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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CGGATCTCCTGGCACTGGAAAAACTATGCTTGCCAAAGCAGTAGCAACTAAAGTAGGCGCTAATTTCATCAATATATCAATGTCGAGCATTACATGTAAGgtattatttcacctaatgggcaactgatgagattcactactgtctcaaggctaaccagtggtttgttaactttcag

Basic information

species Zea mays
transcript GRMZM2G170037_T01
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G170037_T01 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os11g43970.1 (Oryza sativa), 5'ss of exon 22
CGGATCTCCTGGCACTGGAAAAACTATGCTTGCCAAAGCAGTAGCAACTAAAGTAGGCGCTAATTTCATCAATATATCAATGTCGAGCATTACATGTAAGgtattatttcacctaa-tgggcaactgatgagattcac----tactgt------ctcaaggctaaccagtggtttgttaactttcag
 ||| ||||||| ||||| ||||| |||||||| || |||||||||||| ||| ||| ||||| ||||| || ||||||||||| ||||||||||  ||||||| ||  || | || |     | | ||||| |  ||    |||| |      ||||| |||||    || ||| |  ||||||||
TGGACCTCCTGGTACTGGGAAAACCATGCTTGCTAAGGCAGTAGCAACTGAAGCAGGTGCTAACTTCATTAACATATCAATGTCAAGCATTACATCGAAGgtatgatggcatccaaattttgcattaatgaggtgtacagtgtactatgtgattctcaaagctaaatgctgttttttctactttcag

upper sequence: GRMZM2G170037_T01 (Zea mays), 5'ss of exon 4
lower sequence: AT4G02480.1 (Arabidopsis thaliana), 5'ss of exon 21
CGGATCTCCTGGCACTGGAAAAACTATGCTTGCCAAAGCAGTAGCAACTAAAGTAGGCGCTAATTTCATCAATATATCAATGTCGAGCATTACATGTAAGgtattatttcacctaatgggcaactgatgagattcactactgtctcaaggctaac-cagtggtttgttaactttcag----------
 ||| ||||||| |||||||| || ||||| || ||||||||||||||| | |  ||||| |||||||||||||| |||||||| |||||||| |  ||||||   | |||   | ||   |  ||||    ||   | || |||       |    | | |    || ||  | |           
TGGACCTCCTGGTACTGGAAAGACGATGCTGGCAAAAGCAGTAGCAACTGAGGCTGGCGCAAATTTCATCAATATCTCAATGTCCAGCATTACTTCGAAGgtaac-tctcataaagtg---atatgatttccttttatgctttcttttaatgattgtacttgaccatttacactaaatgctttgcag

upper sequence: GRMZM2G170037_T01 (Zea mays), 5'ss of exon 4
lower sequence: Vv07s0005g00200.t01 (Vitis vinifera), 5'ss of exon 21
CGGATCTCCTGGCACTGGAAAAACTATGCTTGCCAAAGCAGTAGCAACTAAAGTAGGCGCTAATTTCATCAATATATCAATGTCGAGCATTACATGTAAGgtat-tattt-cacctaatgggcaactgatgagattc--------actactgtctcaaggctaaccagtggtttgtta--actttcag
 ||  ||||||| ||||||||||| |||||||| || || || |||||| | | ||| || ||||| ||||| ||||||||||| || || || |  ||||||  ||| | || | ||  ||  |||    || |          | |  ||| |  |   ||          || ||   ||| |||
TGGGCCTCCTGGGACTGGAAAAACAATGCTTGCGAAGGCGGTTGCAACTGAGGCAGGTGCAAATTTTATCAACATATCAATGTCTAGTATCACTTCAAAGgtaaatatgtgcatcaaaatggtgactatgcagctctcttttgcaagtcttgttttgaaaatatttgacatcctgatattgcttgcag

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: 40 (upstream exon), 48 (downstream exon)
Score: 203

CGGATCTCCTGGCACTGGAAAAACTATGCTTGCCAAAGCAGTAGCAACTAAAGTAGGCGCTAATTTCATCAATATATCAATGTCGAGCATTACATGTAAGgtattatttc ... taactttcagTGGTTTGGTGAAGGGGAGAAGTATGTAAAGGCTATTTTCTCACTAGCAAGTAAAATAGCACCCAGTGTTATATTTTATTGATGAGGTATGCAAGCACACA


Block sizes: 41 (upstream exon), 49 (downstream exon)
Score: 253

CGGATCTCCTGGCACTGGAAAAACTATGCTTGCCAAAGCAGTAGCAACTAAAGTAGGCGCTAATTTCATCAATATATCAATGTCGAGCATTACATGTAAGgtattatttc ... taactttcagTGGTTTGGTGAAGGGGAGAAGTATGTAAAGGCTATTTTCTCACTAGCAAGTAAAATAGCACCCAGTGTTATATTTTATTGATGAGGTATGCAAGCACACA


Block sizes: 41 (upstream exon), 49 (downstream exon)
Score: 174

CGGATCTCCTGGCACTGGAAAAACTATGCTTGCCAAAGCAGTAGCAACTAAAGTAGGCGCTAATTTCATCAATATATCAATGTCGAGCATTACATGTAAGgtattatttc ... taactttcagTGGTTTGGTGAAGGGGAGAAGTATGTAAAGGCTATTTTCTCACTAGCAAGTAAAATAGCACCCAGTGTTATATTTTATTGATGAGGTATGCAAGCACACA


Block sizes: 41 (upstream exon), 47 (downstream exon)
Score: 225

CGGATCTCCTGGCACTGGAAAAACTATGCTTGCCAAAGCAGTAGCAACTAAAGTAGGCGCTAATTTCATCAATATATCAATGTCGAGCATTACATGTAAGgtattatttc ... taactttcagTGGTTTGGTGAAGGGGAGAAGTATGTAAAGGCTATTTTCTCACTAGCAAGTAAAATAGCACCCAGTGTTATATTTTATTGATGAGGTATGCAAGCACACA