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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTCGATTACTACCTGAGGAACAAGGTGGCGTCCAACAAGATCGACCTTGACGTCATAAAAGACGTCGATCTGTACAAAATTGAGCCCTGGGATCTCCAAGgtaagaagtacattaattctgaaacaagtatatatatacatacatagctgctgctaaatagacacatgcattttggaatgggcatgcag

Basic information

species Zea mays
transcript GRMZM2G354151_T01
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G354151_T01 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os02g42970.1 (Oryza sativa), 5'ss of exon 1
GTCGATTACTACCTGAGGAACAAGGTGGCGTCCAACAAGATCGACCTTGACGTCATAAAAGACGTCGATCTGTACAAAATTGAGCCCTGGGATCTCCAAGgtaagaagta--cattaattctgaaacaagtat--atatatacatacatag--ctgctgctaaatagacacatgcattttggaatgggcatgcag
|||||||||||||||||||| |||||||| || || || |||||||| ||||| |||||||||||||| ||||||||||| |||||||||||||||||||||||  || |  |||  |   |||   ||| ||  | | |  || |  |||   |||   | ||| ||  ||| ||   || |       |||||
GTCGATTACTACCTGAGGAAGAAGGTGGCATCGAAGAAAATCGACCTCGACGTTATAAAAGACGTCGACCTGTACAAAATCGAGCCCTGGGATCTCCAAGgtaattagcatgcatgcaagttgatcgaagaatcaaaaaaatcaaagttaggtttgcgattgaattga-gcatccaacatgtacaaatattgcag

upper sequence: GRMZM2G354151_T01 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA09G36600.1 (Glycine max), 5'ss of exon 1
GTCGATTACTACCTGAGGAACAAGGTGGCGTCCAACAAGATCGACCTTGACGTCATAAAAGACGTCGATCTGTACAAAATTGAGCCCTGGGATCTCCAAGgtaagaagtacattaattctgaaaca-agtatatatatacatacatagctgctgctaaatagacacatgcattttggaatgggcatgcag---------------------------
|| ||||||||||| ||||| ||  | || || |  | ||| || || || || |||||||| || || || |||||||||||||| |||||||| ||||||| ||| |  ||  | |   |  || || || || || |       ||   |        || | ||  ||| |  | |  ||||                               
GTTGATTACTACCTTAGGAAGAAAATTGCTTCAAGGAGGATTGATCTAGATGTGATAAAAGATGTTGACCTCTACAAAATTGAGCCATGGGATCTTCAAGgta-gaactg-atcgagttcaattcatagcatctaaattctagaggggcgattttattggtgaaagatatattgttaactttgcattgtttttttcttttcgttttaaattttaaag

upper sequence: GRMZM2G354151_T01 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA12G00760.1 (Glycine max), 5'ss of exon 1
GTCGATTACTACCTGAGGAACAAGGTGGCGTCCAACAAGATCGACCTTGACGTCATAAAAGACGTCGATCTGTACAAAATTGAGCCCTGGGATCTCCAAGgtaagaagtacattaattctgaaacaagtatatatat-acatacatagctgctgctaaatagacacatgcattttggaatgggcatgcag--------------------------------
|| ||||||||||| ||||| ||  |  | ||    | ||| ||||| || ||||||||||| || || || |||||||||||||| |||||||| |||||||  |     ||  | |    | ||  || ||  |  |   |||    |  || | || ||| | ||    ||||  |    | | ||                                 
GTTGATTACTACCTTAGGAAGAAAATTACTTCAGGGAGGATTGACCTAGATGTCATAAAAGATGTTGACCTCTACAAAATTGAGCCATGGGATCTTCAAGgtagta--ctgatcgagttcatagcatctaaattcaagagggacaattttattggtgaa-agatatatattatttgttaacttc-ttcatttttttttcttttttgtttttaaattttaaag

upper sequence: GRMZM2G354151_T01 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA17G14700.1 (Glycine max), 5'ss of exon 1
GTCGATTACTACCTGAGGAACAAGGTGGCGTCCAACAAGATCGACCTTGACGTCATAAAAGACGTCGATCTGTACAAAATTGAGCCCTGGGATCTCCAAGgtaa----------gaag--tacattaat-------tctgaaacaagtatatatatacatacatagctgctgctaaatagacacatgcattttggaatgg-gcatgcag
|||| ||||||||| ||||| ||||| ||||| || | ||| || || || ||||| ||||| |||||||| || |||||||| || |||||||||||||||||           |||  | |||||||       |   | |||| ||   | ||  || |||||    |     ||| | ||   |||||   | |   | |  |||
GTCGGTTACTACCTTAGGAAAAAGGTAGCGTCTAAAAGGATTGATCTAGATGTCATCAAAGATGTCGATCTCTATAAAATTGAACCATGGGATCTCCAAGgtaattcttcatacaaagctttcattaatcaaagcattacatacaattaagaacatgtat-catagtatatatagtatataaactcacatttgttactcatgtaaacag

