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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgtttgttgtcaacaatttggcatattgtttgtggcgttcatggacaggttttgttcttagtgttgtctgtgtggacagCTTTTGGACCGGATCGGCCCTCCTACTGAAGACCTTAAGAAGAAAGGGATCGACTTCTCGTTGTGGTTCAAGCCTGACAAGTACCCGACTGACTTTTGAG

Basic information

species Zea mays
transcript GRMZM2G051276_T01
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G051276_T01 (Zea mays), 3'ss of exon 9
lower sequence: LOC_Os02g07350.1 (Oryza sativa), 3'ss of exon 9
-------gtt-tgtttgttgtcaacaatttggcatattgtttgtggcgttcatggacaggtttt-----gttcttagt-------gttgtctgtgtggacagCTTTTGGACCGGATCGGCCCTCCTACTGAAGACCTTAAGAAGAAAGGGATCGACTTCTCGTTGTGGTTCAAGCCTGACAAGTACCCGACTGACTTTTGAG
       ||  | |   |   ||| | |   |   ||| || || |  ||  |||| |  ||||     |||  |  |       |||   ||  | | ||||||||||| ||||| |||||| | || ||||| |||||||||||||| || || ||||| |||||||| || || ||||| ||||| || ||||||| ||
gacggtagtagtatgcatcaccaagagtaatgataatttttggtcgtcttt-tggagaaattttatggagttgctgatcaaccctgttacttgacttg-cagCTTTTGGATCGGATTGGCCCTGCCACAGAAGATCTTAAGAAGAAAGGAATTGATTTCTCCTTGTGGTTTAAACCCGACAAATACCCTACCGACTTTTAAG
















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|32921727|gb|CF026539.1|CF026539
EST:     CGGTCTTCGATCGCTCTGTTCTTGTTTCCAACGGACTTGTTCATGGACAG                         CTTTTGGACCGGATCGGCCCTCCTACTGAAGACCTTAAGAAGAAAGGGATC
genomic: CGGTCTTCGATCGCTCTGTTCTTGTTTCCAACGGACTTGTTCATGGACAGgtttgtttgt ... gtgtggacagCTTTTGGACCGGATCGGCCCTCCTACTGAAGACCTTAAGAAGAAAGGGATC
EST: gi|32921409|gb|CF026221.1|CF026221
EST:     CGGTCTTCGATCGCTCTGTTCTTGTTTCCAACGGACTTGTTCATGGACAG                         CTTTTGGACCGGATCGGCCCTCCTACTGAAGACCTTAAGAAGAAAGGGATC
genomic: CGGTCTTCGATCGCTCTGTTCTTGTTTCCAACGGACTTGTTCATGGACAGgtttgtttgt ... gtgtggacagCTTTTGGACCGGATCGGCCCTCCTACTGAAGACCTTAAGAAGAAAGGGATC
EST: gi|32849542|gb|CD989223.1|CD989223
EST:     CGGTCTTCGATCGCTCTGTTCTTGTTTCCAACGGACTTGTTCATGGACAG                         CTTTTGGACCGGATCGGCCCTCCTACTGAAGACCTTAAGAAGAAAGGGATC
genomic: CGGTCTTCGATCGCTCTGTTCTTGTTTCCAACGGACTTGTTCATGGACAGgtttgtttgt ... gtgtggacagCTTTTGGACCGGATCGGCCCTCCTACTGAAGACCTTAAGAAGAAAGGGATC
EST: gi|32921295|gb|CF026107.1|CF026107
EST:     CGGTCTTCGATCGCTCTGTTCTTGTTTCCAACGGACTTGTTCATGGACAG                         CTTTTGGACCGGATCGGCCCTCCTACTGAAGACCTTAAGAAGAAAGGGATC
genomic: CGGTCTTCGATCGCTCTGTTCTTGTTTCCAACGGACTTGTTCATGGACAGgtttgtttgt ... gtgtggacagCTTTTGGACCGGATCGGCCCTCCTACTGAAGACCTTAAGAAGAAAGGGATC

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: 46 (upstream exon), 47 (downstream exon)
Score: 10

AGTAGAGGAAGCTGGTGGGGTGGTAACTCGCATGGACGGTGGAGAGTTTACGGTCTTCGATCGCTCTGTTCTTGTTTCCAACGGACTTGTTCATGGACAGgtttgtttgt ... gtgtggacagCTTTTGGACCGGATCGGCCCTCCTACTGAAGACCTTAAGAAGAAAGGGATCGACTTCTCGTTGTGGTTCAAGCCTGACAAGTACCCGACTGACTTTTGAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 41

AGTAGAGGAAGCTGGTGGGGTGGTAACTCGCATGGACGGTGGAGAGTTTACGGTCTTCGATCGCTCTGTTCTTGTTTCCAACGGACTTGTTCATGGACAGgtttgtttgt ... gtgtggacagCTTTTGGACCGGATCGGCCCTCCTACTGAAGACCTTAAGAAGAAAGGGATCGACTTCTCGTTGTGGTTCAAGCCTGACAAGTACCCGACTGACTTTTGAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 28

AGTAGAGGAAGCTGGTGGGGTGGTAACTCGCATGGACGGTGGAGAGTTTACGGTCTTCGATCGCTCTGTTCTTGTTTCCAACGGACTTGTTCATGGACAGgtttgtttgt ... gtgtggacagCTTTTGGACCGGATCGGCCCTCCTACTGAAGACCTTAAGAAGAAAGGGATCGACTTCTCGTTGTGGTTCAAGCCTGACAAGTACCCGACTGACTTTTGAG


Block sizes: 49 (upstream exon), 43 (downstream exon)
Score: 32

AGTAGAGGAAGCTGGTGGGGTGGTAACTCGCATGGACGGTGGAGAGTTTACGGTCTTCGATCGCTCTGTTCTTGTTTCCAACGGACTTGTTCATGGACAGgtttgtttgt ... gtgtggacagCTTTTGGACCGGATCGGCCCTCCTACTGAAGACCTTAAGAAGAAAGGGATCGACTTCTCGTTGTGGTTCAAGCCTGACAAGTACCCGACTGACTTTTGAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attgtttgtggcgttcatggacaggttttgttcttagtgttgtctgtgtggacagCTTTTGGACCGGATCGGCCCTCCTACTGAAGACCTTAAGAAGAAAGGGATCGACTTCTCGTTGTGGTTCAAGCCTGACAAGTACCCGACTGACTTTTGAG
                         ttttgtt  TA-rich tract