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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttgtattgtgctttgaacctactttttgtgtggggaacaattgtatagtgcttattacctaaccttattggtttgaaaacatgtatttttgtgactgcagATTGGTGATTGTCTAGGCACTCTCGTTAAAACCTTCAAGACTTCTTTTATTCCGTTCTTCGATGAACTCTCCATGTATTTGACACCTATGTTG

Basic information

species Zea mays
transcript GRMZM2G033619_T02
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G033619_T02 (Zea mays), 3'ss of exon 11
lower sequence: LOC_Os03g49420.2 (Oryza sativa), 3'ss of exon 11
ttgtattgtgctttgaacctactttttgtgtggggaacaattgtatagtgcttattacctaaccttattgg------tttgaaaacatgtat-ttttgtgact---gcagATTGGTGATTGTCTAGGCACTCTCGTTAAAACCTTCAAGACTTCTTTTATTCCGTTCTTCGATGAACTCTCCATGTATTTGACACCTATGTTG
    ||||| |||  ||| ||   | |      |  |||  |||  | | ||  || || | | |||||||       ||  | | || ||| |||||||| |    ||||||||||||||| | |||||||| ||||| || |||||||||| |||  |||| ||||| |||||||| ||| | ||||||||||||||||||
----attgtacttccaacttaaactgta-----gacacagctgtg-acttctactttccaagctttattggaaataacttatacagatttatcttttgtgattttcacagATTGGTGATTGTTTGGGCACTCTTGTTAAGACGTTCAAGACTTATTTCCTTCCATTCTTTGATGAACTTTCCGTCTATTTGACACCTATGTTG
















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|19272579|gb|BM888835.1|BM888835
EST:     AGGAGCTACTCAGAGAAGAAAACGAACAGGAAGATGAAATCTTTGACCAA                         ATTGGTGATTGGCTAGGCACTCTCGTTAAAACCTTCAAGACTTCTTTTATT
genomic: AGGAGCTACTCAGAGAAGAAAACGAACAGGAAGATGAAATCTTTGACCAAgtaagctacc ... gtgactgcagATTGGTGATTGTCTAGGCACTCTCGTTAAAACCTTCAAGACTTCTTTTATT
EST: gi|93284006|gb|EB676270.1|EB676270
EST:     AGGAGCTACTCAGAGAAGAAAACGAACAGGAAGATGAAATCTTTGACCAA                         ATTGGTGATTGTCTAGGCACTCCTCGTTAAAACCTTCAAGACTTCTTTTAT
genomic: AGGAGCTACTCAGAGAAGAAAACGAACAGGAAGATGAAATCTTTGACCAAgtaagctacc ... gtgactgcagATTGGTGATTGTCTAGGCACTC-TCGTTAAAACCTTCAAGACTTCTTTTAT

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), 48 (downstream exon)
Score: 76

GATAGAACGAACAGAAAGGGCAAGGGCTGAGGACTTTGATTCTGAAGAAGAGGAGCTACTCAGAGAAGAAAACGAACAGGAAGATGAAATCTTTGACCAAgtaagctacc ... gtgactgcagATTGGTGATTGTCTAGGCACTCTCGTTAAAACCTTCAAGACTTCTTTTATTCCGTTCTTCGATGAACTCTCCATGTATTTGACACCTATGTTG


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 94

GATAGAACGAACAGAAAGGGCAAGGGCTGAGGACTTTGATTCTGAAGAAGAGGAGCTACTCAGAGAAGAAAACGAACAGGAAGATGAAATCTTTGACCAAgtaagctacc ... gtgactgcagATTGGTGATTGTCTAGGCACTCTCGTTAAAACCTTCAAGACTTCTTTTATTCCGTTCTTCGATGAACTCTCCATGTATTTGACACCTATGTTG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 72

GATAGAACGAACAGAAAGGGCAAGGGCTGAGGACTTTGATTCTGAAGAAGAGGAGCTACTCAGAGAAGAAAACGAACAGGAAGATGAAATCTTTGACCAAgtaagctacc ... gtgactgcagATTGGTGATTGTCTAGGCACTCTCGTTAAAACCTTCAAGACTTCTTTTATTCCGTTCTTCGATGAACTCTCCATGTATTTGACACCTATGTTG


Block sizes: 49 (upstream exon), 44 (downstream exon)
Score: 49

GATAGAACGAACAGAAAGGGCAAGGGCTGAGGACTTTGATTCTGAAGAAGAGGAGCTACTCAGAGAAGAAAACGAACAGGAAGATGAAATCTTTGACCAAgtaagctacc ... gtgactgcagATTGGTGATTGTCTAGGCACTCTCGTTAAAACCTTCAAGACTTCTTTTATTCCGTTCTTCGATGAACTCTCCATGTATTTGACACCTATGTTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tagtgcttattacctaaccttattggtttgaaaacatgtatttttgtgactgcagATTGGTGATTGTCTAGGCACTCTCGTTAAAACCTTCAAGACTTCTTTTATTCCGTTCTTCGATGAACTCTCCATGTATTTGACACCTATGTTG
           acctaac  putative branch site (score: 49)
                                        tttttgt  putative PPT
                              aaaacatgtattttt  TA-rich tract