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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatctgctctactctctgtttcttttggttgttttatggtatcatgacacagtcagctgtgcagGCAACAGTTGCCTATTATTTACTCTTGGACAATAGGCTTCGTACAACCAGTGGTTATCTTGGATCTGAGTTTCAAGAATCTATG

Basic information

species Zea mays
transcript GRMZM2G077278_T01
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G077278_T01 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os05g45420.3 (Oryza sativa), 3'ss of exon 7
gtatctgctctactct-ctgtttcttttggttgttttatggtat---catgacacagtcagc------tgtgcagGCAACAGTTGCCTATTATTTACTCTTGGACAATAGGCTTCGTACAACCAGTGGTTATCTTGGATCTGAGTTTCAAGAATCTATG
|| | ||||  ||||   || | || || |||||||  |||      ||||||| |||          ||||||||| ||||||||||| |||||||| |||||||||||||| || ||||||||||| || |||||| ||||||| || |||||||||
gtgtttgcttcactccattgctcctctttgttgtttcttggggaatgcatgacaaagtttctgaataatgtgcagGCGACAGTTGCCTACTATTTACTATTGGACAATAGGCTGCGCACAACCAGTGGCTACCTTGGAGCTGAGTTCCATGAATCTATG
















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|211090137|gb|FL283399.1|FL283399
EST:     TTGACAAGAATCAGCTAATTGAATCTCTGCAAAACAGATTGCAGAATGAG                         GCAACAGTTGCCTATTATTTACTCTTGGACAATAGGCTTCGTACAACCAGT
genomic: TTGACAAGAATCAGCTAATTGAATCTCTGCAAAACAGATTGCAGAATGAGgtatctgctc ... agctgtgcagGCAACAGTTGCCTATTATTTACTCTTGGACAATAGGCTTCGTACAACCAGT
EST: gi|76934830|gb|DV174040.1|DV174040
EST:     TTGACAAGAATCAGCTAATTGAATCTCTGCAAAACAGATTGCAGAATGAG                         GCAACAGTTGCCTATTATTTACTCTTGGACAATAGGCTTCGTACAACCAGT
genomic: TTGACAAGAATCAGCTAATTGAATCTCTGCAAAACAGATTGCAGAATGAGgtatctgctc ... agctgtgcagGCAACAGTTGCCTATTATTTACTCTTGGACAATAGGCTTCGTACAACCAGT
EST: gi|76933421|gb|DV173441.1|DV173441
EST:     TTGACAAGAATCAGCTAATTGAATCTCTGCAAAACAGATTGCAGAATGAG                         GCAACAGTTGCCTATTATTTACTCTTGGACAATAGGCTTCGTACAACCAGT
genomic: TTGACAAGAATCAGCTAATTGAATCTCTGCAAAACAGATTGCAGAATGAGgtatctgctc ... agctgtgcagGCAACAGTTGCCTATTATTTACTCTTGGACAATAGGCTTCGTACAACCAGT
EST: gi|15312951|gb|BI478479.1|BI478479
EST:     TTGACAAGAATCAGCTAATTGAATCTCTGCAAAACAGATTGCAGAATGAG                         GCAACAGTTGCCTATTATTTACTCTTGGACAATAGGCTTCGTACAACCAGT
genomic: TTGACAAGAATCAGCTAATTGAATCTCTGCAAAACAGATTGCAGAATGAGgtatctgctc ... agctgtgcagGCAACAGTTGCCTATTATTTACTCTTGGACAATAGGCTTCGTACAACCAGT
EST: gi|67028292|gb|CO457041.1|CO457041
EST:     TTGACAAGAATCAGCTAATTGAATCTCTGCAAAACAGATTGCAGAATGAG                         GCAACAGTTGCCTATTATTTACTCTTGGACAATAGGCTTCGTACAACCAGT
genomic: TTGACAAGAATCAGCTAATTGAATCTCTGCAAAACAGATTGCAGAATGAGgtatctgctc ... agctgtgcagGCAACAGTTGCCTATTATTTACTCTTGGACAATAGGCTTCGTACAACCAGT
EST: gi|211429825|gb|FL327475.1|FL327475
EST:     TTGACAAGAATCAGCTAATTGAATCTCTGCAAAACAGATTGCAGAATGAG                         GCAACAGTTGCCTATTATTTACTCTTGGACAATAGGCTTCGTACAACCAGT
genomic: TTGACAAGAATCAGCTAATTGAATCTCTGCAAAACAGATTGCAGAATGAGgtatctgctc ... agctgtgcagGCAACAGTTGCCTATTATTTACTCTTGGACAATAGGCTTCGTACAACCAGT

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: 161

GTCGACGAGGAAACTCTTAATGATGTTATTAAGATGGGTTTTGACAAGAATCAGCTAATTGAATCTCTGCAAAACAGATTGCAGAATGAGgtatctgctc ... agctgtgcagGCAACAGTTGCCTATTATTTACTCTTGGACAATAGGCTTCGTACAACCAGTGGTTATCTTGGATCTGAGTTTCAAGAATCTATG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 118

GTCGACGAGGAAACTCTTAATGATGTTATTAAGATGGGTTTTGACAAGAATCAGCTAATTGAATCTCTGCAAAACAGATTGCAGAATGAGgtatctgctc ... agctgtgcagGCAACAGTTGCCTATTATTTACTCTTGGACAATAGGCTTCGTACAACCAGTGGTTATCTTGGATCTGAGTTTCAAGAATCTATG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 295

GTCGACGAGGAAACTCTTAATGATGTTATTAAGATGGGTTTTGACAAGAATCAGCTAATTGAATCTCTGCAAAACAGATTGCAGAATGAGgtatctgctc ... agctgtgcagGCAACAGTTGCCTATTATTTACTCTTGGACAATAGGCTTCGTACAACCAGTGGTTATCTTGGATCTGAGTTTCAAGAATCTATG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 133

GTCGACGAGGAAACTCTTAATGATGTTATTAAGATGGGTTTTGACAAGAATCAGCTAATTGAATCTCTGCAAAACAGATTGCAGAATGAGgtatctgctc ... agctgtgcagGCAACAGTTGCCTATTATTTACTCTTGGACAATAGGCTTCGTACAACCAGTGGTTATCTTGGATCTGAGTTTCAAGAATCTATG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tactctctgtttcttttggttgttttatggtatcatgacacagtcagctgtgcagGCAACAGTTGCCTATTATTTACTCTTGGACAATAGGCTTCGTACAACCAGTGGTTATCTTGGATCTGAGTTTCAAGAATCTATG
                   ttgttttat  TA-rich tract