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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTACGCTGAGGTTGATTGTCCAGTTGCAGCTCCAGATGGCTTCCCGAAAGATGATGAACTTCAATTTGAGATTGAAATGTTGGATTTCTTTAAAGCCAAGgttaatctcattaaatggtgacttgagtatgacttcagatatatatttcattactttcagagaactggcaaacagtttacatgtctattttaacaatttt...

Basic information

species Zea mays
transcript AC216247.3_FGT005
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AC216247.3_FGT005 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os03g25140.1 (Oryza sativa), 5'ss of exon 5
CTACGCTGAGGTTGATTGTCCAGTTGCAGCTCCAGATGGCTTCCCGAAAGATGATGAACTTCAATTTGAGATTGAAATGTTGGATTTCTTTAAAGCCAAGgttaatctcattaaatggtgacttgagtatgacttcagatatatatttcattactttcagagaactggcaaacagtttacatgtctattttaacaatttt------
||| || ||||  |||||||||||| ||||||| || ||||| || ||||||||||||||||||||||||||||| |||||||||||||| |||||||| |||| |||  || |||  || ||| ||| |||||| |    |  | ||  |   | |  |||| ||     |   | | || | || ||   |||| ||       
CTATGCAGAGGAGGATTGTCCAGTTACAGCTCCTGACGGCTTTCCAAAAGATGATGAACTTCAATTTGAGATTGAGATGTTGGATTTCTTCAAAGCCAAAgttagtcttgttgaataatggcttcagtgtgacttaaatccttaaattgctgtatatttgagagct-----attctgtgcaag-ctgttaggacaaattctcatga

upper sequence: AC216247.3_FGT005 (Zea mays), 5'ss of exon 5
lower sequence: GLYMA03G16440.1 (Glycine max), 5'ss of exon 5
CTACGCTGAGGTTGATTGTCCAGTTGCAGCTCCAGATGGCTTCCCGAAAGATGATGAACTTCAATTTGAGATTGAAATGTTGGATTTCTTTAAAGCCAAGgttaatctcattaaatggtgacttgagtatgacttcagatatatatttcattactttcagagaactggcaaacagtttacatgtctattttaacaatttt---
 || | ||||| ||||||||| ||| | ||||| ||||| || || || |||||||||||||| ||||| |||||  || | || || || ||||||||||  |   |    | || | || |||  | | | |  | || | ||| || |   | |  |  | |  |   |   |||   | ||||| |  ||| || |   
TTATGGTGAGGATGATTGTCCTGTTTCTGCTCCTGATGGTTTTCCTAAGGATGATGAACTTCATTTTGAAATTGAGCTGATAGAATTTTTCAAAGCCAAGgcaaggatgtgaacattgagatttgttttttattcta-atgtttatgtcctgtgtctttgttatcctgatgattattttggtttctatct--acacttgtgca

upper sequence: AC216247.3_FGT005 (Zea mays), 5'ss of exon 5
lower sequence: AT3G54010.2 (Arabidopsis thaliana), 5'ss of exon 4
CTACGCTGAGGTTGATTGTCCAGTTGCAGCTCCAGATGGCTTCCCGAAAGATGATGAACTTCAATTTGAGATTGAAATGTTGGATTTCTTTAAAGCCAAGgtta-atctcatta-----------aatggtgacttgagtatgacttcaga-tatatatttcattactttcagagaactggcaaacagtttacatgtctattttaacaatttt---
||| || ||| |||||||||||||  ||||||||||    || || ||||||||||| ||||| |||||||||||  |||||||||| | |||||||||||  | ||||||| |           ||  ||| | | |||  | |   ||| | |  | ||    | ||     |   || |  |  | || | | ||  || |   |||||    
CTATGCAGAGATTGATTGTCCAGTCTCAGCTCCAGAAAATTTTCCAAAAGATGATGAGCTTCATTTTGAGATTGAGTTGTTGGATTTTTCTAAAGCCAAGgcgagatctcatcactaaccaagataacagtg-cattagttagccgaaagactctgaaattttgcatttcatctgttttgacttat-gctttcctttcctttgtgttaatttccag

upper sequence: AC216247.3_FGT005 (Zea mays), 5'ss of exon 5
lower sequence: Vv08s0007g01460.t01 (Vitis vinifera), 5'ss of exon 6
CTACGCTGAGGTTGATTGTCCAGTTGCAGCTCCAGATGGCTTCCCGAAAGATGATGAACTTCAATTTGAGATTGAAATGTTGGATTTCTTTAAAGCCAAGgttaatctca---ttaaatggtgacttgagtatgacttcagatatatatttcattactttca-gagaactggcaaacagtttacatgtc-tattttaacaatttt
||| | ||||| | |||||||  ||   | ||| |||   || ||||| |||||||| ||||| ||||||||||| |||||||| |||||||||| |||||  |     |   |  |    |  || || | |||  | | ||  | ||| |    | | || ||  |||       |  || | || | ||||||||  |||  
CTATGGTGAGGCTAATTGTCCTCTTATGGTTCCTGATAATTTTCCGAAGGATGATGAGCTTCATTTTGAGATTGAGATGTTGGACTTCTTTAAAGTCAAGgcaagaaagagtttctatctttatctagactttgatatgatat-caaattcctccccctacatgatgacttatgttaaaattccttggcatattttaa--att--

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: 49 (upstream exon), 33 (downstream exon)
Score: 278

CTACGCTGAGGTTGATTGTCCAGTTGCAGCTCCAGATGGCTTCCCGAAAGATGATGAACTTCAATTTGAGATTGAAATGTTGGATTTCTTTAAAGCCAAGgttaatctca ... tctttgtcagGTTGTGGCAGAGGATTTGGGGGTGGTAAAGAAG


Block sizes: 48 (upstream exon), 33 (downstream exon)
Score: 203

CTACGCTGAGGTTGATTGTCCAGTTGCAGCTCCAGATGGCTTCCCGAAAGATGATGAACTTCAATTTGAGATTGAAATGTTGGATTTCTTTAAAGCCAAGgttaatctca ... tctttgtcagGTTGTGGCAGAGGATTTGGGGGTGGTAAAGAAG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 208

CTACGCTGAGGTTGATTGTCCAGTTGCAGCTCCAGATGGCTTCCCGAAAGATGATGAACTTCAATTTGAGATTGAAATGTTGGATTTCTTTAAAGCCAAGgttaatctca ... tctttgtcagGTTGTGGCAGAGGATTTGGGGGTGGTAAAGAAG


Block sizes: 49 (upstream exon), 33 (downstream exon)
Score: 203

CTACGCTGAGGTTGATTGTCCAGTTGCAGCTCCAGATGGCTTCCCGAAAGATGATGAACTTCAATTTGAGATTGAAATGTTGGATTTCTTTAAAGCCAAGgttaatctca ... tctttgtcagGTTGTGGCAGAGGATTTGGGGGTGGTAAAGAAG