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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatcaaaaagctaacggaaagtatatacctctgctgtgtccttttcttaggaacctccttatacttgattctgctgtttgaatgaattcatatgcctgcctttctagGAAGATCTAATGGAACTAGAAGATGAAGATCTTGCTTCACAAATGTTAAAACACCAGGAACGAGCAATTGACTTTTGGCAAAAGCATTGG

Basic information

species Zea mays
transcript GRMZM5G807767_T01
intron # 3
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|211020790|gb|FL433478.1|FL433478
EST:     TTTG-TGCTGGCACCAAAG                         GAAGATCTTATGGAACTAGAAGATGAAGATCTTGCTTCACAAATGTTAAAA
genomic: TTTGCTGCTGGCACCAAAGgtatcaaaaa ... gcctttctagGAAGATCTAATGGAACTAGAAGATGAAGATCTTGCTTCACAAATGTTAAAA
EST: gi|13557817|gb|BG549173.1|BG549173
EST:     ATTTTTTGCCAAGTGTTGATGAATGCACTAGTTTGCTGCTGGCACCAAAG                         GAAGATCTAATGGAACTAGAAGATGAAGATCTTGCTTCACAAATGTTAAAA
genomic: ATTTTTTGCCAAGTGTTGATGAATGCACTAGTTTGCTGCTGGCACCAAAGgtatcaaaaa ... gcctttctagGAAGATCTAATGGAACTAGAAGATGAAGATCTTGCTTCACAAATGTTAAAA

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: 51

TCTTCTATATGCATTTGATATAGAAGACAACTTTTGGCAGTTATATTCTGATTTTTTGCCAAGTGTTGATGAATGCACTAGTTTGCTGCTGGCACCAAAGgtatcaaaaa ... gcctttctagGAAGATCTAATGGAACTAGAAGATGAAGATCTTGCTTCACAAATGTTAAAACACCAGGAACGAGCAATTGACTTTTGGCAAAAGCATTGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 116

TCTTCTATATGCATTTGATATAGAAGACAACTTTTGGCAGTTATATTCTGATTTTTTGCCAAGTGTTGATGAATGCACTAGTTTGCTGCTGGCACCAAAGgtatcaaaaa ... gcctttctagGAAGATCTAATGGAACTAGAAGATGAAGATCTTGCTTCACAAATGTTAAAACACCAGGAACGAGCAATTGACTTTTGGCAAAAGCATTGG


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 17

TCTTCTATATGCATTTGATATAGAAGACAACTTTTGGCAGTTATATTCTGATTTTTTGCCAAGTGTTGATGAATGCACTAGTTTGCTGCTGGCACCAAAGgtatcaaaaa ... gcctttctagGAAGATCTAATGGAACTAGAAGATGAAGATCTTGCTTCACAAATGTTAAAACACCAGGAACGAGCAATTGACTTTTGGCAAAAGCATTGG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 51

TCTTCTATATGCATTTGATATAGAAGACAACTTTTGGCAGTTATATTCTGATTTTTTGCCAAGTGTTGATGAATGCACTAGTTTGCTGCTGGCACCAAAGgtatcaaaaa ... gcctttctagGAAGATCTAATGGAACTAGAAGATGAAGATCTTGCTTCACAAATGTTAAAACACCAGGAACGAGCAATTGACTTTTGGCAAAAGCATTGG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acctccttatacttgattctgctgtttgaatgaattcatatgcctgcctttctagGAAGATCTAATGGAACTAGAAGATGAAGATCTTGCTTCACAAATGTTAAAACACCAGGAACGAGCAATTGACTTTTGGCAAAAGCATTGG
          acttgat  putative branch site (score: 51)
                                          cctgcctttct  putative PPT
                                aattcatat  TA-rich tract