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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTGCTCTTGTTAATGGGCTTGTCATGGGTGGTGGCGCTGCAATGGTTGCGCCACTAAAGTTTGCAGTTGTCACAGAGAAAACAgtatgtgccaacaatacaccattgaggcctatattatttacaatctattttaccttaactcttctacatgaattatcttcattgcatcgctcatgataaa...

Basic information

species Zea mays
transcript GRMZM2G042818_T01
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G042818_T01 (Zea mays), 5'ss of exon 6
lower sequence: LOC_Os01g54860.1 (Oryza sativa), 5'ss of exon 6
GTTGCTCTTGTTAATGGGCTTGTCATGGGTGGTGGCGCTGCAATGGTTGCGCCACTAAAGTTTGCAGTTGTCACAGAGAAAACAgtatgtgccaacaatacaccattgaggcctatattatttacaatctattttaccttaactcttctacatgaattatcttcattgcatcgctcatg-ataaa-
|| |||||||||||||| ||||||||||||||||| || || |||||||| ||||| ||||||||||||||||||||||||||||||||   ||  | | ||   |  ||  || |   |       | ||||  |  ||   | || ||  |   ||   |   ||||     | ||   |||| 
GTGGCTCTTGTTAATGGACTTGTCATGGGTGGTGGTGCAGCCATGGTTGCTCCACTGAAGTTTGCAGTTGTCACAGAGAAAACAgtatgcaacactagtccatagtccagttcttttggaggctttttttattccatattg--tgttatatgtttgtttgttggtttgctgtatttatctgtaaaa
















