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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GATACATTCCGTGGAAGAGTTTGCGAGTGTCCAGTTGTGAAAGGCGTCAAATTTGTTGGCGATGGCTATACTCACTGTGAAGgtatgctacacaaggcataaggagattcatcttttggcattttcttttactatgtgttaagagagcttctgaattataacatttgtgttttaag

Basic information

species Zea mays
transcript GRMZM2G347541_T01
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G347541_T01 (Zea mays), 5'ss of exon 7
lower sequence: LOC_Os12g02390.1 (Oryza sativa), 5'ss of exon 7
GATACATTCCGTGGAAGAGTTTGCGAGTGTCCAGTTGTGAAAGGCGTCAAATTTGTTGGCGATGGCTATACTCACTGTGAAGgtatgctacacaaggcataaggagat---tcatcttttggcattttcttttactatgtgt-taagagagcttctgaattataacatttgtgttttaag-----
|| || || |||||||||||||| || ||||||||||||||||| || ||||||||||| |||||||| ||||||||||||||||||||||   || ||| |||  ||   | |||  |||| || ||  ||  ||   ||| ||    || ||   ||  ||| | | |||   ||||      
GACACTTTTCGTGGAAGAGTTTGTGAATGTCCAGTTGTGAAAGGTGTTAAATTTGTTGGTGATGGCTACACTCACTGTGAAGgtatgctacc--agacattagggcataagttatcagttgggatatttgttgtctgcatgtgtagttaagatttaaaagcata-cttatgtagattaataagaa

upper sequence: GRMZM2G347541_T01 (Zea mays), 5'ss of exon 7
lower sequence: LOC_Os11g02464.1 (Oryza sativa), 5'ss of exon 7
GATACATTCCGTGGAAGAGTTTGCGAGTGTCCAGTTGTGAAAGGCGTCAAATTTGTTGGCGATGGCTATACTCACTGTGAAGgtatgctacacaaggcataaggagat---tcatcttttggcattttcttttactatgtgt-taagagagcttctgaattataacatttgtgttttaag-----
|| || || |||||||||||||| || ||||||||||| ||||| || ||||||||||| |||||||| ||||||||||||||||||||||   || ||| |||  ||   | |||  |||| || ||  ||  ||   ||| ||    || ||   ||  ||| | | |||   ||||      
GACACTTTTCGTGGAAGAGTTTGTGAATGTCCAGTTGTAAAAGGTGTTAAATTTGTTGGTGATGGCTACACTCACTGTGAAGgtatgctacc--agacattagggcataagttatcagttgggatatttgttgtctgcatgtgtagttaagatttaaaagcata-cttatgtagattaataagaa

upper sequence: GRMZM2G347541_T01 (Zea mays), 5'ss of exon 7
lower sequence: GLYMA18G44580.1 (Glycine max), 5'ss of exon 7
-GATACATTCCGTGGAAGAGTTTGCGAGTGTCCAGTTGTGAAAGGCGTCAAATTTGTTGGCGATGGCTATACTCACTGTGAAGgtatgcta---cacaaggcataaggagattcatct-tttggcatttt-cttttactatgtgttaagagagcttctgaattataacatttgtgttttaag-
 || || ||||| |||||||| || || || ||| ||||  ||   || ||||||||||| ||||| ||||| |||||||||||||   ||       |     |   | |||  ||| ||   || | | | | |  || || ||   ||| ||  |||    |   ||||   ||  |   
GGACACTTTCCGAGGAAGAGTATGTGAATGCCCAATTGTTCAAAATGTGAAATTTGTTGGAGATGGATATACCCACTGTGAAggtaaattaatttttcaaattcagataaattgctctgttctccactctacatattttaagttttccaaga-ctagtgagcctttcaatttaacttccagat

upper sequence: GRMZM2G347541_T01 (Zea mays), 5'ss of exon 7
lower sequence: EFJ22768 (Selaginella moellendorffii), 5'ss of exon 7
GATACATTCCGTGGAAGAGTTTGCGAGTGTCCAGTTGTGAAAGGCGTCAAATTTGTTGGCGATGGCTATACTCACTGTGAAGgtatgctacacaaggcataaggagattcatcttttggcattttcttttactatgt-gttaagagagcttctgaattataacatttgtgttttaag
||||| |||||||||||||| |||||||||||  ||||| |||||||  | |     || ||||| || | ||||||||||||||   |    ||   ||        |  ||| |     || |  | | ||  || ||| ||                                 
GATACTTTCCGTGGAAGAGTGTGCGAGTGTCCCATTGTGCAAGGCGTGCAGTACAGCGGAGATGGATACAGTCACTGTGAAGgtac-ttgtgaaatctat-------cttctctgtgatagttctaatgtcctgcgttgtttag---------------------------------

