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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaatgcgatgatacccacaagtcgtttcctccctacaaataacatttcactctcatataagtttctgtctgcaacacatgtgtgcagGAACGAGAGCGCTCTCAAGTTCGGATGGTTTTTCCTCTTCTACTTG

Basic information

species Zea mays
transcript GRMZM2G011078_T02
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G011078_T01 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os03g38590.1 (Oryza sativa), 3'ss of exon 8
-----------------------------------------gtaaatgcgatgatacccac--aagtcgtttcctcccta----caaataacatttcactctcatataagtttctgtctgcaacacatgtgtgcagGAACGAGAGCGCTCTCAAGTTCGGATGGTTTTTCCTCTTCTACTTG
                                          |   || ||| ||        | ||  | |  |   ||     || ||| || ||  |  |  |||| ||| | ||||||| || | |   |||||| ||||| ||||| || || |||||||||||||| |||||||||
gtaaatgaaatattactacttgtcacacattataatttgcattttttgggatcattttttgtgaggttttctgttgtttagttcgaactaatatctccttggctcataa-tttatttctgcaaaacgtat-cacagGAATGAGAGTGCTCTGAAATTTGGATGGTTTTTCCTGTTCTACTTG
















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|76927248|gb|DV171197.1|DV171197
EST:     TGCCCCGGTGCATACTACCTTTGGTACCGGCCACTATACCGCGCAATGAG                         GAACGAGAGCGCTCTCAAGTTCGGATGGTTTTTCCTCTTCTACTTG
genomic: TGCCCCGGTGCATACTACCTTTGGTACCGGCCACTATACCGCGCAATGAGgtaaatgcga ... atgtgtgcagGAACGAGAGCGCTCTCAAGTTCGGATGGTTTTTCCTCTTCTACTTG
EST: gi|78080153|gb|DV508565.1|DV508565
EST:     TGCCCCGGTGCATACTACCTTTGGTACCGGCCACTATACCGCGCAATGAG                         GAACGAGAGCGCTCTCAAGTTCGGATGGTTTTTCCTCTTCTACTTG
genomic: TGCCCCGGTGCATACTACCTTTGGTACCGGCCACTATACCGCGCAATGAGgtaaatgcga ... atgtgtgcagGAACGAGAGCGCTCTCAAGTTCGGATGGTTTTTCCTCTTCTACTTG

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: 34 (upstream exon), 48 (downstream exon)
Score: 14

GTCCTAAGATATGGTTTCTCGCAATCATATACTTCATCCTCGGATGCCCCGGTGCATACTACCTTTGGTACCGGCCACTATACCGCGCAATGAGgtaaatgcga ... atgtgtgcagGAACGAGAGCGCTCTCAAGTTCGGATGGTTTTTCCTCTTCTACTTG


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 183

GTCCTAAGATATGGTTTCTCGCAATCATATACTTCATCCTCGGATGCCCCGGTGCATACTACCTTTGGTACCGGCCACTATACCGCGCAATGAGgtaaatgcga ... atgtgtgcagGAACGAGAGCGCTCTCAAGTTCGGATGGTTTTTCCTCTTCTACTTG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 211

GTCCTAAGATATGGTTTCTCGCAATCATATACTTCATCCTCGGATGCCCCGGTGCATACTACCTTTGGTACCGGCCACTATACCGCGCAATGAGgtaaatgcga ... atgtgtgcagGAACGAGAGCGCTCTCAAGTTCGGATGGTTTTTCCTCTTCTACTTG


Block sizes: 34 (upstream exon), 47 (downstream exon)
Score: 43

GTCCTAAGATATGGTTTCTCGCAATCATATACTTCATCCTCGGATGCCCCGGTGCATACTACCTTTGGTACCGGCCACTATACCGCGCAATGAGgtaaatgcga ... atgtgtgcagGAACGAGAGCGCTCTCAAGTTCGGATGGTTTTTCCTCTTCTACTTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctacaaataacatttcactctcatataagtttctgtctgcaacacatgtgtgcagGAACGAGAGCGCTCTCAAGTTCGGATGGTTTTTCCTCTTCTACTTG
    aaataac  putative branch site (score: 43)
     aataacattt  TA-rich tract