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|33942681|gb|CF349281.1|CF349281
EST:     GCGCTGCAATGGTTGCGCCACTAAAGTTTGCAGTTGTCACAGAGAAAACA                         ATCTTTGCTACTCCTGAGGCTAGTGTTGGATTGCACACAGATTGTAGCTTT
genomic: GCGCTGCAATGGTTGCGCCACTAAAGTTTGCAGTTGTCACAGAGAAAACAgtatgtgcca ... tttttgatagATCTTTGCTACTCCTGAGGCTAGTGTTGGATTGCACACAGATTGTAGCTTT
EST: gi|101390789|gb|EB817329.1|EB817329
EST:     GCGCTGCAATGGTTGCGCCACTAAAGTTTGCAGTTGTCACAGAGAAAACA                         ATCTTTGCTACTCCTGAGGCTAGTGTTGGATTGCACACAGATTGTAGCTTT
genomic: GCGCTGCAATGGTTGCGCCACTAAAGTTTGCAGTTGTCACAGAGAAAACAgtatgtgcca ... tttttgatagATCTTTGCTACTCCTGAGGCTAGTGTTGGATTGCACACAGATTGTAGCTTT
EST: gi|71448792|gb|DR829842.1|DR829842
EST:     GCGCTGCAATGGTTGCGCCACTAAAGTTTGCAGTTGTCACAGAGAAAACA                         ATCTTTGCTACTCCTGAGGCTAGTGTTGGATTGCACACAGATTGTAGCTTT
genomic: GCGCTGCAATGGTTGCGCCACTAAAGTTTGCAGTTGTCACAGAGAAAACAgtatgtgcca ... tttttgatagATCTTTGCTACTCCTGAGGCTAGTGTTGGATTGCACACAGATTGTAGCTTT
EST: gi|78109535|gb|DV527951.1|DV527951
EST:     GCGCTGCAATGGTTGCGCCACTAAAGTTTGCAGTTGTCACAGAGAAAACA                         ATCTTTGCTACTCCTGAGGCTAGTGTTGGATTGCACACAGATTGTAGCTTT
genomic: GCGCTGCAATGGTTGCGCCACTAAAGTTTGCAGTTGTCACAGAGAAAACAgtatgtgcca ... tttttgatagATCTTTGCTACTCCTGAGGCTAGTGTTGGATTGCACACAGATTGTAGCTTT
EST: gi|211380232|gb|FL081834.1|FL081834
EST:     GCGCTGCAATGGTTGCGCCACTAAAGTTTGCAGTTGTCACAGAGAAAACA                         ATCTTTGCTACTCCTGAGGCTAGTGTTTGGATTGCACACAGATTGT
genomic: GCGCTGCAATGGTTGCGCCACTAAAGTTTGCAGTTGTCACAGAGAAAACAgtatgtgcca ... tttttgatagATCTTTGCTACTCCTGAGGCTAGTGTT-GGATTGCACACAGATTGT
EST: gi|211380228|gb|FL081830.1|FL081830
EST:     GCGCTGCAATGGTTGCGCCACTAAAGTTTGCAGTTGTCACAGAGAAAACA                         ATCTTTGCTACTCCTGAGGCTAGTGTTGGATTGCACACAGATTGTAGCTTT
genomic: GCGCTGCAATGGTTGCGCCACTAAAGTTTGCAGTTGTCACAGAGAAAACAgtatgtgcca ... tttttgatagATCTTTGCTACTCCTGAGGCTAGTGTTGGATTGCACACAGATTGTAGCTTT
EST: gi|211380225|gb|FL081827.1|FL081827
EST:     GCGCTGCAATGGTTGCGCCACTAAAGTTTGCAGTTGTCACAGAGAAAACA                         ATCTTTGCTACTCCTGA
genomic: GCGCTGCAATGGTTGCGCCACTAAAGTTTGCAGTTGTCACAGAGAAAACAgtatgtgcca ... tttttgatagATCTTTGCTACTCCTGA
EST: gi|149000045|gb|EE037146.2|EE037146
EST:     GCGCTGCAATGGTTGCGCCACTAAAGTTTGCAGTTGTCACAGAGAAAACA                         ATCTTTGCTACTCCTGAGGCTAGTGTTGGATTGCACACAGATTGTAGCTTT
genomic: GCGCTGCAATGGTTGCGCCACTAAAGTTTGCAGTTGTCACAGAGAAAACAgtatgtgcca ... tttttgatagATCTTTGCTACTCCTGAGGCTAGTGTTGGATTGCACACAGATTGTAGCTTT
EST: gi|76292518|gb|DV032086.1|DV032086
EST:     GCGCTGCAATGGTTGCGCCACTAAAGTTTGCAGTTGTCACAGAGAAAACA                         ATCTTTGCTACTCCTGAGGCTAGTGTTGGATTGCACACAGATTGTAGCTTT
genomic: GCGCTGCAATGGTTGCGCCACTAAAGTTTGCAGTTGTCACAGAGAAAACAgtatgtgcca ... tttttgatagATCTTTGCTACTCCTGAGGCTAGTGTTGGATTGCACACAGATTGTAGCTTT
EST: gi|74239820|gb|DT647734.1|DT647734
EST:     GCGCTGCAATGGTTGCGCCACTAAAGTTTGCAGTTGTCACAGAGAAAACA                         ATCTTTGCTACTCCTGAGGCTAGTGTTGGATTGCACACAGATTGTAGCTTT
genomic: GCGCTGCAATGGTTGCGCCACTAAAGTTTGCAGTTGTCACAGAGAAAACAgtatgtgcca ... tttttgatagATCTTTGCTACTCCTGAGGCTAGTGTTGGATTGCACACAGATTGTAGCTTT
EST: gi|71304196|gb|DR788218.1|DR788218
EST:     GCGCTGCAATGGTTGCGCCACTAAAGTTTGCAGTTGTCACAGAGAAAACA                         ATCTTTGCTACTCCTGAGGCTAGTGTTGGATTGCACACAGATTGTAGCTTT
genomic: GCGCTGCAATGGTTGCGCCACTAAAGTTTGCAGTTGTCACAGAGAAAACAgtatgtgcca ... tttttgatagATCTTTGCTACTCCTGAGGCTAGTGTTGGATTGCACACAGATTGTAGCTTT
EST: gi|148930999|gb|EC873545.2|EC873545
EST:     GCGCTGCAATGGTTGCGCCACTAAAGTTTGCAGTTGTCACAGAGAAAACA                         ATCTTTGCTACTCCTGAGGCTA
genomic: GCGCTGCAATGGTTGCGCCACTAAAGTTTGCAGTTGTCACAGAGAAAACAgtatgtgcca ... tttttgatagATCTTTGCTACTCCTGAGGCTA
EST: gi|60352184|gb|DN219157.1|DN219157
EST:     GCGCTGCAATGGTTGCGCCACTAAAGTTTGCAGTTGTCACAGAGAAAACA                         ATCTTTGCTACTCCTGAGGCTAGTGTTGGATTGCACACAGATTGTAGCTTT
genomic: GCGCTGCAATGGTTGCGCCACTAAAGTTTGCAGTTGTCACAGAGAAAACAgtatgtgcca ... tttttgatagATCTTTGCTACTCCTGAGGCTAGTGTTGGATTGCACACAGATTGTAGCTTT
EST: gi|30052459|gb|AI065748.2|AI065748
EST:     GCGCTGCAATGGTTGCGCCACTAAAGTTTGCAGTTGTCACAGAGAAAACA                         ATCTTTGCTACTCCTGAGGCTAGTGTTGGATTGCACACAGATTGTAGCTTT
