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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTACTTCGCGGTTTAGGAAATCTTGTAGCCGGTGATGGTTACATGGTTGATTCAGTCCTTATTGTTGGAAACAGTGTAACAGgttcgctcatgattggataatcctttgtagctaattgtatatgagcaccataatttcacttgtaatgatgtttatcatcagctaacagcttgccgttctagagtatgcgttagtctccaagtactaagttactaactaaattttgttccag

Basic information

species Zea mays
transcript GRMZM2G165692_T01
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G165692_T01 (Zea mays), 5'ss of exon 8
lower sequence: LOC_Os01g06470.1 (Oryza sativa), 5'ss of exon 8
GTACTTCGCGGTTTAGGAAATCTTGTAGCCGGTGATGGTTACATGGTTGATTCAGTCCTTATTGTTGGAAACAGTGTAACAGgttcgctcatgattggataatcctttgtagctaattgtatatgagcaccataatttcacttgtaatgatgtttatcatcagctaacag---cttgccgttctagagtatgcgttagtctccaagtactaagttactaactaaattttgtt-ccag
|| ||||| ||||| ||||||||| | |||| |||||  |||||||||||||||||||| | ||||||| ||| | | |  |||   |||        || | |||||                    ||||||  |    ||  |||| |  ||  |||||| ||||||   |||| | |||| ||  ||   |     | ||| |   |||  ||||||||||| |||||   ||
GTGCTTCGTGGTTTGGGAAATCTTATTGCCGCTGATGACTACATGGTTGATTCAGTCCTAACTGTTGGACACAATATCATTGgtaaactcc-------atgacccttttcc----------------taccata--tctgtttacaatgtttatt--catcagttaacagttccttgtctttctggaaaatatatc---ttgcaaattgcaagc-actaactaaatgttgttattag
















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|78080887|gb|DV509299.1|DV509299
EST:     TCAGTCCTTA-TGTTGGAAACAGTTGTAACAG                         ATCAAGCCTTATCAAGTCTTATCAAGTGTTTGAAGAGCGACCATAGGGTT
genomic: TCAGTCCTTATTGTTGGAAACAG-TGTAACAGgttcgctcat ... tttgttccagATCAAGCCTTATCAAGTCTTATCAAGTGTTTGAAGAGCGACCATAGGGTT
EST: gi|86467944|gb|DY234314.1|DY234314
EST:     GAAACAGTGTAACAG                         ATCAAGCCTTATCAAGTCTTATCAAGTGTTTGAAGAGCGACCATAGGGTTC
genomic: GAAACAGTGTAACAGgttcgctcat ... tttgttccagATCAAGCCTTATCAAGTCTTATCAAGTGTTTGAAGAGCGACCATAGGGTTC
EST: gi|60395305|gb|DN228174.1|DN228174
EST:     TGGAAACAGTGTAACAG                         ATCAAGCCTTATCAAGTCTTATCAAGTGTTTGAAGAGCGACCATAGGGTTC
genomic: TGGAAACAGTGTAACAGgttcgctcat ... tttgttccagATCAAGCCTTATCAAGTCTTATCAAGTGTTTGAAGAGCGACCATAGGGTTC

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), 41 (downstream exon)
Score: 35

GTACTTCGCGGTTTAGGAAATCTTGTAGCCGGTGATGGTTACATGGTTGATTCAGTCCTTATTGTTGGAAACAGTGTAACAGgttcgctcat ... tttgttccagATCAAGCCTTATCAAGTCTTATCAAGTGTTTGAAGAGCGACCATAGGGTTCTCAAGAAG


Block sizes: 45 (upstream exon), 47 (downstream exon)
Score: 103

GTACTTCGCGGTTTAGGAAATCTTGTAGCCGGTGATGGTTACATGGTTGATTCAGTCCTTATTGTTGGAAACAGTGTAACAGgttcgctcat ... tttgttccagATCAAGCCTTATCAAGTCTTATCAAGTGTTTGAAGAGCGACCATAGGGTTCTCAAGAAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 126

GTACTTCGCGGTTTAGGAAATCTTGTAGCCGGTGATGGTTACATGGTTGATTCAGTCCTTATTGTTGGAAACAGTGTAACAGgttcgctcat ... tttgttccagATCAAGCCTTATCAAGTCTTATCAAGTGTTTGAAGAGCGACCATAGGGTTCTCAAGAAG


Block sizes: 45 (upstream exon), 45 (downstream exon)
Score: 26

GTACTTCGCGGTTTAGGAAATCTTGTAGCCGGTGATGGTTACATGGTTGATTCAGTCCTTATTGTTGGAAACAGTGTAACAGgttcgctcat ... tttgttccagATCAAGCCTTATCAAGTCTTATCAAGTGTTTGAAGAGCGACCATAGGGTTCTCAAGAAG