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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTTGTTGTTGGACTGGGGGATAAAGTGTCTCCAACTGACATCGAGGAAGGGATGAGGGTCGGgtatgccaccctgtattttcagtttaagctttctctgtttagtatatcaatacttagtccttcatttctactacagcactgtgatgcatttatgtgctca...

Basic information

species Zea mays
transcript GRMZM2G181359_T01
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G181359_T01 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os02g54340.2 (Oryza sativa), 5'ss of exon 5
TTTGTTGTTGGACTGGGGGATAAAGTGTCTCCAACTGACATCGAGGAAGGGATGAGGGTCGGgtatgccacc-ctgtattttcagtttaagctttctctgtttagtatatc--aatacttagtccttcatttcta-ctacagcactgtgatgcatttatgtgctca
||||| ||||| || ||||||||||| |||||||||||||| |||||||||||||| || ||||| | |||  |||| ||||  || |  | | | ||   ||| | |  |  ||| ||   || | || ||| | || | |   |        |||   |||   
TTTGTGGTTGGCCTAGGGGATAAAGTTTCTCCAACTGACATTGAGGAAGGGATGAGAGTGGGgtaggtcactgctgtttttttggtctttgatgtatcatattattctccctgaattctatctcatgcaattcgatctgctgt-ttccacctttttttgatgc---
















