic: AAACAGGACGATCCAGAGGGTTTGGTTTTGTTTCTTTCAGGAACCAGCAGgtagtgtcgc ... tccttaacagGATGCTCAAAGTGCGATAAATGACTTGAATG
EST: gi|71436375|gb|DR817425.1|DR817425
EST:     AAACAGGACGATCCAGAGGGTTTGGTTTTGTTTCTTTCAGGAACCAGCAG                         GATGCTCAAAGTGCGATAAATGACTTGAATG
genomic: AAACAGGACGATCCAGAGGGTTTGGTTTTGTTTCTTTCAGGAACCAGCAGgtagtgtcgc ... tccttaacagGATGCTCAAAGTGCGATAAATGACTTGAATG
EST: gi|71324258|gb|DR798829.1|DR798829
EST:     AAACAGGACGATCCAGAGGGTTTGGTTTTGTTTCTTTCAGGAACCAGCAG                         GATGCTCAAAGTGCGATAAATGACTTGAATG
genomic: AAACAGGACGATCCAGAGGGTTTGGTTTTGTTTCTTTCAGGAACCAGCAGgtagtgtcgc ... tccttaacagGATGCTCAAAGTGCGATAAATGACTTGAATG
EST: gi|31361403|gb|CD445760.1|CD445760
EST:     AAACAGGACGATCCAGAGGGTTTGGTTTTGTTTCTTTCAGGAACCAGCAG                         GATGCTCAAAGTGCGATAAATGACTTGAATG
genomic: AAACAGGACGATCCAGAGGGTTTGGTTTTGTTTCTTTCAGGAACCAGCAGgtagtgtcgc ... tccttaacagGATGCTCAAAGTGCGATAAATGACTTGAATG
EST: gi|22546594|gb|BU098905.1|BU098905
EST:     AAACAGGACGATCCAGAGGGTTTGGTTTTGTTTCTTTCAGGAACCAGCAG                         GATGCTCAAAGTGCGATAAATGACTTGAATG
genomic: AAACAGGACGATCCAGAGGGTTTGGTTTTGTTTCTTTCAGGAACCAGCAGgtagtgtcgc ... tccttaacagGATGCTCAAAGTGCGATAAATGACTTGAATG
EST: gi|22545671|gb|BU098030.1|BU098030
EST:     AAACAGGACGATCCAGAGGGTTTGGTTTTGTTTCTTTCAGGAACCAGCAG                         GATGCTCAAAGTGCGATAAATGACTTGAATG
genomic: AAACAGGACGATCCAGAGGGTTTGGTTTTGTTTCTTTCAGGAACCAGCAGgtagtgtcgc ... tccttaacagGATGCTCAAAGTGCGATAAATGACTTGAATG
EST: gi|29544652|gb|CB605032.1|CB605032
EST:     AAACAGGACGATCCAGAGGGTTTGGTTTTGTTTCTTTCAGGAACCAGCAG                         GATGCTCAAAGTGCGATAAATGACTTGAATG
genomic: AAACAGGACGATCCAGAGGGTTTGGTTTTGTTTCTTTCAGGAACCAGCAGgtagtgtcgc ... tccttaacagGATGCTCAAAGTGCGATAAATGACTTGAATG
EST: gi|71317247|gb|DR795307.1|DR795307
EST:     AAACAGGACGATCCAGAGGGTTTGGTTTTGTTTCTTTCAGGAACCAGCAG                         GATGCTCAAAGTGCGATAAATGACTTGAATG
genomic: AAACAGGACGATCCAGAGGGTTTGGTTTTGTTTCTTTCAGGAACCAGCAGgtagtgtcgc ... tccttaacagGATGCTCAAAGTGCGATAAATGACTTGAATG
EST: gi|194717059|gb|FK934212.1|FK934212
EST:     AAACAGGACGATCCAGAGGGTTTGGTTTTGTTTCTTTCAGGAACCAGCAG                         GATGCTCAAAGTGCGATAAATGACTTGAATG
genomic: AAACAGGACGATCCAGAGGGTTTGGTTTTGTTTCTTTCAGGAACCAGCAGgtagtgtcgc ... tccttaacagGATGCTCAAAGTGCGATAAATGACTTGAATG
EST: gi|5268356|gb|AI770320.1|AI770320
EST:     AAACAGGACGATCCAGAGGGTTTGGTTTTGTTTCTTTCAGGAACCAGCAG                         GATGCTCAAAGTGCGATAAATGACTTGAATG
genomic: AAACAGGACGATCCAGAGGGTTTGGTTTTGTTTCTTTCAGGAACCAGCAGgtagtgtcgc ... tccttaacagGATGCTCAAAGTGCGATAAATGACTTGAATG
EST: gi|26456698|gb|CA828281.1|CA828281
EST:     AACAGGACGATCCAGAGGGTTTGGTCTTTGTTTCTTTCAGGAACCAGCAG                         GATGCTCAAAGTGCGATAAATGACTTGAATG
genomic: AACAGGACGATCCAGAGGGTTTGGT-TTTGTTTCTTTCAGGAACCAGCAGgtagtgtcgc ... tccttaacagGATGCTCAAAGTGCGATAAATGACTTGAATG
EST: gi|32850339|gb|CD990020.1|CD990020
EST:     AAACAGGACGATCCAGAGGGTTTGGTTTTGTTTCTTTCAGGAACCAGCAG                         GATGCTCAAAGTGCGATAAATGACTTGAATG
genomic: AAACAGGACGATCCAGAGGGTTTGGTTTTGTTTCTTTCAGGAACCAGCAGgtagtgtcgc ... tccttaacagGATGCTCAAAGTGCGATAAATGACTTGAATG
EST: gi|32866442|gb|CF006124.1|CF006124
EST:     AAACAGGACGATCCAGAGGGTTTGGTTTTGTTTCTTTCAGGAACCAGCAG                         GATGCTCAAAGTGCGATAAATGACTTGAATG
genomic: AAACAGGACGATCCAGAGGGTTTGGTTTTGTTTCTTTCAGGAACCAGCAGgtagtgtcgc ... tccttaacagGATGCTCAAAGTGCGATAAATGACTTGAATG

