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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATGGCCTCTTGTCAAGGTCGGACCAGAGAATTCTTGTTCTTGCTGCGACCAACAGGCCTTTTGATCTTGATGAGGCTATTATCCGTAGGTTCGAGCGAAGgtttgtatattttctccaagatactagtaacgtttatgcatccctcagtttgttccctgagctgtgtcctcttcctttaaacag

Basic information

species Zea mays
transcript GRMZM2G159307_T01
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G159307_T01 (Zea mays), 5'ss of exon 11
lower sequence: LOC_Os01g12660.1 (Oryza sativa), 5'ss of exon 11
ATGGCCTCTTGTCAAGGTCGGACCAGAGAATTCTTGTTCTTGCTGCGACCAACAGGCCTTTTGATCTTGATGAGGCTATTATCCGTAGGTTCGAGCGAAGgtttgtatattttctcca--agatactagtaacgtttatgcatccctcagtttgttccctgagctgtgtcctcttcctttaaacag-------------------------------
||||||||||||||||  | || || | ||||||||| ||||||||||||||| | || |||||||||||||| ||||| || || ||||| ||||| ||||||| || | |||      |||| |||||  |  | ||   |  || |  || ||     |||    | |  ||  |  ||                                   
ATGGCCTCTTGTCAAGACCAGATCAAAAAATTCTTGTCCTTGCTGCGACCAACCGACCCTTTGATCTTGATGAAGCTATCATTCGAAGGTTTGAGCGCAGgtttgcatctcttccttgctagatgctagtt-ctctcatctgtatctaaactttttttt--agcccctttcgattgttccaagttccatgcctgagtgtattgccttgcttctttag

upper sequence: GRMZM2G159307_T01 (Zea mays), 5'ss of exon 11
lower sequence: GLYMA20G30360.1 (Glycine max), 5'ss of exon 10
ATGGCCTCTTGTCAAGGTCGGACCAGAGAATTCTTGTTCTTGCTGCGACCAACAGGCCTTTTGATCTTGATGAGGCTATTATCCGTAGGTTCGAGCGAAGgtttg--tatatttt---ctccaagatactagtaacgtttatgcatccctcagtttgttccctgagctgtgtcctcttcctttaaacag-----------
|||| || ||| ||    |  |  |  ||||||| |||||||| || ||||||||||| ||||| |||||||| || || ||  |  |||| ||||| ||||  |   | | |||   ||    | |   || | | | | |  ||  ||   ||   | |   || | | |  ||||  ||  ||||            
ATGGGCTATTGACAGAACCCAATGAACGAATTCTGGTTCTTGCCGCAACCAACAGGCCATTTGACCTTGATGAAGCAATCATAAGACGGTTTGAGCGCAGgtaagaccacacttttgtcttatggttggcaggatcttctgttgattacttgcttctgttcaacagttatattttctttattagaacaaccacaatcatt

upper sequence: GRMZM2G159307_T01 (Zea mays), 5'ss of exon 11
lower sequence: GLYMA10G37380.1 (Glycine max), 5'ss of exon 10
ATGGCCTCTTGTCAAGGTCGGACCAGAGAATTCTTGTTCTTGCTGCGACCAACAGGCCTTTTGATCTTGATGAGGCTATTATCCGTAGGTTCGAGCGAAGgt----ttgtatattt-tctccaagatactagtaacgtttatgcatccctca-gtttgttccctgagctgtgtcctcttcctttaaacag-----------
||||  | ||| |||   | |   || ||||||| ||||||||||| ||||||||||| ||||| |||||||| || |||||  |  |||| ||||| ||||        |  ||| |||    | |   |  | | | | |  ||  ||   || |||||    |||| | |  ||||  ||  ||||            
ATGGAATATTGACAAAACCTGGTGAGCGAATTCTGGTTCTTGCTGCAACCAACAGGCCATTTGACCTTGATGAAGCAATTATAAGACGGTTTGAGCGCAGgtaagaccacacctttgtcttatggttggcatgatcttctgttgattacttgtgtctgttcagc-agctatattttctttattagaacaatcacaatcatt

