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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AACTTCCTTTTCAAATCGAACAAGGAGGATTCACCACTAAAGGCGACAGATTTTGGTTTGTCAGATTTCATTAAGCCAGgtatctacttggggccatctgaatctgtcgggaatctgataggggcaagtctgcagtttagctgaccattttgttgtctaatgcatgctttag

Basic information

species Zea mays
transcript GRMZM2G053868_T02
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G053868_T02 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os02g03410.2 (Oryza sativa), 5'ss of exon 5
AACTTCCTTTTCAAATCGAACAAGGAGGATTCACCACTAAAGGCGACAGATTTTGGTTTGTCAGATTTCATTAAGCCAGgtatctactt-ggggccatctgaatctgtcgggaatctgataggggc----aa-----gtctgcagttt-agctgaccattttgttgtctaatgcatgctttag------------------
||||||||||||||||| | ||||||||| |||||  ||||||| |||||||||||| ||||||| ||||| || |||||||| || ||   |  | | ||  | ||| |    | || || | ||    ||     |  |    ||| ||  |  |||     | |  | | ||| | ||                    
AACTTCCTTTTCAAATCAACCAAGGAGGACTCACCTTTAAAGGCAACAGATTTTGGTCTGTCAGACTTCATAAAACCAGgtatttatttcaagagcttttgcttatgt-gcatctttgctatgtgcttccaattgttgcttctgatttgagtaggacatacaagtctgcagttcattcattgttttctttcattactgtag

upper sequence: GRMZM2G053868_T02 (Zea mays), 5'ss of exon 5
lower sequence: GLYMA02G05440.1 (Glycine max), 5'ss of exon 5
AACTTCCTTTTCAAATCGAACAAGGAGGATTCACCACTAAAGGCGACAGATTTTGGTTTGTCAGATTTCATTAAGCCAGgt------atctacttggggccat-ctgaatctgtcgggaatctgataggggcaagtct----gcagtttag--ctgaccattttgttgtctaat---gcatgctttag----------------------------------------------
|| || ||||| ||||| | ||| || ||||||||  ||||||| |||||||||||||||||||||||||| || || |||      |  |  |      ||| || ||| | |      |    |     ||  | |    ||||  | |  ||     ||| ||||  | ||   ||||||| | |                                              
AATTTTCTTTTTAAATCAATCAAAGAAGATTCACCTTTAAAGGCCACAGATTTTGGTTTGTCAGATTTCATAAAACCTGgtgagggaaagtcttgattttcatgctcaatttctttatttttcttttcttccattttttgttgcaggcttgttctatttctttggttgagttatcaagcatgctcttgtaattttatttgagatttatttttctctatctgaaaaaaaatgcag

upper sequence: GRMZM2G053868_T02 (Zea mays), 5'ss of exon 5
lower sequence: GLYMA16G23870.1 (Glycine max), 5'ss of exon 7
AACTTCCTTTTCAAATCGAACAAGGAGGATTCACCACTAAAGGCGACAGATTTTGGTTTGTCAGATTTCATTAAGCCAGgta--------tcta----cttggggcca-------tctgaatctgtcgggaatctgataggggcaagtctgcagtttagctgaccattttgttgtctaatgcatgctttag-------------------------------------------------
|| || ||||| ||||| | ||| || ||||||||  ||||||| || ||||||||||||||||||||||| || || |||         |||      ||| || ||       |||   ||| |        |  | |   || |  ||   |     |       |||   | | | ||||||| | |                                                 
AATTTTCTTTTTAAATCAACCAAAGAAGATTCACCTTTAAAGGCCACTGATTTTGGTTTGTCAGATTTCATAAAACCTGgtgagggaaagtcttgatttttgtggtcaatttctttctttttcttttcttccattttttgtttcaggcttgttctcctatttcttcagttgagttatcaggcatgctcttgccatttttatttgagatttgtttttctctatctttgaaaaaaaatgcag

