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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTGGGAAGGAACTTGAAAGATTTGCCATCACCTACTTTGGCCATTGTATCAGAAAGGCTGAAACTGTCTACTGTACATGAAGgtggtgttgtatatattgtgtattgtaatgtactccattccaaattatatgaaattttgggttttctatttgtatagcttttgctatgcatgttgatata...

Basic information

species Zea mays
transcript GRMZM2G009849_T03
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G009849_T01 (Zea mays), 5'ss of exon 12
lower sequence: LOC_Os01g60040.1 (Oryza sativa), 5'ss of exon 30
GTGGGAAGGAACTTGAAAGATTTGCCATCACCTACTTTGGCCATTGTATCAGAAAGGCTGAAACTGTCTACTGTACATGAAGgtggtgttgtatatattgtgtattgtaatgtactccattccaaattatatgaaattttgggttttctatttgtatagcttttgctatgcatgttgatata-
|| |  | |||||||||||||||||||||||||||||||||||||||| ||||  || | |||||||| |||||||| |||||||   ||| || ||| |||  |   ||  |  | |  |     | | |||   |      || | || |  | |   | |  || | | | |||| ||| 
GTTGCGAAGAACTTGAAAGATTTGCCATCACCTACTTTGGCCATTGTAGCAGAGCGGTTAAAACTGTCCACTGTACACGAAGgtgtccttg-at-tatcgtgcttcacaa-atgtttctgtttttctgaaatgttgtcaacatttgtgtactcatttga-tatcactgt-cttattgaaatag
















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|17970269|gb|BM277032.1|BM277032
EST:     TACTTTGGCCATTGTATCAGAAAGGCTGAAACTGTCTACTGTACATGAAG                         GATTTTCTGAATCTGTTAAGGTGGTGTCAACAAGCATGAGTTTGCCATCAA
genomic: TACTTTGGCCATTGTATCAGAAAGGCTGAAACTGTCTACTGTACATGAAGgtggtgttgt ... ctttcatcagGATTTTCTGAATCTGTTAAGGTGGTGTCAACAAGCATGAGTTTGCCATCAA
EST: gi|22491327|gb|BU051250.1|BU051250
EST:     TACTTTGGCCATTGTATCAGAAAGGCTGAAACTGTCTACTGTACATGAAG                         GATTTTCTGAATCTGTTAAGGTGGTGTCAACAAGCATGAGTTTGCCATCAA
genomic: TACTTTGGCCATTGTATCAGAAAGGCTGAAACTGTCTACTGTACATGAAGgtggtgttgt ... ctttcatcagGATTTTCTGAATCTGTTAAGGTGGTGTCAACAAGCATGAGTTTGCCATCAA
EST: gi|19351752|gb|BM896284.1|BM896284
EST:     TACTTTGGCCATTGTATCAGAAAGGCTGAAACTGTCTACTGTACATGAAG                         GATTTTCTGAATCTGTTAAGGTGGTGTCAACAAGCATGAGTTTGCCATCAA
genomic: TACTTTGGCCATTGTATCAGAAAGGCTGAAACTGTCTACTGTACATGAAGgtggtgttgt ... ctttcatcagGATTTTCTGAATCTGTTAAGGTGGTGTCAACAAGCATGAGTTTGCCATCAA
EST: gi|32806646|gb|CD958880.1|CD958880
EST:     TACTTTGGCCATTGTATCAGAAAGGCTGAAACTGTCTACTGTACATGAAG                         GATTTTCTGAATCTGTTA
genomic: TACTTTGGCCATTGTATCAGAAAGGCTGAAACTGTCTACTGTACATGAAGgtggtgttgt ... ctttcatcagGATTTTCTGAATCTGTTA
EST: gi|87153866|gb|DY398655.1|DY398655
EST:     TACTTTGGCCATTGTATCAGAAAGGCTGAAACTGTCTACTGTACATGAAG                         GATTTTCTGAATCTGTTAAGGTGGTGTCAACAAGCATGAGTTTGCCATCAA
genomic: TACTTTGGCCATTGTATCAGAAAGGCTGAAACTGTCTACTGTACATGAAGgtggtgttgt ... ctttcatcagGATTTTCTGAATCTGTTAAGGTGGTGTCAACAAGCATGAGTTTGCCATCAA
EST: gi|22489504|gb|BU049427.1|BU049427
EST:     TACTTTGGCCATTGTATCAGAAAGGCTGAAACTGTCTACTGTACATGAAG                         GATTTTCTGAATCTGTTAAGGTGGTGTCAACAAGCATGAGTTTGCCATCAA
genomic: TACTTTGGCCATTGTATCAGAAAGGCTGAAACTGTCTACTGTACATGAAGgtggtgttgt ... ctttcatcagGATTTTCTGAATCTGTTAAGGTGGTGTCAACAAGCATGAGTTTGCCATCAA
EST: gi|87153811|gb|DY398600.1|DY398600
EST:     TACTTTGGCCATTGTATCAGAAAGGCTGAAACTGTCTACTGTACATGAAG                         GATTTTCTGAATCTGTTAAGGTGGTGTCAACAAGCATGAGTTTGCCATCAA
genomic: TACTTTGGCCATTGTATCAGAAAGGCTGAAACTGTCTACTGTACATGAAGgtggtgttgt ... ctttcatcagGATTTTCTGAATCTGTTAAGGTGGTGTCAACAAGCATGAGTTTGCCATCAA

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: 116

GTGGGAAGGAACTTGAAAGATTTGCCATCACCTACTTTGGCCATTGTATCAGAAAGGCTGAAACTGTCTACTGTACATGAAGgtggtgttgt ... ctttcatcagGATTTTCTGAATCTGTTAAGGTGGTGTCAACAAGCATGAGTTTGCCATCAAAAGCTGGTTTAAAGAACAATAAACATGGTCCTAACGATCGTGGTTCTAA


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 48

GTGGGAAGGAACTTGAAAGATTTGCCATCACCTACTTTGGCCATTGTATCAGAAAGGCTGAAACTGTCTACTGTACATGAAGgtggtgttgt ... ctttcatcagGATTTTCTGAATCTGTTAAGGTGGTGTCAACAAGCATGAGTTTGCCATCAAAAGCTGGTTTAAAGAACAATAAACATGGTCCTAACGATCGTGGTTCTAA


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

GTGGGAAGGAACTTGAAAGATTTGCCATCACCTACTTTGGCCATTGTATCAGAAAGGCTGAAACTGTCTACTGTACATGAAGgtggtgttgt ... ctttcatcagGATTTTCTGAATCTGTTAAGGTGGTGTCAACAAGCATGAGTTTGCCATCAAAAGCTGGTTTAAAGAACAATAAACATGGTCCTAACGATCGTGGTTCTAA


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 83

GTGGGAAGGAACTTGAAAGATTTGCCATCACCTACTTTGGCCATTGTATCAGAAAGGCTGAAACTGTCTACTGTACATGAAGgtggtgttgt ... ctttcatcagGATTTTCTGAATCTGTTAAGGTGGTGTCAACAAGCATGAGTTTGCCATCAAAAGCTGGTTTAAAGAACAATAAACATGGTCCTAACGATCGTGGTTCTAA