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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagtttttctcttttttttcagaattaatttagtgttttaggcataaaataccaaaattgttgtattttcccagGCATTTGAATGGCACCGTTCTTGGATCTTTCGTGCGGCCAGCTGTTCTGATAACTGATGCTTACAATGCTTTGAACAACCAAGGCTATAGAAAAAAGCAG

Basic information

species Zea mays
transcript GRMZM2G036050_T03
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G036050_T05 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os09g39590.1 (Oryza sativa), 3'ss of exon 4
gttagtttttctcttttt--tttcagaattaatttagtgtt---ttaggcataaaataccaaaattgttgtattttcccagGCATTTGAATGGCACCGTTCTTGGATCTTTCGTGCGGCCAGCTGTTCTGATAACTGATGCTTACAATGCTTTGAACAACCAAGGCTATAGAAAAAAGCAG
||||  |  |  |||| |  |||     | | |||||| ||   ||    |  |||||  || |    |||  ||| |||||||||||||||| || | ||||||||| || || |||||||||||||||||||||||||| |||||||| ||||||||||| | ||| | ||   |||||
gttaaatccttcctttgtcatttacttgtcattttagttttctctttattagcaaataataacagcaatgtgcttttccagGCATTTGAATGGTACTGCTCTTGGATCATTTGTACGGCCAGCTGTTCTGATAACTGATGCATACAATGCCTTGAACAACCATGTCTACAAAAGGCAGCAG

upper sequence: GRMZM2G036050_T05 (Zea mays), 3'ss of exon 4
lower sequence: Vv16s0050g00590.t01 (Vitis vinifera), 3'ss of exon 4
----------------------------------gttagtttttctcttttttttcagaattaatttagtgttt-------taggcataaaataccaaaattgttgta-----ttttcccagGCATTTGAATGGCACCGTTCTTGGATCTTTCGTGCGGCCAGCTGTTCTGATAACTGATGCTTACAATGCTTTGAACAACCAAGGCTATAGAAAAAAGCAG
                                  ||    ||||    || ||||  | || || ||    ||        || |||  ||  | || | ||  | |      || |  ||||| ||||||||| || ||| | | |||||| || ||||| |||||| | ||||| ||||| || |||||||||||||| ||    | ||||    |   |
gtgagccttaatttgctagttgcaactacctgcagtggacttttagacttcttttatgcataaaatttacattcatgtaagtaagcaagaataagcatacttagtattgcggtttatttcagGCTTTTGAATGGAACTGTTTTAGAATCTTTTGTTCGGCCTGCTGTTTTAATAACAGATGCCTATAATGCTTTGAACAATCAGCCTTCTAGACGCCAAAGG
















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|31361140|gb|CD445497.1|CD445497
EST:     GATGGGGAGGATGTTGTGTATGCTGTTGACTTCAACCATCGGAAAGAGAG                         GCATTTGAATGGCACCGTTCTTGGATCTTTCGTGCGGCCAGCTGTTCTGAT
genomic: GATGGGGAGGATGTTGTGTATGCTGTTGACTTCAACCATCGGAAAGAGAGgttagttttt ... attttcccagGCATTTGAATGGCACCGTTCTTGGATCTTTCGTGCGGCCAGCTGTTCTGAT




















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: 49 (upstream exon), 45 (downstream exon)
Score: 104

CACATGTGGCTGGGCATCTTTTGGGGGGGACAGTTTGGAAGATTACAAAAGATGGGGAGGATGTTGTGTATGCTGTTGACTTCAACCATCGGAAAGAGAGgttagttttt ... attttcccagGCATTTGAATGGCACCGTTCTTGGATCTTTCGTGCGGCCAGCTGTTCTGATAACTGATGCTTACAATGCTTTGAACAACCAAGGCTATAGAAAAAAGCAG


Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 91

CACATGTGGCTGGGCATCTTTTGGGGGGGACAGTTTGGAAGATTACAAAAGATGGGGAGGATGTTGTGTATGCTGTTGACTTCAACCATCGGAAAGAGAGgttagttttt ... attttcccagGCATTTGAATGGCACCGTTCTTGGATCTTTCGTGCGGCCAGCTGTTCTGATAACTGATGCTTACAATGCTTTGAACAACCAAGGCTATAGAAAAAAGCAG


Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 82

CACATGTGGCTGGGCATCTTTTGGGGGGGACAGTTTGGAAGATTACAAAAGATGGGGAGGATGTTGTGTATGCTGTTGACTTCAACCATCGGAAAGAGAGgttagttttt ... attttcccagGCATTTGAATGGCACCGTTCTTGGATCTTTCGTGCGGCCAGCTGTTCTGATAACTGATGCTTACAATGCTTTGAACAACCAAGGCTATAGAAAAAAGCAG


Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 56

CACATGTGGCTGGGCATCTTTTGGGGGGGACAGTTTGGAAGATTACAAAAGATGGGGAGGATGTTGTGTATGCTGTTGACTTCAACCATCGGAAAGAGAGgttagttttt ... attttcccagGCATTTGAATGGCACCGTTCTTGGATCTTTCGTGCGGCCAGCTGTTCTGATAACTGATGCTTACAATGCTTTGAACAACCAAGGCTATAGAAAAAAGCAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cagaattaatttagtgttttaggcataaaataccaaaattgttgtattttcccagGCATTTGAATGGCACCGTTCTTGGATCTTTCGTGCGGCCAGCTGTTCTGATAACTGATGCTTACAATGCTTTGAACAACCAAGGCTATAGAAAAAAGCAG
   aattaat  putative branch site (score: 56)
                                            tattttccc  putative PPT
     ttaatttagtgtttta  TA-rich tract