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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CGCCGTCTCCTAAACCTTAGCCGCGCGGACGCCCACCAGCAGCTGCCCCCTTGCTGTCGCCGCCTCTCCGCGCGACCGATCTACCGCCGCCGCCACCATGgtaacctcctacacttattcctccccgccgactctcgttgtgcagatgtttttgtatcgtgttctgattccgtgacgactgttgccgcag

Basic information

species Zea mays
transcript GRMZM2G178341_T02
intron # 1
splice site 5'
intron type U2

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|15312798|gb|BI478389.1|BI478389
EST:     GATCTACCGCCGCCGCCACCATG                         TCGCTGATCGCCGGCGAGGACTTCCAACATATTCTGCGTCTGCTGAACACC
genomic: GATCTACCGCCGCCGCCACCATGgtaacctcct ... gttgccgcagTCGCTGATCGCCGGCGAGGACTTCCAACATATTCTGCGTCTGCTGAACACC
EST: gi|211506692|gb|FL164921.1|FL164921
EST:     GCTGTCGCCGCCTCTCTCCGCGCGACCGATCTACCGCCGCCGCCACCATG                         TCGCTGATCGCCGGCGAGGACTTCCAACATATTCTGCGTCTGCTGAACACC
genomic: GCTGTCGCCG-C-CTCTCCGCGCGACCGATCTACCGCCGCCGCCACCATGgtaacctcct ... gttgccgcagTCGCTGATCGCCGGCGAGGACTTCCAACATATTCTGCGTCTGCTGAACACC
EST: gi|211504327|gb|FL164902.1|FL164902
EST:     GCTGTCGCCGCCTCTCTCCGCGCGACCGATCTACCGCCGCCGCCACCATG                         TCGCTGATCGCCGGCGAGGACTTCCAACATATTCTGCGTCTGCTGAACACC
genomic: GCTGTCGCCG-C-CTCTCCGCGCGACCGATCTACCGCCGCCGCCACCATGgtaacctcct ... gttgccgcagTCGCTGATCGCCGGCGAGGACTTCCAACATATTCTGCGTCTGCTGAACACC
EST: gi|211004160|gb|FL323112.1|FL323112
EST:     GCTGTCGCCGCCTCTCTCCGCGCGACCGATCTACCGCCGCCGCCACCATG                         TCGCTGATCGCCGGCGAGGACTTCCAACATATTCTGCGTCTGCTGAACACC
genomic: GCTGTCGCCG-C-CTCTCCGCGCGACCGATCTACCGCCGCCGCCACCATGgtaacctcct ... gttgccgcagTCGCTGATCGCCGGCGAGGACTTCCAACATATTCTGCGTCTGCTGAACACC
EST: gi|211506690|gb|FL164919.1|FL164919
EST:     TTGCTGTCGCCGCCTCTCCGCGCGACCGATCTACCGCCGCCGCCACCATG                         TCGCTGATCGCCGGCGAGGACTTCCAACATATTCTGCGTCTGCTGAACACC
genomic: TTGCTGTCGCCGCCTCTCCGCGCGACCGATCTACCGCCGCCGCCACCATGgtaacctcct ... gttgccgcagTCGCTGATCGCCGGCGAGGACTTCCAACATATTCTGCGTCTGCTGAACACC
EST: gi|211075481|gb|FL340028.1|FL340028
EST:     TTGCTGTCGCCGCCTCTCCGCGCGACCGATCTACCGCCGCCGCCACCATG                         TCGCTGATCGCCGGCGAGGACTTCCAACATATTCTGCGTCTGCTGAACACC
genomic: TTGCTGTCGCCGCCTCTCCGCGCGACCGATCTACCGCCGCCGCCACCATGgtaacctcct ... gttgccgcagTCGCTGATCGCCGGCGAGGACTTCCAACATATTCTGCGTCTGCTGAACACC
EST: gi|211506702|gb|FL164931.1|FL164931
EST:     TTGCTGTCGCCGCCTCTCCGCGCGACCGATCTACCGCCGCCGCCACCATG                         TCGCTGATCGCCGGCGAGGACTTCCAACATATTCTGCGTCTGCTGAACACC
genomic: TTGCTGTCGCCGCCTCTCCGCGCGACCGATCTACCGCCGCCGCCACCATGgtaacctcct ... gttgccgcagTCGCTGATCGCCGGCGAGGACTTCCAACATATTCTGCGTCTGCTGAACACC
EST: gi|211415860|gb|FL164865.1|FL164865
EST:     TTGCTGTCGCCGCCTCTCCGCGCGACCGATCTACCGCCGCCGCCACCATG                         TCGCTGATCGCCGGCGAGGACTTCCAACATATTCTGCGTCTGCTGAACACC
genomic: TTGCTGTCGCCGCCTCTCCGCGCGACCGATCTACCGCCGCCGCCACCATGgtaacctcct ... gttgccgcagTCGCTGATCGCCGGCGAGGACTTCCAACATATTCTGCGTCTGCTGAACACC
EST: gi|211504335|gb|FL164910.1|FL164910
EST:     GCTGTCGCCGCCTCTCTCCGCGCGACCGATCTACCGCCGCCGCCACCATG                         TCGCTGATCGCCGGCGAGGACTTCCAACATATTCTGCGTCTGCTGAACACC
genomic: GCTGTCGCCG-C-CTCTCCGCGCGACCGATCTACCGCCGCCGCCACCATGgtaacctcct ... gttgccgcagTCGCTGATCGCCGGCGAGGACTTCCAACATATTCTGCGTCTGCTGAACACC
EST: gi|211504333|gb|FL164908.1|FL164908
EST:     GCTGTCGCCGCCTCTCTCCGCGCGACCGATCTACCGCCGCCGCCACCATG                         TCGCTGATCGCCGGCGAGGACTTCCAACATATTCTGCGTCTGCTGAACACC
genomic: GCTGTCGCCG-C-CTCTCCGCGCGACCGATCTACCGCCGCCGCCACCATGgtaacctcct ... gttgccgcagTCGCTGATCGCCGGCGAGGACTTCCAACATATTCTGCGTCTGCTGAACACC

