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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatggaagtttgtgttatcttggccatttattttatgctcaatgctatggtgtctaaagtttgcttttgaacagGATGCTGTTGAAGCTGCTGATTTGAGGGACTATAGTTCGCGAACTCGTGATTCCTTATCCTGTTGGAATCCTGATTCAATTGGTTTTAATTTAATAGAAA

Basic information

species Zea mays
transcript GRMZM2G373175_T02
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G373175_T02 (Zea mays), 3'ss of exon 9
lower sequence: LOC_Os01g02884.1 (Oryza sativa), 3'ss of exon 3
gtatggaagtt-tgtgttatcttggccatttattttatgctcaatgctatggtgtc-----taaagtttgcttttgaacagGATGCTGTTGAAGCTGCTGATTTGAGGGACTATAGTTCGCGAACTCGTGATTCCTTATCCTGTTGGAATCCTGATTCAATTGGTTTTAATTTAATAGAAA
||||| |  |  ||  || |  || ||| | ||||  || |||  ||| |||| ||     |||| |   ||||||| |||||| | ||| ||||||||||||| |||||||| ||| | ||||||||||| ||  |||||||||||||||||||||| ||||||||||| || |||||||
gtatgtagttcctgcatttttatgcccact-atttcctgttcagagctttggtctcccctctaaactcatcttttgagcagGATACAGTTCAAGCTGCTGATTTAAGGGACTACAGTGCACGAACTCGTGACTCACTATCCTGTTGGAATCCTGATTCGATTGGTTTTAACTTGATAGAAA

upper sequence: GRMZM2G373175_T02 (Zea mays), 3'ss of exon 9
lower sequence: Vv17s0000g03030.t01 (Vitis vinifera), 3'ss of exon 8
gtatggaagttt----gtgttatcttggccatttattttatgctcaatgctatggtgtctaaagtttgcttttgaacagGATGCTGTTGAAGCTGCTGATTTGAGGGACTATAGTTCGCGAACTCGTGATTCCTTATCCTGTTGGAATCCTGATTCAATTGGTTTTAATTTAATAGAAA
||||   |||||      | ||  |       || ||||    | ||||| ||  ||   |   | | ||| ||||||||||||  |||||| |||| ||||    |  |||||  | || || |  || || ||||||||||||||||||||||| |||||||||||  | || ||| 
gtataacagttttatgaggctacatactgttgttgtttttctataaatgc-atcttgaacactttatacttgtgaacagGATGCACTTGAAGTTGCTAATTTTGATGCATATAGCCCACGGACACAAGACTCTTTATCCTGTTGGAATCCTGATTCTATTGGTTTTAACCTTATCGAAC
















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|31351858|gb|CD436215.1|CD436215
EST:     AAAAGCAAGCTCTACAAAAGCGGAAGAGCCAAATCGCTTCTGTTGTGGAA                         GATGCTGTTGAAGCTGCTGATTTGAGGGACTATAGTTCGCGAACTCGTGAT
genomic: AAAAGCAAGCTCTACAAAAGCGGAAGAGCCAAATCGCTTCTGTTGTGGAAgtatggaagt ... ttttgaacagGATGCTGTTGAAGCTGCTGATTTGAGGGACTATAGTTCGCGAACTCGTGAT




















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: 70

TCCATACAATCAAATTGATGACTATGGTCAAGAAAAAAGTTGGAAGATGCAAAAGCAAGCTCTACAAAAGCGGAAGAGCCAAATCGCTTCTGTTGTGGAAgtatggaagt ... ttttgaacagGATGCTGTTGAAGCTGCTGATTTGAGGGACTATAGTTCGCGAACTCGTGATTCCTTATCCTGTTGGAATCCTGATTCAATTGGTTTTAATTTAATAGAAA


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 53

TCCATACAATCAAATTGATGACTATGGTCAAGAAAAAAGTTGGAAGATGCAAAAGCAAGCTCTACAAAAGCGGAAGAGCCAAATCGCTTCTGTTGTGGAAgtatggaagt ... ttttgaacagGATGCTGTTGAAGCTGCTGATTTGAGGGACTATAGTTCGCGAACTCGTGATTCCTTATCCTGTTGGAATCCTGATTCAATTGGTTTTAATTTAATAGAAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 33

TCCATACAATCAAATTGATGACTATGGTCAAGAAAAAAGTTGGAAGATGCAAAAGCAAGCTCTACAAAAGCGGAAGAGCCAAATCGCTTCTGTTGTGGAAgtatggaagt ... ttttgaacagGATGCTGTTGAAGCTGCTGATTTGAGGGACTATAGTTCGCGAACTCGTGATTCCTTATCCTGTTGGAATCCTGATTCAATTGGTTTTAATTTAATAGAAA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 102

TCCATACAATCAAATTGATGACTATGGTCAAGAAAAAAGTTGGAAGATGCAAAAGCAAGCTCTACAAAAGCGGAAGAGCCAAATCGCTTCTGTTGTGGAAgtatggaagt ... ttttgaacagGATGCTGTTGAAGCTGCTGATTTGAGGGACTATAGTTCGCGAACTCGTGATTCCTTATCCTGTTGGAATCCTGATTCAATTGGTTTTAATTTAATAGAAA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttggccatttattttatgctcaatgctatggtgtctaaagtttgcttttgaacagGATGCTGTTGAAGCTGCTGATTTGAGGGACTATAGTTCGCGAACTCGTGATTCCTTATCCTGTTGGAATCCTGATTCAATTGGTTTTAATTTAATAGAAA
                                gtctaaa  putative branch site (score: 102)
                                        tttgctttt  CT-rich tract
      atttattttatgct  TA-rich tract