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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTGAGTTCAAGACAGCTTCAGGGCAAATGTTGGATCTTATCACTACCCACGAGGGTGAAAAGGATCTAACTAAATATAACTTGACAGTgtaagtttatgtttcgctgtatcagtaacataattcacacgctttgtttcctttcatggtttattgtttagtttccagaatgagttattattatgtgtttagcacctcaaatttaggataaaatcttttatttgtgctaatttctctcaatgattttcattttgcacag

Basic information

species Zea mays
transcript GRMZM2G098569_T01
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G098569_T01 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os01g50760.1 (Oryza sativa), 5'ss of exon 5
GTTGAGTTCAAGACAGCTTCAGGGCAAATGTTGGATCTTATCACTACCCACGAGGGTGAAAAGGATCTAACTAAATATAACTTGACAGTgtaagtttatgtttcgctgtatcagtaacataattcacacgctttgtttcctttcatggtttattgtttagtttccagaatgagttattattatgtgtttagcacctcaaatttaggataaaatcttttatttgtgctaatttctctcaatgattttcattttgcacag
|||||||| ||||| |||||||| ||| ||||||||||||| ||||| || ||||| ||||||||||| || || || |||||||||||||||||| || || |  | ||   ||    |  ||      |||| |||| || |||| |||  |||  | ||            ||  | || |  |  | ||   ||||   | |                                                    
GTTGAGTTTAAGACTGCTTCAGGTCAATTGTTGGATCTTATTACTACTCATGAGGGAGAAAAGGATCTCACAAAGTACAACTTGACAGTgtaagttcattttgcatt-tacgtgt----ttgttt-----ctttctttctttgcatgatttcctgtccatttgttt-------ctaaaaataaggttcaaacaaaacaaaggaacg----------------------------------------------------
















