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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGCATCAGACCTCTACCAAGAGCAGATGAAAGGACGTGTTGTTGATTGGGATGTACCTGAACAAGCATCTGGGCAACATGTAATGAAGGACGAACCACAGgtagcttctattccagaacttttttcttgcataatataattctgtaactttagttaagatgtcagtatgctgtccaaatttcag

Basic information

species Zea mays
transcript GRMZM2G001895_T01
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G001895_T01 (Zea mays), 5'ss of exon 11
lower sequence: LOC_Os10g42439.1 (Oryza sativa), 5'ss of exon 17
GGCATCAGACCTCTACCAAGAGCAGATGAAAGGACGTGTTGTTGATTGGGATGTACCTGAACAAGCATCTGGGCAACATGTAATGAAGGACGAACCACAGgtagcttctattccagaacttttttcttgcataatataattctgtaactttagttaagatgtcagtatgctgtccaaatttcag
|||  |||||||||||||||||||||||||||| |||||||||||||||||||| ||||||||||||||||| || |||||||||||||| || ||||||||||  | || || ||||   |  | ||   |    | |||   | |  || |   | ||||    ||||||| ||||||||||
GGCCACAGACCTCTACCAAGAGCAGATGAAAGGGCGTGTTGTTGATTGGGATGTGCCTGAACAAGCATCTGGCCAGCATGTAATGAAGGATGAGCCACAGgtagtgtttagtctagaatcatcctattattt----tcatttcctgaaattgggctatatgttctcatgctgtgcaaatttcag

upper sequence: GRMZM2G001895_T01 (Zea mays), 5'ss of exon 11
lower sequence: GLYMA05G08040.1 (Glycine max), 5'ss of exon 17
GGCATCAGACCTCTACCAAGAGCAGATGAAAGGACGTGTTGTTGATTGGGATGTACCTGAACAAGCATCTGGGCAACATGTAATGAAGGACGAACCACAGgtagcttctattccagaacttttttcttgcataatataattctgtaact-ttagttaagatgtcagtatgc-tgtccaaatttcag---------------
||||| ||| || ||||  ||||||||||| || |||||||||||||||||| | ||||| || |||||||| || || | |||||  || || ||||||||| |  ||  |  |    ||| |    ||| ||| | | |   ||| | ||||| | |   |    |  |  | ||      |                 
GGCATTAGAGCTATACCGTGAGCAGATGAAGGGGCGTGTTGTTGATTGGGATTTGCCTGAGCAGGCATCTGGCCAGCAGGAAATGAGAGATGAGCCACAGgtatcacctgatatatgtttttctataggca-aatgttagttgctaattgttagtgaggggattcaaacccacgacctctccccccttcccttctcccttc

upper sequence: GRMZM2G001895_T01 (Zea mays), 5'ss of exon 11
lower sequence: GLYMA17G12950.1 (Glycine max), 5'ss of exon 18
GGCATCAGACCTCTACCAAGAGCAGATGAAAGGACGTGTTGTTGATTGGGATGTACCTGAACAAGCATCTGGGCAACATGTAATGAAGGACGAACCACAGgtagcttctattccagaacttttttcttgcataatataattctgtaactttagttaagatgtca-gtatgctgtccaaatttcag----------
||||||||| || ||||  |||||||||||||| |||||||||||||||||||| ||||| || |||||||| || || | |||||  || || |||||||||    | |           |||| ||  |||| || ||  | ||   | |  ||   | |||   |||   | ||| |||             
GGCATCAGAGCTATACCGTGAGCAGATGAAAGGGCGTGTTGTTGATTGGGATGTGCCTGAGCAGGCATCTGGACAGCAGGAAATGAGAGATGAGCCACAGgtattcaccagatatatgtgatttttttttataaaattatg-tatagaataatatattttctcataaatggatttcaacttttgtgtggatgcag

upper sequence: GRMZM2G001895_T01 (Zea mays), 5'ss of exon 11
lower sequence: Vv11s0016g04420.t01 (Vitis vinifera), 5'ss of exon 17
GGCATCAGACCTCTACCAAGAGCAGATGAAAGGACGTGTTGTTGATTGGGATGTACCTGAACAAGCATCTGGGCAACATGTAATGAAGGACGAACCACAGgtagcttctattccagaacttttttcttgcataa-tataattctgtaactttagttaagatgtcagtatgctgtccaaatttcag
||| ||||| || || |  || || |||||||| |||||||||||||||||||| ||||| || |||||||| || || | |||||  || || ||||||||| || || ||| |     |  || ||    || |||    |||||   ||   |  ||| |||  ||  |        | |||
GGCTTCAGATCTTTATCGTGAACAAATGAAAGGTCGTGTTGTTGATTGGGATGTGCCTGAGCAGGCATCTGGCCAGCAGGAAATGAGAGATGAGCCACAGgtatctcctgttctattctgtcctttttattcaaatatgtacctgtactgttgagtg-gatttcaa-attttcatggtcatgcag

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: 46 (upstream exon), 48 (downstream exon)
Score: 126

GGCATCAGACCTCTACCAAGAGCAGATGAAAGGACGTGTTGTTGATTGGGATGTACCTGAACAAGCATCTGGGCAACATGTAATGAAGGACGAACCACAGgtagcttcta ... caaatttcagGTTGGTGGAATTTATGTTAGACTTTTTCTTAAGGACCCCAAATTTCCACTGAGAAACCCTAAAAGATTCCTTGAAGGGCTCCTAGATCAATATGTCTCCT


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 123

GGCATCAGACCTCTACCAAGAGCAGATGAAAGGACGTGTTGTTGATTGGGATGTACCTGAACAAGCATCTGGGCAACATGTAATGAAGGACGAACCACAGgtagcttcta ... caaatttcagGTTGGTGGAATTTATGTTAGACTTTTTCTTAAGGACCCCAAATTTCCACTGAGAAACCCTAAAAGATTCCTTGAAGGGCTCCTAGATCAATATGTCTCCT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 133

GGCATCAGACCTCTACCAAGAGCAGATGAAAGGACGTGTTGTTGATTGGGATGTACCTGAACAAGCATCTGGGCAACATGTAATGAAGGACGAACCACAGgtagcttcta ... caaatttcagGTTGGTGGAATTTATGTTAGACTTTTTCTTAAGGACCCCAAATTTCCACTGAGAAACCCTAAAAGATTCCTTGAAGGGCTCCTAGATCAATATGTCTCCT


Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 98

GGCATCAGACCTCTACCAAGAGCAGATGAAAGGACGTGTTGTTGATTGGGATGTACCTGAACAAGCATCTGGGCAACATGTAATGAAGGACGAACCACAGgtagcttcta ... caaatttcagGTTGGTGGAATTTATGTTAGACTTTTTCTTAAGGACCCCAAATTTCCACTGAGAAACCCTAAAAGATTCCTTGAAGGGCTCCTAGATCAATATGTCTCCT