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: 371

CGCCGTCTCCTAAACCTTAGCCGCGCGGACGCCCACCAGCAGCTGCCCCCTTGCTGTCGCCGCCTCTCCGCGCGACCGATCTACCGCCGCCGCCACCATGgtaacctcct ... gttgccgcagTCGCTGATCGCCGGCGAGGACTTCCAACATATTCTGCGTCTGCTGAACACCAACGTGGATGGGAAGCAGAAGATCATGTTCGCCATGACCTCCATAAAGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 237

CGCCGTCTCCTAAACCTTAGCCGCGCGGACGCCCACCAGCAGCTGCCCCCTTGCTGTCGCCGCCTCTCCGCGCGACCGATCTACCGCCGCCGCCACCATGgtaacctcct ... gttgccgcagTCGCTGATCGCCGGCGAGGACTTCCAACATATTCTGCGTCTGCTGAACACCAACGTGGATGGGAAGCAGAAGATCATGTTCGCCATGACCTCCATAAAGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 226

CGCCGTCTCCTAAACCTTAGCCGCGCGGACGCCCACCAGCAGCTGCCCCCTTGCTGTCGCCGCCTCTCCGCGCGACCGATCTACCGCCGCCGCCACCATGgtaacctcct ... gttgccgcagTCGCTGATCGCCGGCGAGGACTTCCAACATATTCTGCGTCTGCTGAACACCAACGTGGATGGGAAGCAGAAGATCATGTTCGCCATGACCTCCATAAAGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 204

CGCCGTCTCCTAAACCTTAGCCGCGCGGACGCCCACCAGCAGCTGCCCCCTTGCTGTCGCCGCCTCTCCGCGCGACCGATCTACCGCCGCCGCCACCATGgtaacctcct ... gttgccgcagTCGCTGATCGCCGGCGAGGACTTCCAACATATTCTGCGTCTGCTGAACACCAACGTGGATGGGAAGCAGAAGATCATGTTCGCCATGACCTCCATAAAGG