genomic: GCGCTGCAATGGTTGCGCCACTAAAGTTTGCAGTTGTCACAGAGAAAACAgtatgtgcca ... tttttgatagATCTTTGCTACTCCTGAGGCTAGTGTTGGATTGCACACAGATTGTAGCTTT
EST: gi|71429840|gb|DR810890.1|DR810890
EST:     GCGCTGCAATGGTTGCGCCACTAAAGTTTGCAGTTGTCACAGAGAAAACA                         ATCTTTGCTACTCCTGAGGCTAGTGTTGGGAT-GCACACAGATTGTAGCTT
genomic: GCGCTGCAATGGTTGCGCCACTAAAGTTTGCAGTTGTCACAGAGAAAACAgtatgtgcca ... tttttgatagATCTTTGCTACTCCTGAGGCTAGTGTTGG-ATTGCACACAGATTGTAGCTT
EST: gi|93012152|gb|EB637672.1|EB637672
EST:     GCGCTGCAATGGTTGCGCCACTAAAGTTTGCAGTTGTCACAGAGAAAACA                         ATCTTTGCTACTCCTGAGGCTAGTGTTGGATTGCACACAGATTGTAGCTTT
genomic: GCGCTGCAATGGTTGCGCCACTAAAGTTTGCAGTTGTCACAGAGAAAACAgtatgtgcca ... tttttgatagATCTTTGCTACTCCTGAGGCTAGTGTTGGATTGCACACAGATTGTAGCTTT
EST: gi|91056953|gb|EB167371.1|EB167371
EST:     GCGCTGCAATGGTTGCGCCACTAAAGTTTGCAGTTGTCACAGAGAAAACA                         ATCTTTGCTACTCCTGAGGCTAGTGTTGGATTGCACACAGATTGTAGCTTT
genomic: GCGCTGCAATGGTTGCGCCACTAAAGTTTGCAGTTGTCACAGAGAAAACAgtatgtgcca ... tttttgatagATCTTTGCTACTCCTGAGGCTAGTGTTGGATTGCACACAGATTGTAGCTTT
EST: gi|40303747|gb|CK348134.1|CK348134
EST:     CACAGAG-AAACC                         ATCTTTGCTACTCCTGAGGCTAGTGTT-GATTGCACACAGATNGTAG-TTT
genomic: CACAGAGAAAACAgtatgtgcca ... tttttgatagATCTTTGCTACTCCTGAGGCTAGTGTTGGATTGCACACAGATTGTAGCTTT
EST: gi|211252499|gb|FL081822.1|FL081822
EST:     GCGCTGCAATGGTTGCGCCACTAAAGTTTGCAGTTGTCACAGAGAAAACA                         ATCTTTGCTACTCCTGAGGCTAGTGTTTGGATTGCACACAGATTGTAGCTT
genomic: GCGCTGCAATGGTTGCGCCACTAAAGTTTGCAGTTGTCACAGAGAAAACAgtatgtgcca ... tttttgatagATCTTTGCTACTCCTGAGGCTAGTGTT-GGATTGCACACAGATTGTAGCTT
EST: gi|211380224|gb|FL081826.1|FL081826
EST:     GCGCTGCAATGGTTGCGCCACTAAAGTTTGCAGTTGTCACAGAGAAAACA                         ATCTTTGCTACTCCTGAAGCTAGTGTT
genomic: GCGCTGCAATGGTTGCGCCACTAAAGTTTGCAGTTGTCACAGAGAAAACAgtatgtgcca ... tttttgatagATCTTTGCTACTCCTGAGGCTAGTGTT
EST: gi|211380235|gb|FL081837.1|FL081837
EST:     GCGCTGCAATGGTTGCGCCACTAAAGTTTGCAGTTGTCACAGAGAAAACA                         ATCTTTGCTACTCCTGAGGCTAGTGTTGGATTGCACACAGATTGTAGCTTT
genomic: GCGCTGCAATGGTTGCGCCACTAAAGTTTGCAGTTGTCACAGAGAAAACAgtatgtgcca ... tttttgatagATCTTTGCTACTCCTGAGGCTAGTGTTGGATTGCACACAGATTGTAGCTTT
EST: gi|149089063|gb|EE178226.2|EE178226
EST:     GCGCTGCAATGGTTGCGCCACTAAAGTTTGCAGTTGTCACAGAGAAAACA                         ATCTTTGCTACTCCTGAGGCTAGTGTTGGATTGCACACAGATTGTAGCTTT
genomic: GCGCTGCAATGGTTGCGCCACTAAAGTTTGCAGTTGTCACAGAGAAAACAgtatgtgcca ... tttttgatagATCTTTGCTACTCCTGAGGCTAGTGTTGGATTGCACACAGATTGTAGCTTT
EST: gi|148959115|gb|EE010592.2|EE010592
EST:     GCGCTGCAATGGTTGCGCCACTAAAGTTTGCAGTTGTCACAGAGAAAACA                         ATCTTTGCTACTCCTGAGGCTAGTGTTGGATTGCACACAGATTGTAGCTTT
genomic: GCGCTGCAATGGTTGCGCCACTAAAGTTTGCAGTTGTCACAGAGAAAACAgtatgtgcca ... tttttgatagATCTTTGCTACTCCTGAGGCTAGTGTTGGATTGCACACAGATTGTAGCTTT
EST: gi|71448491|gb|DR829541.1|DR829541
EST:     GCGCTGCAATGGTTGCGCCACTAAAGTTTGCAGTTGTCACAGAGAAAACA                         ATCTTTGCTACTCCTGAGGCTAGTGTTGGATTGCACACAGATTGTAGCTTT
genomic: GCGCTGCAATGGTTGCGCCACTAAAGTTTGCAGTTGTCACAGAGAAAACAgtatgtgcca ... tttttgatagATCTTTGCTACTCCTGAGGCTAGTGTTGGATTGCACACAGATTGTAGCTTT
EST: gi|74238393|gb|DT646307.1|DT646307
EST:     GCGCTGCAATGGTTGCGCCACTAAAGTTTGCAGTTGTCACAGAGAAAACA                         ATCTTTGCTACTCCTGAGGCTAGTGTTGGATTGCACACAGATTGTAGCTTT
genomic: GCGCTGCAATGGTTGCGCCACTAAAGTTTGCAGTTGTCACAGAGAAAACAgtatgtgcca ... tttttgatagATCTTTGCTACTCCTGAGGCTAGTGTTGGATTGCACACAGATTGTAGCTTT
EST: gi|71447954|gb|DR829004.1|DR829004
EST:     GCGCTGCAATGGTTGCGCCACTAAAGTTTGCAGTTGTCACAGAGAAAACA                         ATCTTTGCTACTCCTGAGGCTAGTGTTGGATTGCACACAGATTGTAGCTTT
genomic: GCGCTGCAATGGTTGCGCCACTAAAGTTTGCAGTTGTCACAGAGAAAACAgtatgtgcca ... tttttgatagATCTTTGCTACTCCTGAGGCTAGTGTTGGATTGCACACAGATTGTAGCTTT
EST: gi|22472580|gb|BU037060.1|BU037060
EST:     GCGCTGCAATGGTTGCGCCACTAAAGTTTGCAGTTGTCACAGAGAAAACA                         ATCTTTGCTACTCCTGAGGCTA
genomic: GCGCTGCAATGGTTGCGCCACTAAAGTTTGCAGTTGTCACAGAGAAAACAgtatgtgcca ... tttttgatagATCTTTGCTACTCCTGAGGCTA

