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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTATTTGATACGCTCAGGATAATTATGGTTGTATTGGGCATGACATTTGTCTTTGTTGGGATCTCCTTGCTAGCACCCGATGACACTAAAGgtttgtaaaaggttgattttcatgtgctttcacacagaagattttgactcttggacaattgtcaccag

Basic information

species Zea mays
transcript GRMZM2G144254_T06
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G144254_T04 (Zea mays), 5'ss of exon 8
lower sequence: LOC_Os02g31874.1 (Oryza sativa), 5'ss of exon 11
GTATTTGATACGCTCAGGATAATTATGGTTGTATTGGGCATGACATTTGTCTTTGTTGGGATCTCCTTGCTAGCACCCGATGACACTAAAGgtttgtaaaaggttgattttcatgtgctttcacacagaagattttgactct---tggacaattgtcaccag
||||||||||| || |||||| | ||| |||||||||||||||||| ||||||| | || |||||||| || |||||||| |||| ||||||||||| ||  ||| | |  | |||||||| ||| | |      ||||| |   | || |||| |   |||
GTATTTGATACCCTGAGGATAGTGATGTTTGTATTGGGCATGACATCTGTCTTTATAGGCATCTCCTTACTGGCACCCGACGACAGTAAAGgtttgtgaa--gttcactgccgtgtgcttttacagaaatatacatgactttaacttgagaattcttggcag

upper sequence: GRMZM2G144254_T04 (Zea mays), 5'ss of exon 8
lower sequence: LOC_Os02g31874.2 (Oryza sativa), 5'ss of exon 11
GTATTTGATACGCTCAGGATAATTATGGTTGTATTGGGCATGACATTTGTCTTTGTTGGGATCTCCTTGCTAGCACCCGATGACACTAAAGgtttgtaaaaggttgattttcatgtgctttcacacagaagattttgactct---tggacaattgtcaccag------------
||||||||||| || |||||| | ||| |||||||||||||||||| ||||||| | || |||||||| || |||||||| |||| ||||||||||| ||  ||| | |  | |||||||| ||| | |      ||||| |   | || |||| |   |||            
GTATTTGATACCCTGAGGATAGTGATGTTTGTATTGGGCATGACATCTGTCTTTATAGGCATCTCCTTACTGGCACCCGACGACAGTAAAGgtttgtgaa--gttcactgccgtgtgcttttacagaaatatacatgactttaacttgagaattcttggcagttgacaccaaag
