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|31998161|gb|CD661959.1|CD661959
EST:     CTGGGGGATAAAGTGTCTCCAACTGACATCGAGGAAGGGATGAGGGTCGG                         TGTTGATCGCAACAAGTACCAGATTCAAATCCCTCTTCCACCAAAAATTGA
genomic: CTGGGGGATAAAGTGTCTCCAACTGACATCGAGGAAGGGATGAGGGTCGGgtatgccacc ... cttgttgcagTGTTGATCGCAACAAGTACCAGATTCAAATCCCTCTTCCACCAAAAATTGA
EST: gi|148939474|gb|EC884049.2|EC884049
EST:     CTGGGGGATAAAGTGTCTCCAACTGACATCGAGGAAGGGATGAGGGTCGG                         TGTTGATCGCAACAAGTACCAGATTCAAATCCCTCTTCCACCAAAAATTGA
genomic: CTGGGGGATAAAGTGTCTCCAACTGACATCGAGGAAGGGATGAGGGTCGGgtatgccacc ... cttgttgcagTGTTGATCGCAACAAGTACCAGATTCAAATCCCTCTTCCACCAAAAATTGA
EST: gi|32909117|gb|CF013929.1|CF013929
EST:     CTGGGGGATAAAGTGTCTCCAACTGACATCGAGGAAGGGATGAGGGTCGG                         TGTTGATCGCAACAAGTACCAGATTCAAATCCCTCTTCCACCAAAAATTGA
genomic: CTGGGGGATAAAGTGTCTCCAACTGACATCGAGGAAGGGATGAGGGTCGGgtatgccacc ... cttgttgcagTGTTGATCGCAACAAGTACCAGATTCAAATCCCTCTTCCACCAAAAATTGA
EST: gi|148930441|gb|EE284947.2|EE284947
EST:     CTGGGGGATAAAGTGTCTCCAACTGACATCGAGGAAGGGATGAGGGTCGG                         TGTTGATCGCAACAAGTACCAGATTCAAATCCCTCTTCCACCAAAAATTGA
genomic: CTGGGGGATAAAGTGTCTCCAACTGACATCGAGGAAGGGATGAGGGTCGGgtatgccacc ... cttgttgcagTGTTGATCGCAACAAGTACCAGATTCAAATCCCTCTTCCACCAAAAATTGA
EST: gi|148986522|gb|EE030276.2|EE030276
EST:     CTGGGGGATAAAGTGTCTCCAACTGACATCGAGGAAGGGATGAGGGTCGG                         TGTTGATCGCAACAAGTACCAGATTCAAATCCCTCTTCCACCAAAAATTGA
genomic: CTGGGGGATAAAGTGTCTCCAACTGACATCGAGGAAGGGATGAGGGTCGGgtatgccacc ... cttgttgcagTGTTGATCGCAACAAGTACCAGATTCAAATCCCTCTTCCACCAAAAATTGA
EST: gi|148941059|gb|EC885918.2|EC885918
EST:     CTGGGGGATAAAGTGTCTCCAACTGACATCGAGGAAGGGATGAGGGTCGG                         TGTTGATCGCAACAAGTACCAGATTCAAATCCCTCTTCCACCAAAAATTGA
genomic: CTGGGGGATAAAGTGTCTCCAACTGACATCGAGGAAGGGATGAGGGTCGGgtatgccacc ... cttgttgcagTGTTGATCGCAACAAGTACCAGATTCAAATCCCTCTTCCACCAAAAATTGA
EST: gi|148940274|gb|EC885053.2|EC885053
EST:     CTGGGGGATAAAGTGTCTCCAACTGACATCGAGGAAGGGATGAGGGTCGG                         TGTTGATCGCAACAAGTACCAGATTCAAATCCCTCTTCCACCAAAAATTGA
genomic: CTGGGGGATAAAGTGTCTCCAACTGACATCGAGGAAGGGATGAGGGTCGGgtatgccacc ... cttgttgcagTGTTGATCGCAACAAGTACCAGATTCAAATCCCTCTTCCACCAAAAATTGA
EST: gi|149102256|gb|EE287643.2|EE287643
EST:     CTGGGGGATAAAGTGTCTCCAACTGACATCGAGGAAGGGATGAGGGTCGG                         TGTTGATCGCAACAAGTACCAGATTCAAATCCCTCTTCCACCAAAAATTGA
genomic: CTGGGGGATAAAGTGTCTCCAACTGACATCGAGGAAGGGATGAGGGTCGGgtatgccacc ... cttgttgcagTGTTGATCGCAACAAGTACCAGATTCAAATCCCTCTTCCACCAAAAATTGA
EST: gi|148940455|gb|EC885254.2|EC885254
EST:     CTGGGGGATAAAGTGTCTCCAACTGACATCGAGGAAGGGATGAGGGTCGG                         TGTTGATCGCAACAAGTACCAGATTCAAATCCCTCTTCCACCAAAAATTGA
genomic: CTGGGGGATAAAGTGTCTCCAACTGACATCGAGGAAGGGATGAGGGTCGGgtatgccacc ... cttgttgcagTGTTGATCGCAACAAGTACCAGATTCAAATCCCTCTTCCACCAAAAATTGA
EST: gi|148981623|gb|EE027766.2|EE027766
EST:     CTGGGGGATAAAGTGTCTCCAACTGACATCGAGGAAGGGATGAGGGTCGG                         TGTTGATCGCAACAAGTACCAGATTCAAATCCCTCTTCCACCAAAAATTGA
genomic: CTGGGGGATAAAGTGTCTCCAACTGACATCGAGGAAGGGATGAGGGTCGGgtatgccacc ... cttgttgcagTGTTGATCGCAACAAGTACCAGATTCAAATCCCTCTTCCACCAAAAATTGA
EST: gi|26457221|gb|CA828804.1|CA828804
EST:     CTGGGGGATAAAGTGTCTCCAACTGACATCGAGGAAGGGATGAGGGTCGG                         TGTTGATCGCAACAAGTACCAGATTCAAATCCCTCT
genomic: CTGGGGGATAAAGTGTCTCCAACTGACATCGAGGAAGGGATGAGGGTCGGgtatgccacc ... cttgttgcagTGTTGATCGCAACAAGTACCAGATTCAAATCCCTCT
EST: gi|149078548|gb|EE167330.2|EE167330
EST:     CTGGGGGATAAAGTGTCTCCAACTGACATCGAGGAAGGGATGAGGGTCGG                         TGTTGATCGCAACAAGTACCAGATTCAAATCCCTCTTCCACCAAAAATTGA
genomic: CTGGGGGATAAAGTGTCTCCAACTGACATCGAGGAAGGGATGAGGGTCGGgtatgccacc ... cttgttgcagTGTTGATCGCAACAAGTACCAGATTCAAATCCCTCTTCCACCAAAAATTGA
EST: gi|148933068|gb|EE285985.2|EE285985
EST:     CTGGGGGATAAAGTGTCTCCAACTGACATCGAGGAAGGGATGAGGGTCGG                         TGTTGATCGCAACAAGTACCAGATTCAAATCCCTCTTCCACCAAAAATTGA
genomic: CTGGGGGATAAAGTGTCTCCAACTGACATCGAGGAAGGGATGAGGGTCGGgtatgccacc ... cttgttgcagTGTTGATCGCAACAAGTACCAGATTCAAATCCCTCTTCCACCAAAAATTGA
EST: gi|67042393|gb|CO468648.1|CO468648
EST:     CTGGGGGATAAAGTGTCTCCAACTGACATCGAGGAAGGGATGAGGGTCGG                         TGTTGATCGCAACAAGTACCAGATTCAAATCCCTCTTCCACCAAAAATTGA
genomic: CTGGGGGATAAAGTGTCTCCAACTGACATCGAGGAAGGGATGAGGGTCGGgtatgccacc ... cttgttgcagTGTTGATCGCAACAAGTACCAGATTCAAATCCCTCTTCCACCAAAAATTGA
EST: gi|67020716|gb|CO449465.1|CO449465
EST:     AGTGTCTTTAACTGACATCGAGGGAA-GGATGAGGGTCGG                         TGTTGATCGCAACAAGTACCAGATTCAAATCCCTCTTCCACCAAAAATTGA
genomic: AGTGTCTCCAACTGACATCGA-GGAAGGGATGAGGGTCGGgtatgccacc ... cttgttgcagTGTTGATCGCAACAAGTACCAGATTCAAATCCCTCTTCCACCAAAAATTGA
EST: gi|148943018|gb|EC888066.2|EC888066
EST:     CTGGGGGATAAAGTGTCTCCAACTGACATCGAGGAAGGGATGAGGGTCGG                         TGTTGATCGCAACAAGTACCAGATTCAAATCCCTCTTCCACCAAAAATTGA
genomic: CTGGGGGATAAAGTGTCTCCAACTGACATCGAGGAAGGGATGAGGGTCGGgtatgccacc ... cttgttgcagTGTTGATCGCAACAAGTACCAGATTCAAATCCCTCTTCCACCAAAAATTGA
EST: gi|148952264|gb|EC898073.2|EC898073
EST:     CTGGGGGATAAAGTGTCTCCAACTGACATCGAGGAAGGGATGAGGGTCGG                         TGTTGATCGCAACAAGTACCAGATTCAAATCCCTCTTCCACCAAAAATTGA
genomic: CTGGGGGATAAAGTGTCTCCAACTGACATCGAGGAAGGGATGAGGGTCGGgtatgccacc ... cttgttgcagTGTTGATCGCAACAAGTACCAGATTCAAATCCCTCTTCCACCAAAAATTGA
EST: gi|60401248|gb|DN234055.1|DN234055
EST:     CTGGGGGATAAAGTGTCTCCAACTGACATCGAGGAAGGGATGAGGGTCGG                         TGTTGATCGCAACAAGTACCAGATTCAAATCCCTCTTCCACCAAAAATTGA
genomic: CTGGGGGATAAAGTGTCTCCAACTGACATCGAGGAAGGGATGAGGGTCGGgtatgccacc ... cttgttgcagTGTTGATCGCAACAAGTACCAGATTCAAATCCCTCTTCCACCAAAAATTGA
EST: gi|149077295|gb|EE165971.2|EE165971
EST:     CTGGGGGATAAAGTGTCTCCAACTGACATCGAGGAAGGGATGAGGGTCGG                         TGTTGATCGCAACAAGTACCAGATTCAAATCCCTCTTCCACCAAAAATTGA
genomic: CTGGGGGATAAAGTGTCTCCAACTGACATCGAGGAAGGGATGAGGGTCGGgtatgccacc ... cttgttgcagTGTTGATCGCAACAAGTACCAGATTCAAATCCCTCTTCCACCAAAAATTGA
EST: gi|148968071|gb|EE019406.2|EE019406
EST:     CTGGGGGATAAAGTGTCTCCAACTGACATCGAGGAAGGGATGAGGGTCGG                         TGTTGATCGCAACAAGTACCAGATTCAAATCCCTCTTCCACCAAAAATTGA
genomic: CTGGGGGATAAAGTGTCTCCAACTGACATCGAGGAAGGGATGAGGGTCGGgtatgccacc ... cttgttgcagTGTTGATCGCAACAAGTACCAGATTCAAATCCCTCTTCCACCAAAAATTGA
EST: gi|149040621|gb|EE046862.2|EE046862
EST:     CTGGGGGATAAAGTGTCTCCAACTGACATCGAGGAAGGGATGAGGGTCGG                         TGTTGATCGCAACAAGTACCAGATTCAAATCCCTCTTCCACCAAAAATTGA
genomic: CTGGGGGATAAAGTGTCTCCAACTGACATCGAGGAAGGGATGAGGGTCGGgtatgccacc ... cttgttgcagTGTTGATCGCAACAAGTACCAGATTCAAATCCCTCTTCCACCAAAAATTGA