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|32935750|gb|CF040562.1|CF040562
EST:     GGCGTCAAATTTGTTGGCGATGGCTATACTCACTGTGAAG                         CTTCCGGGTCTGGTCGGTGTGAAATTAACAACGGAGGGTGCTGGAAAGATA
genomic: GGCGTCAAATTTGTTGGCGATGGCTATACTCACTGTGAAGgtatgctaca ... gtgttttaagCTTCCGGATCTGGTCGGTGTGAAATTAACAACGGAGGGTGCTGGAAAGATA
EST: gi|71299569|gb|DR785796.1|DR785796
EST:     AGTTGTGAAAGGCGTCAAATTTGTTGGCGATGGCTATACTCACTGTGAAG                         CTTCCGGATCTGGTCGGTGTGAAATTAACAACGGAGGGTGCTGGAAAGATA
genomic: AGTTGTGAAAGGCGTCAAATTTGTTGGCGATGGCTATACTCACTGTGAAGgtatgctaca ... gtgttttaagCTTCCGGATCTGGTCGGTGTGAAATTAACAACGGAGGGTGCTGGAAAGATA
EST: gi|67021468|gb|CO450217.1|CO450217
EST:     AGTTGTGAAAGGCGTCAAATTTGTTGGCGATGGCTATACTCACTGTGAAG                         CTTCCGGGTCTGGTCGGTGTGAAATTAACAACGGAGGGTGCTGGAAAGATA
genomic: AGTTGTGAAAGGCGTCAAATTTGTTGGCGATGGCTATACTCACTGTGAAGgtatgctaca ... gtgttttaagCTTCCGGATCTGGTCGGTGTGAAATTAACAACGGAGGGTGCTGGAAAGATA
EST: gi|211224453|gb|FL435606.1|FL435606
EST:     TTGTGAAAGGGCGTCAAATTTGTTGGCGATGGCTATACTCACTGTGAAAG                         CTTCCGGATCTGGTCGGTGTGAAAATTAACAACGGAGGGGTGGCTGG-AA
genomic: TTGTGAAA-GGCGTCAAATTTGTTGGCGATGGCTATACTCACTGTG-AAGgtatgctaca ... gtgttttaagCTTCCGGATCTGGTCGGTGTG-AAATTAACAACGGA-GGGT-GCTGGAAA
EST: gi|67028179|gb|CO456928.1|CO456928
EST:     AGTTGTGAAAGGCGTCAAATTTGTTGGCGATGGCTATACTCACTGTGAAG                         CTTCCGGGTCTGGTCGGTGTGAAATTAACAACGGAGGGTGCTGGAAAGATA
genomic: AGTTGTGAAAGGCGTCAAATTTGTTGGCGATGGCTATACTCACTGTGAAGgtatgctaca ... gtgttttaagCTTCCGGATCTGGTCGGTGTGAAATTAACAACGGAGGGTGCTGGAAAGATA
EST: gi|76292778|gb|DV032346.1|DV032346
EST:     AGTTGTGAAAGGCGTCAAATTTGTTGGCGATGGCTATACTCACTGTGAAG                         CTTCCGGATCTGGTCGGTGTGAAATTAACAACGGAGGGTGCTGGAAAGATA
genomic: AGTTGTGAAAGGCGTCAAATTTGTTGGCGATGGCTATACTCACTGTGAAGgtatgctaca ... gtgttttaagCTTCCGGATCTGGTCGGTGTGAAATTAACAACGGAGGGTGCTGGAAAGATA
EST: gi|211301945|gb|FL333154.1|FL333154
EST:     AGTTGTGAAAGGCGTCAAATTTGTTGGCGATGGCTATACTCACTGTGAAG                         CTTCCGGATCTGGTCGGTGTGAAATTAACAACGGAGGGTGCTGGAAAGATA
genomic: AGTTGTGAAAGGCGTCAAATTTGTTGGCGATGGCTATACTCACTGTGAAGgtatgctaca ... gtgttttaagCTTCCGGATCTGGTCGGTGTGAAATTAACAACGGAGGGTGCTGGAAAGATA

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), 48 (downstream exon)
Score: 91

GATACATTCCGTGGAAGAGTTTGCGAGTGTCCAGTTGTGAAAGGCGTCAAATTTGTTGGCGATGGCTATACTCACTGTGAAGgtatgctaca ... gtgttttaagCTTCCGGATCTGGTCGGTGTGAAATTAACAACGGAGGGTGCTGGAAAGATACCAAGAATGGTCGGACATACTCTGCCTGTACT


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 62

GATACATTCCGTGGAAGAGTTTGCGAGTGTCCAGTTGTGAAAGGCGTCAAATTTGTTGGCGATGGCTATACTCACTGTGAAGgtatgctaca ... gtgttttaagCTTCCGGATCTGGTCGGTGTGAAATTAACAACGGAGGGTGCTGGAAAGATACCAAGAATGGTCGGACATACTCTGCCTGTACT


Block sizes: 44 (upstream exon), 45 (downstream exon)
Score: 29

GATACATTCCGTGGAAGAGTTTGCGAGTGTCCAGTTGTGAAAGGCGTCAAATTTGTTGGCGATGGCTATACTCACTGTGAAGgtatgctaca ... gtgttttaagCTTCCGGATCTGGTCGGTGTGAAATTAACAACGGAGGGTGCTGGAAAGATACCAAGAATGGTCGGACATACTCTGCCTGTACT


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 97

GATACATTCCGTGGAAGAGTTTGCGAGTGTCCAGTTGTGAAAGGCGTCAAATTTGTTGGCGATGGCTATACTCACTGTGAAGgtatgctaca ... gtgttttaagCTTCCGGATCTGGTCGGTGTGAAATTAACAACGGAGGGTGCTGGAAAGATACCAAGAATGGTCGGACATACTCTGCCTGTACT