upper sequence: GRMZM2G053868_T02 (Zea mays), 5'ss of exon 5
lower sequence: GLYMA01G37100.1 (Glycine max), 5'ss of exon 6
AACTTCCTTTTCAAATCGAACAAGGAGGATTCACCACTAAAGGCGACAGATTTTGGTTTGTCAGATTTCATTAAGCCAGgtatctact--tggggccatctgaatctgt-cgggaatctgataggggcaagtctgcagtttagctgaccattttgttgtctaatgcatgctttag--------------------
|| || |||||||| || | ||| || ||||||||  ||||||| || |||||||||||||| |||||||| || || |||    |    || |   |||   |||| |       | | ||       ||  | ||   |       || | | || | | |   ||| |||                      
AATTTTCTTTTCAAGTCAACCAAAGAAGATTCACCTTTAAAGGCTACCGATTTTGGTTTGTCTGATTTCATAAAACCTGgtgagcaaaaatgtgttgatcattatctttgtttcctttttatccctcttagcattcaaaatgttcttgcaatct-ttatttgagttatggttttctctctttgcaaacaaaacag

upper sequence: GRMZM2G053868_T02 (Zea mays), 5'ss of exon 5
lower sequence: AT4G36070.1 (Arabidopsis thaliana), 5'ss of exon 5
AACTTCCTTTTCAAATCGAACAAGGAGGATTCACCACTAAAGGCGACAGATTTTGGTTTGTCAGATTTCATTAAGCCAGgtatctacttggggccatctgaatctgtcgggaatctgataggggcaagtctgcagttta-gctgaccattttgttgtctaatgcatgctttag
|| || || |||||||| | | | || | |||| | |||||||| |||||||||||| |||| || ||||| ||||||||||   | ||       ||      ||||      ||||   | |||     | || | | |  |   |||||||     ||||   |      
AATTTTCTGTTCAAATCAACCGAAGAAGGTTCATCTCTAAAGGCTACAGATTTTGGTCTGTCGGACTTCATAAAGCCAGgtaaa-agtttcacttgtcaagtcttgtc-----cctga---gagcagaatggtagataatggaggtgattttgtgaa--aatggcag------

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), 49 (downstream exon)
Score: 113

AACTTCCTTTTCAAATCGAACAAGGAGGATTCACCACTAAAGGCGACAGATTTTGGTTTGTCAGATTTCATTAAGCCAGgtatctactt ... catgctttagGGAAGAAGTTCCATGACATTGTTGGAAGTGCTTACTATGTCGCACCAGAAGTACTAAAACGACGGTCTGGTCCTGAGTCAGATGTTTGGAGCATAGGAGT


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 241

AACTTCCTTTTCAAATCGAACAAGGAGGATTCACCACTAAAGGCGACAGATTTTGGTTTGTCAGATTTCATTAAGCCAGgtatctactt ... catgctttagGGAAGAAGTTCCATGACATTGTTGGAAGTGCTTACTATGTCGCACCAGAAGTACTAAAACGACGGTCTGGTCCTGAGTCAGATGTTTGGAGCATAGGAGT


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 401

AACTTCCTTTTCAAATCGAACAAGGAGGATTCACCACTAAAGGCGACAGATTTTGGTTTGTCAGATTTCATTAAGCCAGgtatctactt ... catgctttagGGAAGAAGTTCCATGACATTGTTGGAAGTGCTTACTATGTCGCACCAGAAGTACTAAAACGACGGTCTGGTCCTGAGTCAGATGTTTGGAGCATAGGAGT


Block sizes: 48 (upstream exon), 45 (downstream exon)
Score: 233

AACTTCCTTTTCAAATCGAACAAGGAGGATTCACCACTAAAGGCGACAGATTTTGGTTTGTCAGATTTCATTAAGCCAGgtatctactt ... catgctttagGGAAGAAGTTCCATGACATTGTTGGAAGTGCTTACTATGTCGCACCAGAAGTACTAAAACGACGGTCTGGTCCTGAGTCAGATGTTTGGAGCATAGGAGT