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: 47 (upstream exon), 49 (downstream exon)
Score: 55

GTTGCTCTTGTTAATGGGCTTGTCATGGGTGGTGGCGCTGCAATGGTTGCGCCACTAAAGTTTGCAGTTGTCACAGAGAAAACAgtatgtgcca ... tttttgatagATCTTTGCTACTCCTGAGGCTAGTGTTGGATTGCACACAGATTGTAGCTTTTCCTACATCCATTCCCGGCTCCCTGGATATTTAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 108

GTTGCTCTTGTTAATGGGCTTGTCATGGGTGGTGGCGCTGCAATGGTTGCGCCACTAAAGTTTGCAGTTGTCACAGAGAAAACAgtatgtgcca ... tttttgatagATCTTTGCTACTCCTGAGGCTAGTGTTGGATTGCACACAGATTGTAGCTTTTCCTACATCCATTCCCGGCTCCCTGGATATTTAG


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

GTTGCTCTTGTTAATGGGCTTGTCATGGGTGGTGGCGCTGCAATGGTTGCGCCACTAAAGTTTGCAGTTGTCACAGAGAAAACAgtatgtgcca ... tttttgatagATCTTTGCTACTCCTGAGGCTAGTGTTGGATTGCACACAGATTGTAGCTTTTCCTACATCCATTCCCGGCTCCCTGGATATTTAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 148

GTTGCTCTTGTTAATGGGCTTGTCATGGGTGGTGGCGCTGCAATGGTTGCGCCACTAAAGTTTGCAGTTGTCACAGAGAAAACAgtatgtgcca ... tttttgatagATCTTTGCTACTCCTGAGGCTAGTGTTGGATTGCACACAGATTGTAGCTTTTCCTACATCCATTCCCGGCTCCCTGGATATTTAG