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|76293424|gb|DV032992.1|DV032992
EST:     ATCACTACCCACGAGGGTGAAAAGGATCTAACTAAATATAACTTGACAGT                         TCACCGCCGCATCGTTCAGTACAAGACAGCTTATTATTCATTCTACCTTCC
genomic: ATCACTACCCACGAGGGTGAAAAGGATCTAACTAAATATAACTTGACAGTgtaagtttat ... ttttgcacagTCACCGCCGCATCGTTCAGTACAAGACAGCTTATTATTCATTCTACCTTCC
EST: gi|71306846|gb|DR789579.1|DR789579
EST:     ATCACTACCCACGAGGGTGAAAAGGATCTAACTAAATATAACTTGACAGT                         TCACCGCCGCATCGTTCAGT
genomic: ATCACTACCCACGAGGGTGAAAAGGATCTAACTAAATATAACTTGACAGTgtaagtttat ... ttttgcacagTCACCGCCGCATCGTTCAGT
EST: gi|76293423|gb|DV032991.1|DV032991
EST:     ATCACTACCCACGAGGGTGAAAAGGATCTAACTAAATATAACTTGACAGT                         TCACCGCCGCATCGTTCAGTACAAGACAGCTTATTATTCATTCTACCTTCC
genomic: ATCACTACCCACGAGGGTGAAAAGGATCTAACTAAATATAACTTGACAGTgtaagtttat ... ttttgcacagTCACCGCCGCATCGTTCAGTACAAGACAGCTTATTATTCATTCTACCTTCC
EST: gi|78117581|gb|DV535968.1|DV535968
EST:     ATCACTACCCACGAGGGTGAAAAGGATCTAACTAAATATAACTTGACAGT                         TCACCGCCGCATCGTTCAGTACAAGACAGCTTATTATTCATTCTACCTTCC
genomic: ATCACTACCCACGAGGGTGAAAAGGATCTAACTAAATATAACTTGACAGTgtaagtttat ... ttttgcacagTCACCGCCGCATCGTTCAGTACAAGACAGCTTATTATTCATTCTACCTTCC
EST: gi|149100778|gb|EE186872.2|EE186872
EST:     ATCACTACCCACGAGGGTGAAAAGGATCTAACTAAATATAACTTGACAGT                         TCACCGCCGCATCGTTCAGTACAAGACAGCTTATTATTCATTCTACCTTCC
genomic: ATCACTACCCACGAGGGTGAAAAGGATCTAACTAAATATAACTTGACAGTgtaagtttat ... ttttgcacagTCACCGCCGCATCGTTCAGTACAAGACAGCTTATTATTCATTCTACCTTCC
EST: gi|211448759|gb|FL324438.1|FL324438
EST:     ATCACTACCCACGAAGGTGAAAAGGATCTAACTAAATATAACTTGACAGT                         TCACCGCCGCATCGTTCAGTACAAGACAGCTTTAT-ATTCATTCTACCTTC
genomic: ATCACTACCCACGAGGGTGAAAAGGATCTAACTAAATATAACTTGACAGTgtaagtttat ... ttttgcacagTCACCGCCGCATCGTTCAGTACAAGACAGCTT-ATTATTCATTCTACCTTC
EST: gi|149100779|gb|EE186873.2|EE186873
EST:     ATCACTACCCACGAGGGTGAAAAGGATCTAACTAAATATAACTTGACAGT                         TCACCGCCGCATCGTTCAGTACAAGACAGCTTATTATTCATTCTACCTTCC
genomic: ATCACTACCCACGAGGGTGAAAAGGATCTAACTAAATATAACTTGACAGTgtaagtttat ... ttttgcacagTCACCGCCGCATCGTTCAGTACAAGACAGCTTATTATTCATTCTACCTTCC
EST: gi|60339232|gb|DN206205.1|DN206205
EST:     CACTACCCACGAGGGTGAAAAGGATCTAACTAAATATAACTTGACAGT                         TCACCGCCGCATCGTTCAGTACAAGACAGCTTATTATTCATTCTACCTTCC
genomic: CACTACCCACGAGGGTGAAAAGGATCTAACTAAATATAACTTGACAGTgtaagtttat ... ttttgcacagTCACCGCCGCATCGTTCAGTACAAGACAGCTTATTATTCATTCTACCTTCC
EST: gi|60359240|gb|DN226213.1|DN226213
EST:     ATCACTACCCACGAGGGTGAAAAGGATCTAACTAAATATAACTTGACAGT                         TCACCGCCGCATCGTTCAGTACAAGACAGCTTATTATTCATTCTACCTTCC
genomic: ATCACTACCCACGAGGGTGAAAAGGATCTAACTAAATATAACTTGACAGTgtaagtttat ... ttttgcacagTCACCGCCGCATCGTTCAGTACAAGACAGCTTATTATTCATTCTACCTTCC
EST: gi|60355012|gb|DN221985.1|DN221985
EST:     TCACTACCCACGAGGGTGAAAAGGATCTAACTAAATATAACTTGACAGT                         TCACCGCCGCATCGTTCAGTACAAGACAGCTTATTATTCATTCTACCTTCC
genomic: TCACTACCCACGAGGGTGAAAAGGATCTAACTAAATATAACTTGACAGTgtaagtttat ... ttttgcacagTCACCGCCGCATCGTTCAGTACAAGACAGCTTATTATTCATTCTACCTTCC
EST: gi|148951737|gb|EC897492.2|EC897492
EST:     ATCACTACCCACGAGGGTGAAAAGGATCTAACTAAATATAACTTGACAGT                         TCACCGCCGCATCGTTCAGTACAAGACAGCTTATTATTCATTCTACCTTCC
genomic: ATCACTACCCACGAGGGTGAAAAGGATCTAACTAAATATAACTTGACAGTgtaagtttat ... ttttgcacagTCACCGCCGCATCGTTCAGTACAAGACAGCTTATTATTCATTCTACCTTCC
EST: gi|148950117|gb|EC895653.2|EC895653
EST:     ATCACTACCCACGAGGGTGAAAAGGATCTAACTAAATATAACTTGACAGT                         TCACCGCCGCATCGTTCAGTACAAGACAGCTTATTATTCATTCTACCTTCC
genomic: ATCACTACCCACGAGGGTGAAAAGGATCTAACTAAATATAACTTGACAGTgtaagtttat ... ttttgcacagTCACCGCCGCATCGTTCAGTACAAGACAGCTTATTATTCATTCTACCTTCC
EST: gi|60341646|gb|DN208619.1|DN208619
EST:     ATCACTACCCACGAGGGTGAAAAGGATCTAACTAAATATAACTTGACAGT                         TCACCGCCGCATCGTTCAGTACAAGACAGCTTATTATTCATTCTACCTTCC
genomic: ATCACTACCCACGAGGGTGAAAAGGATCTAACTAAATATAACTTGACAGTgtaagtttat ... ttttgcacagTCACCGCCGCATCGTTCAGTACAAGACAGCTTATTATTCATTCTACCTTCC
EST: gi|71310911|gb|DR791758.1|DR791758
EST:     ATCACTACCCACGAGGGTGAAAAGGATCTAACTAAATATAACTTGACAGT                         TCACCGCCGCATCGTTCAGTACAAGACAGCTTATTATTCATTCTACCTTCC
genomic: ATCACTACCCACGAGGGTGAAAAGGATCTAACTAAATATAACTTGACAGTgtaagtttat ... ttttgcacagTCACCGCCGCATCGTTCAGTACAAGACAGCTTATTATTCATTCTACCTTCC
EST: gi|211504975|gb|FL314285.1|FL314285
EST:     ATCACTACCCACGAGGGTGAAAAGGATCTAACTAAATATAACTTGACAGT                         TCACCGCCGCATCGTTCAGTACAAGACAGCTTATTATTCATTCTACCTTCC
genomic: ATCACTACCCACGAGGGTGAAAAGGATCTAACTAAATATAACTTGACAGTgtaagtttat ... ttttgcacagTCACCGCCGCATCGTTCAGTACAAGACAGCTTATTATTCATTCTACCTTCC
EST: gi|71310909|gb|DR791757.1|DR791757
EST:     ATCACTACCCACGAGGGTGAAAAGGATCTAACTAAATATAACTTGACAGT                         TCACCGCCGCATCGTTCAGTACAAGACAGCTTATTATTCATTCTACCTTCC
genomic: ATCACTACCCACGAGGGTGAAAAGGATCTAACTAAATATAACTTGACAGTgtaagtttat ... ttttgcacagTCACCGCCGCATCGTTCAGTACAAGACAGCTTATTATTCATTCTACCTTCC
EST: gi|148964886|gb|EE015748.2|EE015748
EST:     ATCACTACCCACGAGGGTGAAAAGGATCTAACTAAATATAACTTGACAGT                         TCACCGCCGCATCGTTCAGTACAAGACAGCTTATTATTCATTCTACCTTCC
genomic: ATCACTACCCACGAGGGTGAAAAGGATCTAACTAAATATAACTTGACAGTgtaagtttat ... ttttgcacagTCACCGCCGCATCGTTCAGTACAAGACAGCTTATTATTCATTCTACCTTCC
EST: gi|78117582|gb|DV535969.1|DV535969
EST:     ATCACTACCCACGAGGGTGAAAAGGATCTAACTAAATATAACTTGACAGT                         TCACCGCCGCATCGTTCAGTACAAGACAGCTTATTATTCATTCTACCTTCC
genomic: ATCACTACCCACGAGGGTGAAAAGGATCTAACTAAATATAACTTGACAGTgtaagtttat ... ttttgcacagTCACCGCCGCATCGTTCAGTACAAGACAGCTTATTATTCATTCTACCTTCC
EST: gi|60353036|gb|DN220009.1|DN220009
EST:     TCACTACCCCACGAGGGTGAAAAGGATCTAACTAAATATAACTTGACAGT                         TCACCGCCGCATCGTTCAGTACAAGACAGCTTATTATTCATTCTACCTTCC
genomic: TCACTA-CCCACGAGGGTGAAAAGGATCTAACTAAATATAACTTGACAGTgtaagtttat ... ttttgcacagTCACCGCCGCATCGTTCAGTACAAGACAGCTTATTATTCATTCTACCTTCC

