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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACTTCCTGAACGTTGCTATGCTCTTACTGTGAATTATCCCCTTATGATTGTTGGAACTGCTGACCGTCATCTTGTTGTCTTCAATTTGCAGAATCCTCAGgtgattgtgttgttaagctgggcatgcatttgttgattcattttgagttagacattgatgacttctgttgtccaaatggcttatttcatggcttctgtttgaattattag

Basic information

species Zea mays
transcript GRMZM2G058498_T01
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G058498_T01 (Zea mays), 5'ss of exon 6
lower sequence: LOC_Os08g07960.1 (Oryza sativa), 5'ss of exon 6
ACTTCCTGAACGTTGCTATGCTCTTACTGTGAATTATCCCCTTATGATTGTTGGAACTGCTGACCGTCATCTTGTTGTCTTCAATTTGCAGAATCCTCAGgtgattgtgttgttaa-gctgggcatg--catttgt--tgattcattttga------gttagacattgatgacttctgttgtccaaatggcttatttcatggcttc-tgtttgaattattag
||||||||| || || || || ||||| ||||||||||||||||||||||| ||||||||||| ||| |||| || |||||||| |||||||||||||||||   | | |||| ||    |  ||||  ||||     ||| | ||   ||      |||   |||     ||||||  | |  || ||  |  ||| || | ||| |||||   | |||||
ACTTCCTGAGCGCTGTTACGCACTTACAGTGAATTATCCCCTTATGATTGTGGGAACTGCTGATCGTAATCTGGTCGTCTTCAACTTGCAGAATCCTCAGgttggtct-ttgtgaacatcgcacatgtccattaaaaatgaataatggggatcactcgtttttcatctgcaacttctcatattgaactgagtgtttttattgtttcctgttttggtcattag
















