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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGATCTCTCTGAATTTGATGAATCTCGAGAGATAATAGAGAGCCTAGTTGATGAATACAAGGCCTGTGAGTCGCCAGACTACATTAAATGGGGAATGGAGgtaagtttaatgaagtttaaatgttgttctttgcgctatataaaatgctgagcaatctgttccaaagcag

Basic information

species Zea mays
transcript GRMZM2G085970_T02
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G085970_T01 (Zea mays), 5'ss of exon 10
lower sequence: LOC_Os05g06450.1 (Oryza sativa), 5'ss of exon 10
TGATCTCTCTGAATTTGATGAATCTCGAGAGATAATAGAGAGCCTAGTTGATGAATACAAGGCCTGTGAGTCGCCAGACTACATTAAATGGGGAATGGAGgtaagt-ttaatgaagtttaaatg---ttgttctttgcgctatataaaatgctgagcaatctgttccaaagcag
|||||||||||||||||||||||||||||| |||||||||||| |||||||||| |||||||| || || || ||||||||||| |||||||| ||||||||| || ||       ||| | |    ||||| ||| |  ||| | |||||||||||||||||||  |||  ||
TGATCTCTCTGAATTTGATGAATCTCGAGAAATAATAGAGAGCTTAGTTGATGAGTACAAGGCTTGCGAATCACCAGACTACATCAAATGGGGGATGGAGgtacgtctttgctccatttcagtatatttgttatttactttatgtgaaatgctgagcaatctgttggaaaatag

upper sequence: GRMZM2G085970_T01 (Zea mays), 5'ss of exon 10
lower sequence: GLYMA03G41670.2 (Glycine max), 5'ss of exon 10
TGATCTCTCTGAATTTGATGAATCTCGAGAGATAATAGAGAGCCTAGTTGATGAATACAAGGCCTGTGAGTCGCCAGACTACATTAAATGGGGAATGGAGgtaagtttaatgaagtttaaatgttgttctttgcgc-tatataaaatgctgagcaatctgttccaaagcag----
||| ||||| ||||||||||||||  | || ||||| |||||  | |||||||||||||||||||||||||| ||||| || || ||||||||||||||||||  ||   |  |  |   | ||     |||  ||  || |    |  ||   | | | | ||     |     
TGACCTCTCAGAATTTGATGAATCAAGGGACATAATTGAGAGTTTGGTTGATGAATACAAGGCCTGTGAGTCCCCAGATTATATCAAATGGGGAATGGAGgtagattctctacaaatcccacgtaccattttaagcacatctttcgtattgctaattttttgccgtcttatttag

upper sequence: GRMZM2G085970_T01 (Zea mays), 5'ss of exon 10
lower sequence: GLYMA19G44260.2 (Glycine max), 5'ss of exon 11
TGATCTCTCTGAATTTGATGAATCTCGAGAGATAATAGAGAGCCTAGTTGATGAATACAAGGCCTGTGAGTCGCCAGACTACATTAAATGGGGAATGGAGgtaagtttaatgaagtttaaatgttgttctttgcgc-tatataaaatgctgagcaatctgt----tccaaagcag
||| ||||| ||||||||||||||  | || ||||| ||||   | |||||||||||||||||||||||||| ||||| || || ||||||||||||||||||  ||   |  |  |    |||     |||  ||  ||||    |  ||   | | | |    ||  |   ||
TGACCTCTCAGAATTTGATGAATCAAGGGACATAATTGAGACTTTGGTTGATGAATACAAGGCCTGTGAGTCCCCAGATTATATCAAATGGGGAATGGAGgtagattctctacaaatcccttgtaccattttaagcacatattgcgtattgctaattttttgctctcttatttag

upper sequence: GRMZM2G085970_T01 (Zea mays), 5'ss of exon 10
lower sequence: AT3G61650.1 (Arabidopsis thaliana), 5'ss of exon 9
TGATCTCTCTGAATTTGATGAATCTCGAGAGATAATAGAGAGCCTAGTTGATGAATACAAGGCCTGTGAGTCGCCAGACTACATTAAATGGGGAATGGAGgta----agtttaatgaagtttaaatgttgttctttgcgctatataaaatgctgagca-atctgt-tccaaagcag
|||||| || || ||||| |||||  | || ||||| |||||  | || ||||||||||||||||||||||| ||||| ||||| ||||||||||||||||||    || ||     |     ||| ||  |  | |    |    ||||| | |    |||||| ||     |||
TGATCTTTCAGAGTTTGACGAATCAAGGGACATAATTGAGAGTTTGGTAGATGAATACAAGGCCTGTGAGTCTCCAGATTACATCAAATGGGGAATGGAGgtatataagcttttcccatcaataatcttacttatggatgaactcgaaatgataactgtatctgtgtctgtctcag

