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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCTTAGAGACAATTATTTGGTTTTACTGGCCCTAATTTATTGTGTAACCGGCATAGGTTACTCTTTTGCTATTTGGTTTGAGCTCGGATTAGCACAGTTGgtaagtagggcatctcttttttgtaatcatgatattaactctactgaaggtggctaatgaactataatgttgtag

Basic information

species Zea mays
transcript GRMZM2G430675_T02
intron # 12
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G430675_T03 (Zea mays), 5'ss of exon 12
lower sequence: LOC_Os10g30610.1 (Oryza sativa), 5'ss of exon 11
TCTTAGAGACAATTATTTGGTTTTACTGGCCCTAATTTATTGTGTAACCGGCATAGGTTACTCTTTTGCTATTTGGTTTGAGCTCGGATTAGCACAGTTGgtaagtagggcatctctt--ttttgtaatcatgatattaactctactgaaggtggctaa-tgaactataatgttgtag
  ||| |||||| |||||||| ||  |||| ||  ||||||||||||| |||||||||||  ||||||||||||||||||||||||||||||| || |||||||| |    | ||     | |  | ||| ||| |||  |  |     |  ||||||| |||||| |  | ||| ||
ATTTAAAGACAACTATTTGGTGTTTTTGGCACTGGTTTATTGTGTAACTGGCATAGGTTATACTTTTGCTATTTGGTTTGAGCTCGGATTAGCTCAATTGgtaagcataataacttaaaatatcttcatcctgacattggcggtgtc--atttggctaaatgaacttttctcttgcag
















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|32923118|gb|CF027930.1|CF027930
EST:     GCATAGGTTACTCTTTTGCTATTTGGTTTGAGCTCGGATTAGCACAGTTG                         AGCTCTGCAATAGTA
genomic: GCATAGGTTACTCTTTTGCTATTTGGTTTGAGCTCGGATTAGCACAGTTGgtaagtaggg ... aatgttgtagAGCTCTGCAATAGTA
EST: gi|32921859|gb|CF026671.1|CF026671
EST:     GCATAGGTTACTCTTTTGCTATTTGGTTTGAGCTCGGATTAGCACAGTTG                         AGCTCTGCAATAGT
genomic: GCATAGGTTACTCTTTTGCTATTTGGTTTGAGCTCGGATTAGCACAGTTGgtaagtaggg ... aatgttgtagAGCTCTGCAATAGT
EST: gi|32920474|gb|CF025286.1|CF025286
EST:     GCATAGGTTACTCTTTTGCTATTTGGTTTGAGCTCGGATTAGCACAGTTG                         AGCTCTGCAATAGTA
genomic: GCATAGGTTACTCTTTTGCTATTTGGTTTGAGCTCGGATTAGCACAGTTGgtaagtaggg ... aatgttgtagAGCTCTGCAATAGTA
EST: gi|32922329|gb|CF027141.1|CF027141
EST:     GCATAGGTTACTCTTTTGCTATTTGGTTTGAGCTCGGATTAGCACAGTTG                         AGCTCTGCAATAGTA
genomic: GCATAGGTTACTCTTTTGCTATTTGGTTTGAGCTCGGATTAGCACAGTTGgtaagtaggg ... aatgttgtagAGCTCTGCAATAGTA
EST: gi|32922314|gb|CF027126.1|CF027126
EST:     GCATAGGTTACTCTTTTGCTATTTGGTTTGAGCTCGGATTAGCACAGTTG                         AGCTCTGCAATAGTA
genomic: GCATAGGTTACTCTTTTGCTATTTGGTTTGAGCTCGGATTAGCACAGTTGgtaagtaggg ... aatgttgtagAGCTCTGCAATAGTA

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 2 RNA-Seq libraries.


Block sizes: 15 (upstream exon), 35 (downstream exon)
Score: 3

TCTTAGAGACAATTATTTGGTTTTACTGGCCCTAATTTATTGTGTAACCGGCATAGGTTACTCTTTTGCTATTTGGTTTGAGCTCGGATTAGCACAGTTGgtaagtaggg ... aatgttgtagAGCTCTGCAATAGTACCTGTTGTTCTGGTCCTGGTGGGCACTAAACCTGACCTTCCGAGGGTTATAAGGGAATTGTGCTATCCAAAGTGGGCTCTAGAAG


Block sizes: 15 (upstream exon), 35 (downstream exon)
Score: 1

TCTTAGAGACAATTATTTGGTTTTACTGGCCCTAATTTATTGTGTAACCGGCATAGGTTACTCTTTTGCTATTTGGTTTGAGCTCGGATTAGCACAGTTGgtaagtaggg ... aatgttgtagAGCTCTGCAATAGTACCTGTTGTTCTGGTCCTGGTGGGCACTAAACCTGACCTTCCGAGGGTTATAAGGGAATTGTGCTATCCAAAGTGGGCTCTAGAAG




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