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|71310172|gb|DR791375.1|DR791375
EST:     TCAATTTGCAGAATCCTCAG                         ACGGAGTTCAAGCGAATCCAATCACCACTAAAATACCAGACACGGTGCCTT
genomic: TCAATTTGCAGAATCCTCAGgtgattgtgt ... gaattattagACGGAGTTCAAGCGAATCCAATCACCACTAAAATACCAGACACGGTGCCTT
EST: gi|71319015|gb|DR796255.1|DR796255
EST:     TTGGAACTGCTGACCGTCATCTTGTTGTCTTCAATTTGCAGAATCCTCAG                         ACGGAGTTCAAGCGAATCCAATCACCACTAAAATACCAGACACGGTGCCTT
genomic: TTGGAACTGCTGACCGTCATCTTGTTGTCTTCAATTTGCAGAATCCTCAGgtgattgtgt ... gaattattagACGGAGTTCAAGCGAATCCAATCACCACTAAAATACCAGACACGGTGCCTT
EST: gi|71435207|gb|DR816257.1|DR816257
EST:     TTGGAACTGCTGACCGTCATCTTGTTGTCTTCAATTTGCAGAATCCTCAG                         ACGGAGTTCAAGCGAATCCAATCACCACTAAAATACCAGACACGGTGCCTT
genomic: TTGGAACTGCTGACCGTCATCTTGTTGTCTTCAATTTGCAGAATCCTCAGgtgattgtgt ... gaattattagACGGAGTTCAAGCGAATCCAATCACCACTAAAATACCAGACACGGTGCCTT
EST: gi|67019316|gb|CO448065.1|CO448065
EST:     TTGGAACTGCTGACCGTCATCTTGTTGTCTTCAATTTGCAGAATCCTCAG                         ACGGAGTTCAAGCGAATCCAATCACCACTAAAATACCAGACACGGTGCCTT
genomic: TTGGAACTGCTGACCGTCATCTTGTTGTCTTCAATTTGCAGAATCCTCAGgtgattgtgt ... gaattattagACGGAGTTCAAGCGAATCCAATCACCACTAAAATACCAGACACGGTGCCTT
EST: gi|31355022|gb|CD439379.1|CD439379
EST:     TTGGAACTGCTGACCGTCATCTTGTTGTCTTCAATTTGCAGAATCCTCAG                         ACGGAGTTCAAGCGAATCCAATCACCACTAAAATACCAGACACGGTGCCTT
genomic: TTGGAACTGCTGACCGTCATCTTGTTGTCTTCAATTTGCAGAATCCTCAGgtgattgtgt ... gaattattagACGGAGTTCAAGCGAATCCAATCACCACTAAAATACCAGACACGGTGCCTT
EST: gi|548062|gb|T25262.1|T25262
EST:     TTGGAACTGCTGACCGTCATCTTGTTGTCTTCAATTTGCAGAATCCTCAG                         ACGGAGTTCAAGCGAATCCAATCACCACTAAAATACCAGACACGGTGCCTT
genomic: TTGGAACTGCTGACCGTCATCTTGTTGTCTTCAATTTGCAGAATCCTCAGgtgattgtgt ... gaattattagACGGAGTTCAAGCGAATCCAATCACCACTAAAATACCAGACACGGTGCCTT
EST: gi|71427496|gb|DR808546.1|DR808546
EST:     TTGGAACTGCTGACCGTCATCTTGTTGTCTTCAATTTGCAGAATCCTCAG                         ACGGAGTTCAAGCGAATCCAATCACCACTAAAATACCAGACACGGTGCCTT
genomic: TTGGAACTGCTGACCGTCATCTTGTTGTCTTCAATTTGCAGAATCCTCAGgtgattgtgt ... gaattattagACGGAGTTCAAGCGAATCCAATCACCACTAAAATACCAGACACGGTGCCTT
EST: gi|32838237|gb|CD977915.1|CD977915
EST:     TTGGAACTGCTGACCGTCATCTTGTTGTCTTCAATTTGCAGAATCCTCAG                         ACGGAGTTCAAGCGAATCCAATCACCACTAAAATACCAGACACGGTGCCTT
genomic: TTGGAACTGCTGACCGTCATCTTGTTGTCTTCAATTTGCAGAATCCTCAGgtgattgtgt ... gaattattagACGGAGTTCAAGCGAATCCAATCACCACTAAAATACCAGACACGGTGCCTT
EST: gi|78092605|gb|DV520979.1|DV520979
EST:     TTGGAACTGCTGACCGTCATCTTGTTGTCTTCAATTTGCAGAATCCTCAG                         ACGGAGTTCAAGCGAATCCAATCACCACTAAAATACCAGACACGGTGCCTT
genomic: TTGGAACTGCTGACCGTCATCTTGTTGTCTTCAATTTGCAGAATCCTCAGgtgattgtgt ... gaattattagACGGAGTTCAAGCGAATCCAATCACCACTAAAATACCAGACACGGTGCCTT
EST: gi|71765073|gb|DR963010.1|DR963010
EST:     TTGGAACTGCTGACCGTCATCTTGTTGTCTTCAATTTGCAGAATCCTCAG                         ACGGAGTTCAAGCGAATCCAATCACCACTAAAATACCAGACACGGTGCCTT
genomic: TTGGAACTGCTGACCGTCATCTTGTTGTCTTCAATTTGCAGAATCCTCAGgtgattgtgt ... gaattattagACGGAGTTCAAGCGAATCCAATCACCACTAAAATACCAGACACGGTGCCTT
EST: gi|32868065|gb|CF007747.1|CF007747
EST:     TTGGAACTGCTGACCGTCATCTTGTTGTCTTCAATTTGCAGAATCCTCAG                         ACGGAGTTCAAGCGAATCCAATCACCACTAAAA
genomic: TTGGAACTGCTGACCGTCATCTTGTTGTCTTCAATTTGCAGAATCCTCAGgtgattgtgt ... gaattattagACGGAGTTCAAGCGAATCCAATCACCACTAAAA
EST: gi|62550552|gb|DN830972.1|DN830972
EST:     TTGGAACTGCTGACCGTCATCTTGTTGTCTTCAATTTGCGGAATCCTCGG                         ACGGAGTTCAAGCGAATCCAATCACCACTAAAATACCAGACACGGTGCCTT
genomic: TTGGAACTGCTGACCGTCATCTTGTTGTCTTCAATTTGCAGAATCCTCAGgtgattgtgt ... gaattattagACGGAGTTCAAGCGAATCCAATCACCACTAAAATACCAGACACGGTGCCTT
EST: gi|32789124|gb|CD941360.1|CD941360
EST:     CTGGAACTGCTGACCGTCATCTTGTTGTCTTCAATTTGCAGAATCCTCAG                         ACGGAGTTCAAGCGAATCCAATCACCACTAAAATACCAGACACGGAGCCTT
genomic: TTGGAACTGCTGACCGTCATCTTGTTGTCTTCAATTTGCAGAATCCTCAGgtgattgtgt ... gaattattagACGGAGTTCAAGCGAATCCAATCACCACTAAAATACCAGACACGGTGCCTT
EST: gi|32945537|gb|CF050356.1|CF050356
EST:     TTGGAACTGCTGACCGTCATCTTATTGTCTTCAATTTGCAGAATCCTCAG                         ACGGAATTCAAGCGAATCCAATCACCACTAAAATACCAGACACGGTGCCTT
genomic: TTGGAACTGCTGACCGTCATCTTGTTGTCTTCAATTTGCAGAATCCTCAGgtgattgtgt ... gaattattagACGGAGTTCAAGCGAATCCAATCACCACTAAAATACCAGACACGGTGCCTT
EST: gi|50339684|gb|CO534810.1|CO534810
EST:     TTGGAACTGCTGACCGTCATCTTGTTGTCTTCAATTTGCAGAATCCTCAG                         ACGGAGTTCAAGCGAATCCAATCACCACTAAAATACCA
genomic: TTGGAACTGCTGACCGTCATCTTGTTGTCTTCAATTTGCAGAATCCTCAGgtgattgtgt ... gaattattagACGGAGTTCAAGCGAATCCAATCACCACTAAAATACCA
EST: gi|67024188|gb|CO452937.1|CO452937
EST:     TTGGAACTGCTGACCGTCATCTTGTTGTCTTCAATTTGCAGAATCCTCAG                         ACGGAGTTCAAGCGAATCCAATCACCACTAAAATACCAGACACGGTGCCTT
genomic: TTGGAACTGCTGACCGTCATCTTGTTGTCTTCAATTTGCAGAATCCTCAGgtgattgtgt ... gaattattagACGGAGTTCAAGCGAATCCAATCACCACTAAAATACCAGACACGGTGCCTT

