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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaaggcccttctttgagcgatccgttagttgaagcttggcattgttttgtctatttttggctgcgttatgttaatactcggtctgtttcctttgacttagCCTGTCAAGTCTGGATCAGCGGATGCGGCCGCCCCAAATGACGCAATTCCCGCTGTCCAAGA

Basic information

species Zea mays
transcript GRMZM2G023652_T01
intron # 3
splice site 3'
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|31355088|gb|CD439445.1|CD439445
EST:     GACACCTGTCGCTCGCCGGTCGATG                         CCTGTCAAGTCTGGATCAGCGGATGCGGCCGCCCCAAATGACGCAATTCCC
genomic: GACACCTGTCGCTCGCCGGTCGATGgtaaaggccc ... tttgacttagCCTGTCAAGTCTGGATCAGCGGATGCGGCCGCCCCAAATGACGCAATTCCC
EST: gi|21809702|gb|BQ668020.1|BQ668020
EST:     GAAGAAGGCGAATTCAGCGCGGACACCTGTCGCTCGCCGGTCGATG                         CCTGTCAAGTCTGGATCAGCGGATGCGGCCGCCCCAAATGACGCAATTCCC
genomic: GAAGAAGGCGAATTCAGCGCGGACACCTGTCGCTCGCCGGTCGATGgtaaaggccc ... tttgacttagCCTGTCAAGTCTGGATCAGCGGATGCGGCCGCCCCAAATGACGCAATTCCC
EST: gi|21891697|gb|BQ744910.1|BQ744910
EST:     CCGAGAAGAAGGCGAATTCAGCGCGGACACCTGTCGCTCGCCGGTCGATG                         CCTGTCAAGTCTGGATCAGCGGATGCGGCCGCCCCAAATGACGCAATTCCC
genomic: CCGAGAAGAAGGCGAATTCAGCGCGGACACCTGTCGCTCGCCGGTCGATGgtaaaggccc ... tttgacttagCCTGTCAAGTCTGGATCAGCGGATGCGGCCGCCCCAAATGACGCAATTCCC

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), 48 (downstream exon)
Score: 177

GCCGGGCAGCCGAGAAGAAGGCGAATTCAGCGCGGACACCTGTCGCTCGCCGGTCGATGgtaaaggccc ... tttgacttagCCTGTCAAGTCTGGATCAGCGGATGCGGCCGCCCCAAATGACGCAATTCCCGCTGTCCAAGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 114

GCCGGGCAGCCGAGAAGAAGGCGAATTCAGCGCGGACACCTGTCGCTCGCCGGTCGATGgtaaaggccc ... tttgacttagCCTGTCAAGTCTGGATCAGCGGATGCGGCCGCCCCAAATGACGCAATTCCCGCTGTCCAAGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 125

GCCGGGCAGCCGAGAAGAAGGCGAATTCAGCGCGGACACCTGTCGCTCGCCGGTCGATGgtaaaggccc ... tttgacttagCCTGTCAAGTCTGGATCAGCGGATGCGGCCGCCCCAAATGACGCAATTCCCGCTGTCCAAGA


Block sizes: 49 (upstream exon), 44 (downstream exon)
Score: 144

GCCGGGCAGCCGAGAAGAAGGCGAATTCAGCGCGGACACCTGTCGCTCGCCGGTCGATGgtaaaggccc ... tttgacttagCCTGTCAAGTCTGGATCAGCGGATGCGGCCGCCCCAAATGACGCAATTCCCGCTGTCCAAGA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttgtctatttttggctgcgttatgttaatactcggtctgtttcctttgacttagCCTGTCAAGTCTGGATCAGCGGATGCGGCCGCCCCAAATGACGCAATTCCCGCTGTCCAAGA
                                    tctgtttccttt  CT-rich tract
                    ttatgttaata  TA-rich tract