upper sequence: GRMZM2G159307_T01 (Zea mays), 5'ss of exon 11
lower sequence: AT5G52882.1 (Arabidopsis thaliana), 5'ss of exon 9
ATGGCCTCTTGTCAAGGTCGGACCAGAGAATTCTTGTTCTTGCTGCGACCAACAGGCCTTTTGATCTTGATGAGGCTATTATCCGTAGGTTCGAGCGAAGgtttgtat--attttctccaagatactagtaacgtttatgcatccct-cagtttgttccctgagctgtgtcctcttcct--ttaaacag
|||| ||  || | |   | |   | || ||||| |||||||| ||||| ||||| || |||||||||||||| ||||| ||  | ||||| ||| |||||| |  |   | |||    || || | |      |  ||   ||  | || | | ||  ||||  | |||  | |      |  |||||
ATGGGCTAATGACGAAACCCGGTGAAAGGATTCTCGTTCTTGCAGCGACAAACAGACCGTTTGATCTTGATGAAGCTATCATTAGGAGGTTTGAGAGAAGgtataaaagaaattttggtaaaatgcaaaacctctaaatcagtctttacactattttgactgatttttgttttgtgttggatataacag

upper sequence: GRMZM2G159307_T01 (Zea mays), 5'ss of exon 11
lower sequence: Vv16s0050g01850.t01 (Vitis vinifera), 5'ss of exon 13
ATGGCCTCTTGTCAAGGTCGGACCAGAGAATTCTTGTTCTTGCTGCGACCAACAGGCCTTTTGATCTTGATGAGGCTATTATCCGTAGGTTCGAGCGAAGgt----ttgtatattttctc--------caagatactagtaacgtttatgcatccctcagtttgttccctgagctgtgtcc---tcttcctttaaacag-
|||| ||  || |||   | |   |  |||| |||||||||||||| ||||||||||| ||||| ||||| ||||| |||||| |  |||| ||||| ||||    ||||||||| | |         ||  || ||  |    ||  ||||||||| | | |    |   |     | ||   ||||| |  || ||  
ATGGGCTACTGACAAAAGCTGGTGAACGAATCCTTGTTCTTGCTGCAACCAACAGGCCATTTGACCTTGACGAGGCAATTATCAGGCGGTTTGAGCGCAGgtagatttgtatattgtattacactcagcatcattctcatcgttttactgcatcccttaatcttcaactacaaaaaaggccagatcttcatcaaagcatg

upper sequence: GRMZM2G159307_T01 (Zea mays), 5'ss of exon 11
lower sequence: Vv02s0025g00650.t01 (Vitis vinifera), 5'ss of exon 12
ATGGCCTCTTGTCAAGGTCGGACCAGAGAATTCTTGTTCTTGCTGCGACCAACAGGCCTTTTGATCTTGATGAGGCTATTATCCGTAGGTTCGAGCGAAGgt--ttgtatattttctccaagatactagtaacgtttatgcatccctcagtttgttccctgagctgtgtcctcttcctttaaacag------------------
|||| |||||| |||   |||   || | ||||||||||||||||| || |||||||| ||||| |||||||| || || ||| |  | || ||| | ||||   | |  |||| |   || || | |   || || ||| |    | ||||           |  |||  ||||  || |    |                  
ATGGACTCTTGACAAAACCGGGTGAGCGGATTCTTGTTCTTGCTGCAACTAACAGGCCATTTGACCTTGATGAAGCCATAATCAGACGCTTTGAGAGGAGgtaactctgcatttccaagaacattccacacaccttaatggaagtttgagttcaccttt----ccatgttttcttggttgaggaggagaagccaaaattattat