upper sequence: GRMZM2G354151_T01 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA05G04250.1 (Glycine max), 5'ss of exon 1
GTCGATTACTACCTGAGGAACAAGGTGGCGTCCAACAAGATCGACCTTGACGTCATAAAAGACGTCGATCTGTACAAAATTGAGCCCTGGGATCTCCAAGgtaa--------gaagtacattaattctgaaacaagtatatatatacata-catagctgc-tgctaaataga-cacatgcattttggaatgggcatgcag
|| | ||||||||| ||||| ||||| ||||| || | ||| || || || || || ||||| |||||||| || |||||||| || |||||||||||||||||         ||   | ||||||    ||  ||||   ||| ||| | |||   |   |  ||||||   ||     |||||  | |   | |    
GTTGGTTACTACCTTAGGAAAAAGGTAGCGTCTAAAAGGATTGATCTAGATGTGATCAAAGATGTCGATCTCTATAAAATTGAACCATGGGATCTCCAAGgtaattcatcataaaaagctttaattaattaaagagtaatgatacacaaatcatttttttattttaaatatttcatcaatatttttcatttttctttttt

upper sequence: GRMZM2G354151_T01 (Zea mays), 5'ss of exon 3
lower sequence: Vv02s0154g00020.t01 (Vitis vinifera), 5'ss of exon 1
GTCGATTACTACCTGAGGAACAAGGTGGCGTCCAACAAGATCGACCTTGACGTCATAAAAGACGTCGATCTGTACAAAATTGAGCCCTGGGATCTCCAAGgtaagaagtacattaattctgaaacaagtatatatatacatac------atagctgctgctaaat-agacac-atgcattttggaatg-ggcatgcag------------------------
|||||||||||||| || || ||||| || || |  | ||| || || || ||||| ||||| |||||||| |||||||||||||| |||||||| ||||||| | ||  | ||| | ||  |     |   |||  | | |       |||  |    ||  || | | || ||||||  |  |||  | | | ||                         
GTCGATTACTACCTTAGAAAAAAGGTTGCTTCGAGAAGGATTGATCTAGATGTCATTAAAGATGTCGATCTCTACAAAATTGAGCCATGGGATCTTCAAGgtatgtagctc-ttattcctacagtccttccctatgcatacaacagaaaatatgtatatcttgatgaaatactatgcatcataaaatctgacttccatgttcatttttcttaatttgaatag

upper sequence: GRMZM2G354151_T01 (Zea mays), 5'ss of exon 3
lower sequence: PP1S1_447V6.1 (Physcomitrella patens), 5'ss of exon 1
---GTCGATTACTACCTGAGGAACAAGGTGGCGTCCAACAAGATCGACCTTGACGTCATAAAAGACGTCGATCTGTACAAAATTGAGCCCTGGGATCTCCAAGgtaagaa----------------gtacattaattctgaaacaagtatatata-tacatacatagctgct--gctaaatagacacatgcattttggaatgggcatgcag------------------------------------------------------------------------------
   || |  || ||| ||     ||| ||||         |||  ||||   |  ||||  | ||  | || || |||||||| ||||||||||||||||||||||||||                ||  | ||  | ||| || ||  || | |  || | |  |  ||||  | |         ||  |  ||  || ||  |     |                                                                              
CTGGTTGGGTATTACTTGCACGGCAAAGTGGGAAGATCTCAGAGAGACC---AGCTCATTCAGGAGTTGGACCTCTACAAAATCGAGCCCTGGGATCTCCAAGgtaagaatcgatcagaatcctcggtgtactatgtatgacaccagactagaaaacacgtcctcacatgcttcgttgccccatttcagtctattaagattgaactcatggtgtgttcgagccctgggattgcaattagattccatgtccactacgtacacggacaagtaaccccgatgtggtcatcag

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 2 RNA-Seq libraries.


Block sizes: 39 (upstream exon), 11 (downstream exon)
Score: 1

GTCGATTACTACCTGAGGAACAAGGTGGCGTCCAACAAGATCGACCTTGACGTCATAAAAGACGTCGATCTGTACAAAATTGAGCCCTGGGATCTCCAAGgtaagaagta ... gggcatgcagAGAAGTGCAAGATCGGGACGGAGGAGCAGAACGAGTGGTACTTCTTCAGCCACAAGGACAAGAAGTACCCGACGGGCACCCGCACAAACCGGGCGACCAC


Block sizes: 28 (upstream exon), 45 (downstream exon)
Score: 2

GTCGATTACTACCTGAGGAACAAGGTGGCGTCCAACAAGATCGACCTTGACGTCATAAAAGACGTCGATCTGTACAAAATTGAGCCCTGGGATCTCCAAGgtaagaagta ... gggcatgcagAGAAGTGCAAGATCGGGACGGAGGAGCAGAACGAGTGGTACTTCTTCAGCCACAAGGACAAGAAGTACCCGACGGGCACCCGCACAAACCGGGCGACCAC




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