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: 46 (upstream exon), 49 (downstream exon)
Score: 179

GTTGAGTTCAAGACAGCTTCAGGGCAAATGTTGGATCTTATCACTACCCACGAGGGTGAAAAGGATCTAACTAAATATAACTTGACAGTgtaagtttat ... ttttgcacagTCACCGCCGCATCGTTCAGTACAAGACAGCTTATTATTCATTCTACCTTCCT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 565

GTTGAGTTCAAGACAGCTTCAGGGCAAATGTTGGATCTTATCACTACCCACGAGGGTGAAAAGGATCTAACTAAATATAACTTGACAGTgtaagtttat ... ttttgcacagTCACCGCCGCATCGTTCAGTACAAGACAGCTTATTATTCATTCTACCTTCCT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 525

GTTGAGTTCAAGACAGCTTCAGGGCAAATGTTGGATCTTATCACTACCCACGAGGGTGAAAAGGATCTAACTAAATATAACTTGACAGTgtaagtttat ... ttttgcacagTCACCGCCGCATCGTTCAGTACAAGACAGCTTATTATTCATTCTACCTTCCT


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 276

GTTGAGTTCAAGACAGCTTCAGGGCAAATGTTGGATCTTATCACTACCCACGAGGGTGAAAAGGATCTAACTAAATATAACTTGACAGTgtaagtttat ... ttttgcacagTCACCGCCGCATCGTTCAGTACAAGACAGCTTATTATTCATTCTACCTTCCT