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|60359035|gb|DN226008.1|DN226008
EST:     GACATTTGTCTTTGTTGGGATCTCCTTGCTAGCACCCGATGACACTAAAG                         CTGATACGAAAGATGGTTCGAGCACTGCCGAGGAATCTATAATTGATATGG
genomic: GACATTTGTCTTTGTTGGGATCTCCTTGCTAGCACCCGATGACACTAAAGgtttgtaaaa ... ttgtcaccagCTGATACGAAAGATGGTTCGAGCACTGCCGAGGAATCTATAATTGATATGG
EST: gi|93281607|gb|EB673871.1|EB673871
EST:     GACATTTGTCTTTGTTGGGATCTCCTTGCTAGCACCCGATGACACTAAAG                         CTGATACGAAAGATGGTTCGAGCACTGCCGAGGAATCTATAATTGATATGG
genomic: GACATTTGTCTTTGTTGGGATCTCCTTGCTAGCACCCGATGACACTAAAGgtttgtaaaa ... ttgtcaccagCTGATACGAAAGATGGTTCGAGCACTGCCGAGGAATCTATAATTGATATGG
EST: gi|32844477|gb|CD984158.1|CD984158
EST:     GACATTTGTCTTTGTTGGGATCTCCTTGCTAGCACCCGATGACACTAAAG                         CTGATACGAAAGATGGTTCGAGCACTGCCGAGGAATCTATAATTGATATGG
genomic: GACATTTGTCTTTGTTGGGATCTCCTTGCTAGCACCCGATGACACTAAAGgtttgtaaaa ... ttgtcaccagCTGATACGAAAGATGGTTCGAGCACTGCCGAGGAATCTATAATTGATATGG
EST: gi|5296213|gb|AI782893.1|AI782893
EST:     GACATTTGTCTTTGTTGGGATCTCCTTGCTAGCACCCGATGACACTAAAG                         CTGATACGAAAGATGGTTCGAGCACTGCCGAGGAATCTATAATTGATATGG
genomic: GACATTTGTCTTTGTTGGGATCTCCTTGCTAGCACCCGATGACACTAAAGgtttgtaaaa ... ttgtcaccagCTGATACGAAAGATGGTTCGAGCACTGCCGAGGAATCTATAATTGATATGG
EST: gi|32808432|gb|CD960666.1|CD960666
EST:     GATCTCCTTGCTAGCACCCGATGACACTAAAG                         CTGATACGAAAGATGGTTCGAGCACTGCCGAGGAATCTATAATTGATATGG
genomic: GATCTCCTTGCTAGCACCCGATGACACTAAAGgtttgtaaaa ... ttgtcaccagCTGATACGAAAGATGGTTCGAGCACTGCCGAGGAATCTATAATTGATATGG
EST: gi|6828189|gb|AW331832.1|AW331832
EST:     GACATTTGTCTTTGTTGGGATCTCCTTGCTAGCACCCGATGACACTAAAG                         CTGATACGAAAGATGGTTCGAGCNCTGCCGAGGAATCTATAATTGATATGG
genomic: GACATTTGTCTTTGTTGGGATCTCCTTGCTAGCACCCGATGACACTAAAGgtttgtaaaa ... ttgtcaccagCTGATACGAAAGATGGTTCGAGCACTGCCGAGGAATCTATAATTGATATGG
EST: gi|6227147|gb|AW155676.1|AW155676
EST:     GACATTTGTCTTTGTTGGGATCTCCTTGCTAGCACCCGATGACACTAAAG                         CTGATACGAAAGATGGTTCGAGCACTGCCGAGGAATCTATAATTGATATGG
genomic: GACATTTGTCTTTGTTGGGATCTCCTTGCTAGCACCCGATGACACTAAAGgtttgtaaaa ... ttgtcaccagCTGATACGAAAGATGGTTCGAGCACTGCCGAGGAATCTATAATTGATATGG
EST: gi|32792658|gb|CD944894.1|CD944894
EST:     GATCTGCTTGCTAGCACCCGATGACACTAAAG                         CTGATACGAAAGATGGTTCGAGCACTGCCGAGGAATCTATAATTGATATGG
genomic: GATCTCCTTGCTAGCACCCGATGACACTAAAGgtttgtaaaa ... ttgtcaccagCTGATACGAAAGATGGTTCGAGCACTGCCGAGGAATCTATAATTGATATGG
EST: gi|60351321|gb|DN218294.1|DN218294
EST:     CTTTGTTGGGATCTCCTTGCTAGCACCCGATGACACTAAAG                         CTGATACGAAAGATGGTTCGAGCACTGCCGAGGAATCTATAATTGATATGG
genomic: CTTTGTTGGGATCTCCTTGCTAGCACCCGATGACACTAAAGgtttgtaaaa ... ttgtcaccagCTGATACGAAAGATGGTTCGAGCACTGCCGAGGAATCTATAATTGATATGG
EST: gi|113701592|gb|EE679096.1|EE679096
EST:     GACATTTGTCTTTGTTGGGATCTCCTTGCTAGCACCCGATGACACTAAAG                         CTGATACGAAAGATGGTTCGAGCACTGCCGAGGAATCTATAATTGATATGG
genomic: GACATTTGTCTTTGTTGGGATCTCCTTGCTAGCACCCGATGACACTAAAGgtttgtaaaa ... ttgtcaccagCTGATACGAAAGATGGTTCGAGCACTGCCGAGGAATCTATAATTGATATGG
EST: gi|211277446|gb|FL309933.1|FL309933
EST:     GACATTTGTCTTTGTTGGGATCTCCTTGCTAGCACCCGATGACACTAAAG                         CTGATACGAAAGATGGTTCGAGCACTGCCGAGGAATCTATAATTGATATGG
genomic: GACATTTGTCTTTGTTGGGATCTCCTTGCTAGCACCCGATGACACTAAAGgtttgtaaaa ... ttgtcaccagCTGATACGAAAGATGGTTCGAGCACTGCCGAGGAATCTATAATTGATATGG
EST: gi|60350817|gb|DN217790.1|DN217790
EST:     GACATTTGTCTTTGTTGGGATCTCCTTGCTAGCACCCGATGACACTAAAG                         CTGATACGAAAGATGGTTCGAGCACTGCCGAGGAATCTATAATTGATATGG
genomic: GACATTTGTCTTTGTTGGGATCTCCTTGCTAGCACCCGATGACACTAAAGgtttgtaaaa ... ttgtcaccagCTGATACGAAAGATGGTTCGAGCACTGCCGAGGAATCTATAATTGATATGG
EST: gi|60356320|gb|DN223293.1|DN223293
EST:     GACATTTGTCTTTGTTGGGATCTCCTTGCTAGCACCCGATGACACTAAAG                         CTGATACGAAAGATGGTTCGAGCACTGCCGAGGAATCTATAATTGATATGG
genomic: GACATTTGTCTTTGTTGGGATCTCCTTGCTAGCACCCGATGACACTAAAGgtttgtaaaa ... ttgtcaccagCTGATACGAAAGATGGTTCGAGCACTGCCGAGGAATCTATAATTGATATGG
EST: gi|19822362|gb|BQ048386.1|BQ048386
EST:     GACATTTGTCTTTGTTGGGATCTCCTTGCTAGCACCCGATGACACTAAAG                         CTGATACGAAAGATGGTTCGAGCACTGCCGAGGAATCTATAATTGATATGG
genomic: GACATTTGTCTTTGTTGGGATCTCCTTGCTAGCACCCGATGACACTAAAGgtttgtaaaa ... ttgtcaccagCTGATACGAAAGATGGTTCGAGCACTGCCGAGGAATCTATAATTGATATGG
EST: gi|32844487|gb|CD984168.1|CD984168
EST:     GACATTTGTCTTTGTTGGGATCTCCTTGCTAGCACCCGATGACACTAAAG                         CTGATACGAAAGATGGTTCGAGCACTGCCGAGGAATCTATAATTGATATGG
genomic: GACATTTGTCTTTGTTGGGATCTCCTTGCTAGCACCCGATGACACTAAAGgtttgtaaaa ... ttgtcaccagCTGATACGAAAGATGGTTCGAGCACTGCCGAGGAATCTATAATTGATATGG
EST: gi|19822356|gb|BQ048380.1|BQ048380
EST:     GACATTTGTCTTTGTTGGGATCTCCTTGCTAGCACCCGATGACACTAAAG                         CTGATACGAAAGATGGTTCGAGCACTGCCGAGGAATCTATAATTGATATGG
genomic: GACATTTGTCTTTGTTGGGATCTCCTTGCTAGCACCCGATGACACTAAAGgtttgtaaaa ... ttgtcaccagCTGATACGAAAGATGGTTCGAGCACTGCCGAGGAATCTATAATTGATATGG
EST: gi|78022546|gb|DV490933.1|DV490933
EST:     GACATTTGTCTTTGTTGGGATCTCCTTGCTAGCACCCGATGACACTAAAG                         CTGATACGAAAGATGGTTCGAGCACTGCCGAGGAATCTATAATTGATATGG
genomic: GACATTTGTCTTTGTTGGGATCTCCTTGCTAGCACCCGATGACACTAAAGgtttgtaaaa ... ttgtcaccagCTGATACGAAAGATGGTTCGAGCACTGCCGAGGAATCTATAATTGATATGG

