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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttaaaaagctaacatagatattgctaaagaaggtgctaagagtttagtgctatatatctaaatatatgtatctgttcagacattagatttttcgtttcagGTGGTTGGCAATGCAGTGATGCTCGGTGAAATCATAAACTACGTGCAGTCCCTACAATGACAAGTTGAG

Basic information

species Zea mays
transcript GRMZM2G085916_T01
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|67019403|gb|CO448152.1|CO448152
EST:     CAAGGCTGCTAGATATTCATGATAAGATGATGTTGATAAATAATAAAGAG                         GTGGTTGGCAATGCAGTGATGCTCGGTGAAATCATAAACTACGTGCATTCC
genomic: CAAGGCTGCTAGATATTCATGATAAGATGATGTTGATAAATAATAAAGAGgtgagtaaac ... ttcgtttcagGTGGTTGGCAATGCAGTGATGCTCGGTGAAATCATAAACTACGTGCAGTCC
EST: gi|67018831|gb|CO447580.1|CO447580
EST:     CAAGGCTGCTAGATATTCATGATAAGATGATGTTGATAAATAATAAAGAG                         GTGGTTGGCAATGCAGTGATGCTCGGTGAAATCATAAACTACGTGCAGTCC
genomic: CAAGGCTGCTAGATATTCATGATAAGATGATGTTGATAAATAATAAAGAGgtgagtaaac ... ttcgtttcagGTGGTTGGCAATGCAGTGATGCTCGGTGAAATCATAAACTACGTGCAGTCC
EST: gi|56691639|gb|CX129542.1|CX129542
EST:     CAAGGCTGCTAGATATTCATGATAAGATGATGTTGATAAATAATAAAGAG                         GTGGTTGGCAATGCAGTGATGCTCGGTGAAATCATAAACTACGTGCAGTCC
genomic: CAAGGCTGCTAGATATTCATGATAAGATGATGTTGATAAATAATAAAGAGgtgagtaaac ... ttcgtttcagGTGGTTGGCAATGCAGTGATGCTCGGTGAAATCATAAACTACGTGCAGTCC

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: 47 (upstream exon), 26 (downstream exon)
Score: 11

AACAAAGCAGGTTCATGAATTTACCGCAAGGCTGCTAGATATTCATGATAAGATGATGTTGATAAATAATAAAGAGgtgagtaaac ... ttcgtttcagGTGGTTGGCAATGCAGTGATGCTCGGTGAAATCATAAACTACGTGCAGTCCCTACAATGACAAGTTGAG


Block sizes: 47 (upstream exon), 48 (downstream exon)
Score: 7

AACAAAGCAGGTTCATGAATTTACCGCAAGGCTGCTAGATATTCATGATAAGATGATGTTGATAAATAATAAAGAGgtgagtaaac ... ttcgtttcagGTGGTTGGCAATGCAGTGATGCTCGGTGAAATCATAAACTACGTGCAGTCCCTACAATGACAAGTTGAG


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 8

AACAAAGCAGGTTCATGAATTTACCGCAAGGCTGCTAGATATTCATGATAAGATGATGTTGATAAATAATAAAGAGgtgagtaaac ... ttcgtttcagGTGGTTGGCAATGCAGTGATGCTCGGTGAAATCATAAACTACGTGCAGTCCCTACAATGACAAGTTGAG


Block sizes: 49 (upstream exon), 25 (downstream exon)
Score: 7

AACAAAGCAGGTTCATGAATTTACCGCAAGGCTGCTAGATATTCATGATAAGATGATGTTGATAAATAATAAAGAGgtgagtaaac ... ttcgtttcagGTGGTTGGCAATGCAGTGATGCTCGGTGAAATCATAAACTACGTGCAGTCCCTACAATGACAAGTTGAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agtgctatatatctaaatatatgtatctgttcagacattagatttttcgtttcagGTGGTTGGCAATGCAGTGATGCTCGGTGAAATCATAAACTACGTGCAGTCCCTACAATGACAAGTTGAG
          atctaaa  putative branch site (score: 7)
                                          tttttcgtttc  putative PPT
     tatatatctaaatata  TA-rich tract