upper sequence: GRMZM2G159307_T01 (Zea mays), 5'ss of exon 11
lower sequence: Vv16s0050g01830.t01 (Vitis vinifera), 5'ss of exon 11
ATGGCCTCTTGTCAAGGTCGGACCAGAGAATTCTTGTTCTTGCTGCGACCAACAGGCCTTTTGATCTTGATGAGGCTATTATCCGTAGGTTCGAGCGAAGgtttgtatattttctccaagatact-agtaacgtttatg-catccctcagtttgttccctga-gctgtgtcctcttcctttaaacag------------------------------------------------------------------
|||| ||  || |||   | |   |  || | || ||||||||||| ||||||||||| ||||| ||||||||||| |||||| |  |||| ||||  ||||   | |   |  |     | |||  | | | |||    | |    | |  | |   || | || ||||  | |        | |                                                                   
ATGGACTACTGACAAAAGCTGGTGAACGAGTCCTCGTTCTTGCTGCAACCAACAGGCCATTTGACCTTGATGAGGCGATTATCAGGCGGTTTGAGCACAGgtagatttgcatattgtgtcacactcggcatcattttcatcgttttaccgcatttaaactaaagccgtgttgtatggagaaggatatattgaagatagatgaatgtgtcaccatgcttcgagtaggcaaactaatggtatctgtgatgaacag

upper sequence: GRMZM2G159307_T01 (Zea mays), 5'ss of exon 11
lower sequence: Vv16s0050g01840.t01 (Vitis vinifera), 5'ss of exon 12
ATGGCCTCTTGTCAAGGTCGGACCAGAGAATTCTTGTTCTTGCTGCGACCAACAGGCCTTTTGATCTTGATGAGGCTATTATCCGTAGGTTCGAGCGAAGgtttgtatattttctccaagatact-agtaacgtttatg-catccctcagtttgttccctgagctgtgtcctcttcctttaaacag---------------------------------------------------
|||| ||  || |||   | |   |  || | || ||||||||||| ||||||||||| ||||| ||||||||||| |||||| |  |||| || |  ||||   | |   |  |     | ||| || | | |||    | |    |  |         |||  |  |    |     || |                                                      
ATGGACTACTGACAAAAGCTGGTGAACGAGTCCTCGTTCTTGCTGCAACCAACAGGCCATTTGACCTTGATGAGGCGATTATCAGGCGGTTTGACCACAGgtagatttgcatattgtgttacactcagcatcattttcatcgttttactctgaagctatggagaaggatatattaaagatagatgaatgtgtcaccatgctttgagtaggcaaactaatggtatctgtgatgaacag

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: 43 (upstream exon), 46 (downstream exon)
Score: 11

ATGGCCTCTTGTCAAGGTCGGACCAGAGAATTCTTGTTCTTGCTGCGACCAACAGGCCTTTTGATCTTGATGAGGCTATTATCCGTAGGTTCGAGCGAAGgtttgtatat ... ctttaaacagAATCATGGTAGGTCTGCCATCAATGGAAAGCCGGGAACTCATAATGCGGCGACTTCTGTCAAAGGAGAAAGTTGATGAAAGGCTGAACTTCAAGGAGCTA


Block sizes: 46 (upstream exon), 33 (downstream exon)
Score: 9

ATGGCCTCTTGTCAAGGTCGGACCAGAGAATTCTTGTTCTTGCTGCGACCAACAGGCCTTTTGATCTTGATGAGGCTATTATCCGTAGGTTCGAGCGAAGgtttgtatat ... ctttaaacagAATCATGGTAGGTCTGCCATCAATGGAAAGCCGGGAACTCATAATGCGGCGACTTCTGTCAAAGGAGAAAGTTGATGAAAGGCTGAACTTCAAGGAGCTA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 22

ATGGCCTCTTGTCAAGGTCGGACCAGAGAATTCTTGTTCTTGCTGCGACCAACAGGCCTTTTGATCTTGATGAGGCTATTATCCGTAGGTTCGAGCGAAGgtttgtatat ... ctttaaacagAATCATGGTAGGTCTGCCATCAATGGAAAGCCGGGAACTCATAATGCGGCGACTTCTGTCAAAGGAGAAAGTTGATGAAAGGCTGAACTTCAAGGAGCTA


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 7

ATGGCCTCTTGTCAAGGTCGGACCAGAGAATTCTTGTTCTTGCTGCGACCAACAGGCCTTTTGATCTTGATGAGGCTATTATCCGTAGGTTCGAGCGAAGgtttgtatat ... ctttaaacagAATCATGGTAGGTCTGCCATCAATGGAAAGCCGGGAACTCATAATGCGGCGACTTCTGTCAAAGGAGAAAGTTGATGAAAGGCTGAACTTCAAGGAGCTA