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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagttgacatgcttaccacctactccagctacaagtttaagttcttaatgcaacgtttaacaatccttgcagAAATGTCGAAAACAACCAACTCACCGGTTGGATACCCGATAAACTAAAGGGAATCAATAATCTCCA

Basic information

species Zea mays
transcript GRMZM2G121573_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|148955088|gb|EC900600.2|EC900600
EST:     AAATTTAACGGCACAATAGATGTTCTCACTGATCTTCCTCTTACTGACTT                         AAATGTCGAAAACAACCAACTCACCGGTTGGATACCCGATAAACTAAAGGG
genomic: AAATTTAACGGCACAATAGATGTTCTCACTGATCTTCCTCTTACTGACTTgtaagttgac ... atccttgcagAAATGTCGAAAACAACCAACTCACCGGTTGGATACCCGATAAACTAAAGGG




















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: 97

TTACCTTCAGAACAACAAATTTAACGGCACAATAGATGTTCTCACTGATCTTCCTCTTACTGACTTgtaagttgac ... atccttgcagAAATGTCGAAAACAACCAACTCACCGGTTGGATACCCGATAAACTAAAGGGAATCAATAATCTCCA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 248

TTACCTTCAGAACAACAAATTTAACGGCACAATAGATGTTCTCACTGATCTTCCTCTTACTGACTTgtaagttgac ... atccttgcagAAATGTCGAAAACAACCAACTCACCGGTTGGATACCCGATAAACTAAAGGGAATCAATAATCTCCA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 199

TTACCTTCAGAACAACAAATTTAACGGCACAATAGATGTTCTCACTGATCTTCCTCTTACTGACTTgtaagttgac ... atccttgcagAAATGTCGAAAACAACCAACTCACCGGTTGGATACCCGATAAACTAAAGGGAATCAATAATCTCCA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 192

TTACCTTCAGAACAACAAATTTAACGGCACAATAGATGTTCTCACTGATCTTCCTCTTACTGACTTgtaagttgac ... atccttgcagAAATGTCGAAAACAACCAACTCACCGGTTGGATACCCGATAAACTAAAGGGAATCAATAATCTCCA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acctactccagctacaagtttaagttcttaatgcaacgtttaacaatccttgcagAAATGTCGAAAACAACCAACTCACCGGTTGGATACCCGATAAACTAAAGGGAATCAATAATCTCCA
                                     gtttaac  putative branch site (score: 192)
                                              tccttgc  putative PPT
                  tttaagttcttaat  TA-rich tract