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), 49 (downstream exon)
Score: 701

TTTGTTGTTGGACTGGGGGATAAAGTGTCTCCAACTGACATCGAGGAAGGGATGAGGGTCGGgtatgccacc ... cttgttgcagTGTTGATCGCAACAAGTACCAGATTCAAATCCCTCTTCCACCAAAAATTGACCCAAGTGTTACCATGATGACCGTGGAGGAAAAGCCAGATGTGACGTAC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 811

TTTGTTGTTGGACTGGGGGATAAAGTGTCTCCAACTGACATCGAGGAAGGGATGAGGGTCGGgtatgccacc ... cttgttgcagTGTTGATCGCAACAAGTACCAGATTCAAATCCCTCTTCCACCAAAAATTGACCCAAGTGTTACCATGATGACCGTGGAGGAAAAGCCAGATGTGACGTAC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 851

TTTGTTGTTGGACTGGGGGATAAAGTGTCTCCAACTGACATCGAGGAAGGGATGAGGGTCGGgtatgccacc ... cttgttgcagTGTTGATCGCAACAAGTACCAGATTCAAATCCCTCTTCCACCAAAAATTGACCCAAGTGTTACCATGATGACCGTGGAGGAAAAGCCAGATGTGACGTAC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 730

TTTGTTGTTGGACTGGGGGATAAAGTGTCTCCAACTGACATCGAGGAAGGGATGAGGGTCGGgtatgccacc ... cttgttgcagTGTTGATCGCAACAAGTACCAGATTCAAATCCCTCTTCCACCAAAAATTGACCCAAGTGTTACCATGATGACCGTGGAGGAAAAGCCAGATGTGACGTAC