upper sequence: GRMZM2G085970_T01 (Zea mays), 5'ss of exon 10
lower sequence: AT5G05620.1 (Arabidopsis thaliana), 5'ss of exon 9
TGATCTCTCTGAATTTGATGAATCTCGAGAGATAATAGAGAGCCTAGTTGATGAATACAAGGCCTGTGAGTCGCCAGACTACATTAAATGGGGAATGGAGgtaagtttaatgaagtttaaatgttgttctttgcgc--tatataaaatgctgagcaatctgttccaaagcag-------------
|||||| || || |||||||||||  | || ||||| |||||  | || || ||||| |||||||||||||| ||||| ||||| ||||||||||||||||||  |    | |  |||     |   |  |  | |  || |  ||   || |  |   |  || ||   |              
TGATCTTTCAGAGTTTGATGAATCAAGGGACATAATTGAGAGTTTGGTAGACGAATATAAGGCCTGTGAGTCTCCAGATTACATCAAATGGGGAATGGAGgtatataagctaagcttttgccatctatagtcacacactaaaggaagaacttataatgattatcgaatatatgtgactctctcag

upper sequence: GRMZM2G085970_T01 (Zea mays), 5'ss of exon 10
lower sequence: Vv15s0046g01350.t01 (Vitis vinifera), 5'ss of exon 10
TGATCTCTCTGAATTTGATGAATCTCGAGAGATAATAGAGAGCCTAGTTGATGAATACAAGGCCTGTGAGTCGCCAGACTACATTAAATGGGGAATGGAGgtaagtttaatga-agtttaaatgttgttc----tttgcgctatataaaatgc--tgagcaatctgttccaaagcag
|||||| || ||||||||||||||  |||| || || |||||  | ||||||||||||||||| || ||||| |||||||| ||||||||||| |||||||||     | |    |     || |    |    ||||    || || | ||   ||   ||| |        ||||
TGATCTTTCAGAATTTGATGAATCAAGAGACATTATTGAGAGTTTGGTTGATGAATACAAGGCATGCGAGTCCCCAGACTATATTAAATGGGGGATGGAGgtataagaacttctggccctgatctcacccatcttttgtataatttagattgtaatggtaaattttaatttgtgcag

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), 42 (downstream exon)
Score: 24

TGATCTCTCTGAATTTGATGAATCTCGAGAGATAATAGAGAGCCTAGTTGATGAATACAAGGCCTGTGAGTCGCCAGACTACATTAAATGGGGAATGGAGgtaagtttaa ... tccaaagcagGACCCTGGAGAGGCAAACGTTGCAGCAGATCTTGACTCTAAGTTGGTAGTGTAAATATAAAGGTACCATTTCATGAATCATGATCAGGCACTTTATATGC


Block sizes: 44 (upstream exon), 49 (downstream exon)
Score: 16

TGATCTCTCTGAATTTGATGAATCTCGAGAGATAATAGAGAGCCTAGTTGATGAATACAAGGCCTGTGAGTCGCCAGACTACATTAAATGGGGAATGGAGgtaagtttaa ... tccaaagcagGACCCTGGAGAGGCAAACGTTGCAGCAGATCTTGACTCTAAGTTGGTAGTGTAAATATAAAGGTACCATTTCATGAATCATGATCAGGCACTTTATATGC


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 14

TGATCTCTCTGAATTTGATGAATCTCGAGAGATAATAGAGAGCCTAGTTGATGAATACAAGGCCTGTGAGTCGCCAGACTACATTAAATGGGGAATGGAGgtaagtttaa ... tccaaagcagGACCCTGGAGAGGCAAACGTTGCAGCAGATCTTGACTCTAAGTTGGTAGTGTAAATATAAAGGTACCATTTCATGAATCATGATCAGGCACTTTATATGC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 30

TGATCTCTCTGAATTTGATGAATCTCGAGAGATAATAGAGAGCCTAGTTGATGAATACAAGGCCTGTGAGTCGCCAGACTACATTAAATGGGGAATGGAGgtaagtttaa ... tccaaagcagGACCCTGGAGAGGCAAACGTTGCAGCAGATCTTGACTCTAAGTTGGTAGTGTAAATATAAAGGTACCATTTCATGAATCATGATCAGGCACTTTATATGC