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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtataccttgttatgcaactgaaacattcatgtatatccattattcagttttactgatatccgttcatgctgctacatgtagCTACCTCCACCACAACTTGAATTTATGTTGAATAAATATCCCAATCTTCGGACACCTCTTTCTTCCTTTGTTAATCAGCGGAATATGCATAACACCTTGC

Basic information

species Zea mays
transcript GRMZM2G466139_T01
intron # 22
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G466139_T01 (Zea mays), 3'ss of exon 22
lower sequence: LOC_Os01g49940.2 (Oryza sativa), 3'ss of exon 25
------------------------------gtataccttgttatgcaactgaaacattcatgtatatccattattcagttttactgatatccgttcatgctgctacatgtagCTACCTCCACCACAACTTGAATTTATGTTGAATAAATATCCCAATCTTCGGACACCTCTTTCTTCCTTTGTTAATCAGCGGAATATGCATAACACCTTGC
                              | ||   | |||||  ||   |  || || |  |||| || ||  |   | |||||| ||   ||||   |||||| | ||| |||||||||| || |||||| |    |||||||| || |||||||| || || ||||||| ||||||||||||||||||||| ||||| | || |||||
gtacaatgttaagtaactgaatgcattcttgcatgtat-gttataaaaaatatgcactccttgatatacaatacactactgtactgacatggcttcacaatgctacttttagTTACCTCCACCCCAGCTTGAAATAGCTTTGAATAAGTACCCCAATCTACGAACTCCTCTTTGTTCCTTTGTTAATCAGCGGAACATGCACAGCATCTTGC
















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|67029877|gb|CO458626.1|CO458626
EST:     TAAAATTGTCATTCCAGACTCAGCCACGTTCTTTTGATGTCTTATTACAG                         CTACCTCCACCACAACTTGAATTTATGTTGAATAAATATCCCAATCTTCGG
genomic: TAAAATTGTCATTCCAGACTCAGCCACGTTCTTTTGATGTCTTATTACAGgtataccttg ... ctacatgtagCTACCTCCACCACAACTTGAATTTATGTTGAATAAATATCCCAATCTTCGG
EST: gi|60395389|gb|DN228258.1|DN228258
EST:     TAAAATTGTCATTCCAGACTCAGCCACGTTCTTTTGATGTCTTATTACAG                         CTACCTCCACCACAACTTGAATTTATGTTGAATAAATATCCCAATCTTCGG
genomic: TAAAATTGTCATTCCAGACTCAGCCACGTTCTTTTGATGTCTTATTACAGgtataccttg ... ctacatgtagCTACCTCCACCACAACTTGAATTTATGTTGAATAAATATCCCAATCTTCGG
EST: gi|67026985|gb|CO455734.1|CO455734
EST:     TAAAATTGTCATTCCAGACTCAGCCACGTTCTTTTGATGTCTTATTACAG                         CTACCTCCACCACAACTTGAATTTATGTTGAATAAATATCCCAATCTTCGG
genomic: TAAAATTGTCATTCCAGACTCAGCCACGTTCTTTTGATGTCTTATTACAGgtataccttg ... ctacatgtagCTACCTCCACCACAACTTGAATTTATGTTGAATAAATATCCCAATCTTCGG

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), 49 (downstream exon)
Score: 86

ATATGGAAAATGCCGAAGCTCTGGGTTGGGTTTTTAAAATTGTCATTCCAGACTCAGCCACGTTCTTTTGATGTCTTATTACAGgtataccttg ... ctacatgtagCTACCTCCACCACAACTTGAATTTATGTTGAATAAATATCCCAATCTTCGGACACCTCTTTCTTCCTTTGTTAATCAGCGGAATATGCATAACACCTTGC


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 35

ATATGGAAAATGCCGAAGCTCTGGGTTGGGTTTTTAAAATTGTCATTCCAGACTCAGCCACGTTCTTTTGATGTCTTATTACAGgtataccttg ... ctacatgtagCTACCTCCACCACAACTTGAATTTATGTTGAATAAATATCCCAATCTTCGGACACCTCTTTCTTCCTTTGTTAATCAGCGGAATATGCATAACACCTTGC


Block sizes: 46 (upstream exon), 48 (downstream exon)
Score: 67

ATATGGAAAATGCCGAAGCTCTGGGTTGGGTTTTTAAAATTGTCATTCCAGACTCAGCCACGTTCTTTTGATGTCTTATTACAGgtataccttg ... ctacatgtagCTACCTCCACCACAACTTGAATTTATGTTGAATAAATATCCCAATCTTCGGACACCTCTTTCTTCCTTTGTTAATCAGCGGAATATGCATAACACCTTGC


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 68

ATATGGAAAATGCCGAAGCTCTGGGTTGGGTTTTTAAAATTGTCATTCCAGACTCAGCCACGTTCTTTTGATGTCTTATTACAGgtataccttg ... ctacatgtagCTACCTCCACCACAACTTGAATTTATGTTGAATAAATATCCCAATCTTCGGACACCTCTTTCTTCCTTTGTTAATCAGCGGAATATGCATAACACCTTGC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcatgtatatccattattcagttttactgatatccgttcatgctgctacatgtagCTACCTCCACCACAACTTGAATTTATGTTGAATAAATATCCCAATCTTCGGACACCTCTTTCTTCCTTTGTTAATCAGCGGAATATGCATAACACCTTGC
                        tactgat  putative branch site (score: 68)
            attattcagtttta  TA-rich tract