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), 31 (downstream exon)
Score: 1412

AGATGCTAGGGTTATGTGGGACCAGAAAACAGGACGATCCAGAGGGTTTGGTTTTGTTTCTTTCAGGAACCAGCAGgtagtgtcgc ... tccttaacagGATGCTCAAAGTGCGATAAATGACTTGAATG


Block sizes: 49 (upstream exon), 31 (downstream exon)
Score: 568

AGATGCTAGGGTTATGTGGGACCAGAAAACAGGACGATCCAGAGGGTTTGGTTTTGTTTCTTTCAGGAACCAGCAGgtagtgtcgc ... tccttaacagGATGCTCAAAGTGCGATAAATGACTTGAATG


Block sizes: 49 (upstream exon), 35 (downstream exon)
Score: 567

AGATGCTAGGGTTATGTGGGACCAGAAAACAGGACGATCCAGAGGGTTTGGTTTTGTTTCTTTCAGGAACCAGCAGgtagtgtcgc ... tccttaacagGATGCTCAAAGTGCGATAAATGACTTGAATG


Block sizes: 49 (upstream exon), 31 (downstream exon)
Score: 1852

AGATGCTAGGGTTATGTGGGACCAGAAAACAGGACGATCCAGAGGGTTTGGTTTTGTTTCTTTCAGGAACCAGCAGgtagtgtcgc ... tccttaacagGATGCTCAAAGTGCGATAAATGACTTGAATG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gccatgaacttttggagctgctgtttcatctcgttatgtcattattccttaacagGATGCTCAAAGTGCGATAAATGACTTGAATG
                                         ttattcctt  CT-rich tract
                                      tcattatt  TA-rich tract