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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatatctattcccttctatttgtactttcattttttgtttatgcttatttgtatggcatgcagTTCACAAGCATTGTTTCCTGGGAATGAAATTGCCGAGATTTACCATGAAATGGCTAGAAAG

Basic information

species Zea mays
transcript GRMZM2G096553_T03
intron # 14
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|60347237|gb|DN214210.1|DN214210
EST:     CTACCTTTGCCTGG                         TTCACAAGCATTGTTTCCTGGGAATGAAATTGCCGAGATTTACCATGAAAT
genomic: CTACCTTTGCCTGGgtaatatcta ... tggcatgcagTTCACAAGCATTGTTTCCTGGGAATGAAATTGCCGAGATTTACCATGAAAT
EST: gi|13149317|gb|BG319639.1|BG319639
EST:     TTTACTAA-GGGATATACAC-TTTGATGAT-MTMTCCTACC-TTGCCTGG                         TTCACAAGCATTGTTTCCTGGGAATGAAATTGCCGAGATTTACCATGAAAT
genomic: TTTACTAAGGGGATATACACTTTTGATGATGTTGTCCTACCTTTGCCTGGgtaatatcta ... tggcatgcagTTCACAAGCATTGTTTCCTGGGAATGAAATTGCCGAGATTTACCATGAAAT
EST: gi|211061095|gb|FL320235.1|FL320235
EST:     TTTACTAAGGGGATATACACTTTTGATGATGTTGTCCTACCTTTGCCTGG                         TTCACAAGCATTGTTTCMTGGGAATGAAATTGCCGAGATTTACCATGAAAT
genomic: TTTACTAAGGGGATATACACTTTTGATGATGTTGTCCTACCTTTGCCTGGgtaatatcta ... tggcatgcagTTCACAAGCATTGTTTCCTGGGAATGAAATTGCCGAGATTTACCATGAAAT
EST: gi|6031366|gb|AW076223.1|AW076223
EST:     TTTACTAAGGGGATATACACTTTTGATGATGTTGTCCTACCTTTGCCTGG                         TTCACAAGCATTGTTTCCTGGGAATGAAATTGCCGAGATTTACCATGAAAT
genomic: TTTACTAAGGGGATATACACTTTTGATGATGTTGTCCTACCTTTGCCTGGgtaatatcta ... tggcatgcagTTCACAAGCATTGTTTCCTGGGAATGAAATTGCCGAGATTTACCATGAAAT

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: 48 (upstream exon), 49 (downstream exon)
Score: 161

ATAGTTGATTCTGGAGATTTTACTAAGGGGATATACACTTTTGATGATGTTGTCCTACCTTTGCCTGGgtaatatcta ... tggcatgcagTTCACAAGCATTGTTTCCTGGGAATGAAATTGCCGAGATTTACCATGAAATGGCTAGAAAG


Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 35

ATAGTTGATTCTGGAGATTTTACTAAGGGGATATACACTTTTGATGATGTTGTCCTACCTTTGCCTGGgtaatatcta ... tggcatgcagTTCACAAGCATTGTTTCCTGGGAATGAAATTGCCGAGATTTACCATGAAATGGCTAGAAAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 50

ATAGTTGATTCTGGAGATTTTACTAAGGGGATATACACTTTTGATGATGTTGTCCTACCTTTGCCTGGgtaatatcta ... tggcatgcagTTCACAAGCATTGTTTCCTGGGAATGAAATTGCCGAGATTTACCATGAAATGGCTAGAAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 42

ATAGTTGATTCTGGAGATTTTACTAAGGGGATATACACTTTTGATGATGTTGTCCTACCTTTGCCTGGgtaatatcta ... tggcatgcagTTCACAAGCATTGTTTCCTGGGAATGAAATTGCCGAGATTTACCATGAAATGGCTAGAAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcccttctatttgtactttcattttttgtttatgcttatttgtatggcatgcagTTCACAAGCATTGTTTCCTGGGAATGAAATTGCCGAGATTTACCATGAAATGGCTAGAAAG
                     attttttgtttatgct  TA-rich tract