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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCCTAACAGCATCCTCGTCGTCACCATCAACGGCGTCGGGCTCGTCATCGAGGCCATCTACCTCACCATCTTCTTCCTTTACTCTGATGGCCCGAAACGCgtgagtgccacggcgatggcgctgcacaaatgccggccgtgtgttccctcttcggatctagttttgagcttgacgatcccttacgccttattaattctcgttcgcag

Basic information

species Zea mays
transcript GRMZM2G416965_T01
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G416965_T01 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os01g42090.1 (Oryza sativa), 5'ss of exon 2
CCCTAACAGCATCCTCGTCGTCACCATCAACGGCGTCGGGCTCGTCATCGAGGCCATCTACCTCACCATCTTCTTCCTTTACTCTGATGGCCCGAAACGCgtgagtgc-cacggcgatggcgctgcacaaatgc---cggccgtgtgttccctcttcggatct-agttttgagcttgacgatcccttacgcct--tattaattctcgttcgcag
||| |||||||||||||||||||||||||||||| |||| ||| |  |||||| || |||||||  |||||||||||| |||||      |  ||| |||||   | | |    |  |  | ||  | | ||        || | | | | |  ||    |   |  |||||   |  |       ||  | |   ||||||||    | ||||
CCCGAACAGCATCCTCGTCGTCACCATCAACGGCATCGGTCTCATTGTCGAGGGCACCTACCTCTTCATCTTCTTCCTCTACTCCCCCAACAAGAAGCGCgtatatacgcttttccctccctcttgatatatctatatatccatatttcctcgatttaatttcgaaatttgaatctatctgaaatataatcttgacattaattcattgttgcag

upper sequence: GRMZM2G416965_T01 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os01g42110.1 (Oryza sativa), 5'ss of exon 2
CCCTAACAGCATCCTCGTCGTCACCATCAACGGCGTCGGGCTCGTCATCGAGGCCATCTACCTCACCATCTTCTTCCTTTACTCTGATGGCCCGAAACGCgtgagtgccacggcgatggcgctgcacaa-atgccggccgtgtgttccctcttcggatctagttttgagcttgacgatcccttacgccttatta-attctcgttcgcag--
||| ||||| |||||||||||||||||||||||| |||| ||| || |||||| || |||||||  |||||||||||| |||||      |  |||||||||  ||    ||      |  |||  ||  ||  |   | |   |     | |      |  |  ||| ||  |  | ||| |||   | || | ||  ||| |||     
CCCCAACAGTATCCTCGTCGTCACCATCAACGGCATCGGCCTCCTCGTCGAGGGCACCTACCTCCTCATCTTCTTCCTCTACTCCCCCAACAAGAAACGCgtacgtcgatcgatccatgatctgttcattatttccttcctcgatctatacattaatctttatcatgatct-aattaacccgtaccattgatcatatcatcgatcgtgcag

upper sequence: GRMZM2G416965_T01 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os09g08030.1 (Oryza sativa), 5'ss of exon 1
CCCTAACAGCATCCTCGTCGTCACCATCAACGGCGTCGGGCTCGTCATCGAGGCCATCTACCTCACCATCTTCTTCCTTTACTCTGATGGCCCGAAACGCgtgagtgccacggcgatggcgctgcacaaatgccggccgtg-tgttccctcttcggatctag----ttttgagcttgacgatcccttacgccttattaattctcgttcgcag--------------------------------------------------------------------
|   | | ||| | | || | || | ||  |  ||||       || |   | |  |    ||| ||     |  ||||    |  ||   |   ||   |   ||   | | |       | |  |     | ||||    || ||     |  | ||| |    |||   |  |  | |||    || ||      || |||||   ||                                                                     
CATGATCCGCAACGTGGTGGGCATCGTCGGCAACGTCA----TCTCCTTTGGCCTCTTCCTCTCGCCGGTCCCCACCTTCTGGCAAATCATCAAGAATAAGAACgtat-aggacttcaagacagacccgtacctggccacactgctcaactgtatgctctgggacttttacggtctccccatcgtccaccccaacagcatcctcgtcgtcaccatcaacggcattggccttgtcatcgagacctgtctatctcaccatcttcttcctcttctccgacaag

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|211351800|gb|FK980889.1|FK980889
EST:     AGGCCATCTACCTCACCATCTTCTTCCTTTACTCTGATGGCCCGAAACGC                         AGGAAAGCGTTCGGAATCCTGGCCGTGGAGATTTTGTTCATGGTCGCCGTG
genomic: AGGCCATCTACCTCACCATCTTCTTCCTTTACTCTGATGGCCCGAAACGCgtgagtgcca ... tcgttcgcagAGGAAAGCGTTCGGAATCCTGGCCGTGGAGATTTTGTTCATGGTCGCCGTG
EST: gi|211351797|gb|FK980886.1|FK980886
EST:     AGGCCATCTACCTCACCATCTTCTTCCTTTACTCTGATGGCCCGAAACGC                         AGGAAAGCGTTCGGAATCCTGGCCGTGGAGATTTTGTTCATGGTCGCCGTG
genomic: AGGCCATCTACCTCACCATCTTCTTCCTTTACTCTGATGGCCCGAAACGCgtgagtgcca ... tcgttcgcagAGGAAAGCGTTCGGAATCCTGGCCGTGGAGATTTTGTTCATGGTCGCCGTG
EST: gi|149079042|gb|EE167926.2|EE167926
EST:     GGCCATCTACCTCACCATCTTCTTCCTTTACTCTGATGGCCCGAAACCGC                         AGGAAAGCGTTCGGAATCCTGGCCCGTGGAGATTTTGTTCATGGTCGCCG
genomic: GGCCATCTACCTCACCATCTTCTTCCTTTACTCTGATGGCCCGAAAC-GCgtgagtgcca ... tcgttcgcagAGGAAAGCGTTCGGAATCCTGGCC-GTGGAGATTTTGTTCATGGTCGCCG
EST: gi|211351796|gb|FK980885.1|FK980885
EST:     AGGCCATCTACCTCACCATCTTCTTCCTTTACTCTGATGGCCCGAAACGC                         AGGAAAGCGTTCGGAATCCTGGCCGTGGAGATTTTGTTCATGGTCGCCGT
genomic: AGGCCATCTACCTCACCATCTTCTTCCTTTACTCTGATGGCCCGAAACGCgtgagtgcca ... tcgttcgcagAGGAAAGCGTTCGGAATCCTGGCCGTGGAGATTTTGTTCATGGTCGCCGT
EST: gi|211351798|gb|FK980887.1|FK980887
EST:     AGGCCATCTACCTCACCATCTTCTTCCTTTACTCTGATGGCCCGAAACGC                         AGGAAAGCGTTCGGAATCCTGGCCGTGGAGATTTTGTTCATGGTCGCCGTG
genomic: AGGCCATCTACCTCACCATCTTCTTCCTTTACTCTGATGGCCCGAAACGCgtgagtgcca ... tcgttcgcagAGGAAAGCGTTCGGAATCCTGGCCGTGGAGATTTTGTTCATGGTCGCCGTG

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 1 RNA-Seqlibrary.


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 110

CCCTAACAGCATCCTCGTCGTCACCATCAACGGCGTCGGGCTCGTCATCGAGGCCATCTACCTCACCATCTTCTTCCTTTACTCTGATGGCCCGAAACGCgtgagtgcca ... tcgttcgcagAGGAAAGCGTTCGGAATCCTGGCCGTGGAGATTTTGTTCATGGTCGCCGTGGTGCTTGGTGTGATTTTGGGCGCCCACACGCACGAGAAGCGCTCCATGA




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