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: 5

GTATTTGATACGCTCAGGATAATTATGGTTGTATTGGGCATGACATTTGTCTTTGTTGGGATCTCCTTGCTAGCACCCGATGACACTAAAGgtttgtaaaa ... ttgtcaccagCTGATACGAAAGATGGTTCGAGCACTGCCGAGGAATCTATAATTGATATGGACAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 14

GTATTTGATACGCTCAGGATAATTATGGTTGTATTGGGCATGACATTTGTCTTTGTTGGGATCTCCTTGCTAGCACCCGATGACACTAAAGgtttgtaaaa ... ttgtcaccagCTGATACGAAAGATGGTTCGAGCACTGCCGAGGAATCTATAATTGATATGGACAG


Block sizes: 49 (upstream exon), 40 (downstream exon)
Score: 6

GTATTTGATACGCTCAGGATAATTATGGTTGTATTGGGCATGACATTTGTCTTTGTTGGGATCTCCTTGCTAGCACCCGATGACACTAAAGgtttgtaaaa ... ttgtcaccagCTGATACGAAAGATGGTTCGAGCACTGCCGAGGAATCTATAATTGATATGGACAG


Block sizes: 49 (upstream exon), 40 (downstream exon)
Score: 6

GTATTTGATACGCTCAGGATAATTATGGTTGTATTGGGCATGACATTTGTCTTTGTTGGGATCTCCTTGCTAGCACCCGATGACACTAAAGgtttgtaaaa ... ttgtcaccagCTGATACGAAAGATGGTTCGAGCACTGCCGAGGAATCTATAATTGATATGGACAG