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), 47 (downstream exon)
Score: 285

ACTTCCTGAACGTTGCTATGCTCTTACTGTGAATTATCCCCTTATGATTGTTGGAACTGCTGACCGTCATCTTGTTGTCTTCAATTTGCAGAATCCTCAGgtgattgtgt ... gaattattagACGGAGTTCAAGCGAATCCAATCACCACTAAAATACCAGACACGGTGCCTTGCTGCATTCCCTGATCAACAAGGGTTTTTG


Block sizes: 48 (upstream exon), 44 (downstream exon)
Score: 184

ACTTCCTGAACGTTGCTATGCTCTTACTGTGAATTATCCCCTTATGATTGTTGGAACTGCTGACCGTCATCTTGTTGTCTTCAATTTGCAGAATCCTCAGgtgattgtgt ... gaattattagACGGAGTTCAAGCGAATCCAATCACCACTAAAATACCAGACACGGTGCCTTGCTGCATTCCCTGATCAACAAGGGTTTTTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 204

ACTTCCTGAACGTTGCTATGCTCTTACTGTGAATTATCCCCTTATGATTGTTGGAACTGCTGACCGTCATCTTGTTGTCTTCAATTTGCAGAATCCTCAGgtgattgtgt ... gaattattagACGGAGTTCAAGCGAATCCAATCACCACTAAAATACCAGACACGGTGCCTTGCTGCATTCCCTGATCAACAAGGGTTTTTG


Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 174

ACTTCCTGAACGTTGCTATGCTCTTACTGTGAATTATCCCCTTATGATTGTTGGAACTGCTGACCGTCATCTTGTTGTCTTCAATTTGCAGAATCCTCAGgtgattgtgt ... gaattattagACGGAGTTCAAGCGAATCCAATCACCACTAAAATACCAGACACGGTGCCTTGCTGCATTCCCTGATCAACAAGGGTTTTTG