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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tattactttgcttgatctcggtttagcttctttagcatgctttaaggacatttcatttagtaaagctgcactctctaacgacttttctttttattttaagGTTGAAGCCATTCGCAATCTATTTGCAGCACTCTTCCTTGCAAGCATTGGAATGCTCATACATGTTAAGTTCTTGTGGAATCATGTTGACATATTACTTG

Basic information

species Zea mays
transcript GRMZM2G040158_T03
intron # 15
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G040158_T03 (Zea mays), 3'ss of exon 15
lower sequence: LOC_Os03g03590.2 (Oryza sativa), 3'ss of exon 5
tattactttgcttgatctcggtttagcttctttagcatgctttaaggacatttcatt-tagtaaagctgcactctctaacgacttttctttttatttt-----aagGTTGAAGCCATTCGCAATCTATTTGCAGCACTCTTCCTTGCAAGCATTGGAATGCTCATACATGTTAAGTTCTTGTGGAATCATGTTGACATATTACTTG
  || |||  || |       ||| | || | ||||    |   || ||||||  || |  |  | || |||||||||||   |  | | ||| ||||     ||||| ||  | ||||| ||  |||||||||||||||||||||||||||| || |||||||||||||| ||||||||||||||||||||||||||||| ||||
-gtttcttccctag--tgtaattttgtttttgtagctaaatc--agtacattttgttctgattgaact-cactctctaacatgtaatttctttgtttttattcaagGTGGAGCCAATTCGTAACTTATTTGCAGCACTCTTCCTTGCAAGCATCGGCATGCTCATACATGTCAAGTTCTTGTGGAATCATGTTGACATATTGCTTG

upper sequence: GRMZM2G040158_T03 (Zea mays), 3'ss of exon 15
lower sequence: GLYMA16G32820.1 (Glycine max), 3'ss of exon 9
--tattactttgcttgatctcggtt-tagcttctttagcatgctttaag-gacatttcatttagtaaagctgcactctctaacgacttttctttttattttaagGTTGAAGCCATTCGCAATCTATTTGCAGCACTCTTCCTTGCAAGCATTGGAATGCTCATACATGTTAAGTTCTTGTGGAATCATGTTGACATATTACTTG
     || ||| ||   | |   || |    | |  |  ||| || |   | ||    ||| |  |||   |  ||||  || |    |  || || |    |||| ||| | ||||| || ||||||||||| ||||| ||  |||| ||||||||||||||||||||  | ||| | ||||| ||||| || || ||  | |
taggataatttactgcttttgaattatgaactatgaactatgtttcagttgtcacaagattaaagaaaaacgttctcttaaaagtgcatatttgttgt----agGTGGAACCAATTCGTAACCTATTTGCAGCTCTCTTTCTCTCAAGTATTGGAATGCTCATACATGTGCACTTCCTTTGGAACCATGTGGATATTTTGTTGG

upper sequence: GRMZM2G040158_T03 (Zea mays), 3'ss of exon 15
lower sequence: Vv16s0022g02060.t01 (Vitis vinifera), 3'ss of exon 15
tattactttgcttgatctcggtttagcttctttagcatgctttaaggacatttcattta--gtaaagctgcactctcta-acgacttttctttttat-tttaagGTTGAAGCCATTCGCAATCTATTTGCAGCACTCTTCCTTGCAAGCATTGGAATGCTCATACATGTTAAGTTCTTGTGGAATCATGTTGACATATTACTTG
   | |  |  ||  |     | |||  |  |   || | ||| |  |  |||| |||    |||   || | | |||  |    |    ||| ||| ||  |||||||| | || || || ||||||||||| ||||||||| |||| ||||||||||||||||| ||  ||||| | ||||  ||||| || ||||| || |
--gttccctctttacttcaactgtagaattctc--caagtttttatcatgtttcttttgtcataagaatgaattttctgtatctgtcgcttttctatgttctagGTTGAACCGATCCGGAACCTATTTGCAGCTCTCTTCCTTTCAAGTATTGGAATGCTCATACACGTGCAGTTCCTATGGACCCATGTGGATATATTGCTAG

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: 47 (upstream exon), 44 (downstream exon)
Score: 17

TGCAGTGACTATTGTGGATTGAGTCTTGAGTTGGGGTCATTTCTTGCTGGTGTTATGATATCAACCACAGATTTTGCTCATCATACTATGGAGCAGgtggtattct ... ttattttaagGTTGAAGCCATTCGCAATCTATTTGCAGCACTCTTCCTTGCAAGCATTGGAATGCTCATACATGTTAAGTTCTTGTGGAATCATGTTGACATATTACTTG


Block sizes: 45 (upstream exon), 39 (downstream exon)
Score: 18

TGCAGTGACTATTGTGGATTGAGTCTTGAGTTGGGGTCATTTCTTGCTGGTGTTATGATATCAACCACAGATTTTGCTCATCATACTATGGAGCAGgtggtattct ... ttattttaagGTTGAAGCCATTCGCAATCTATTTGCAGCACTCTTCCTTGCAAGCATTGGAATGCTCATACATGTTAAGTTCTTGTGGAATCATGTTGACATATTACTTG


Block sizes: 48 (upstream exon), 46 (downstream exon)
Score: 32

TGCAGTGACTATTGTGGATTGAGTCTTGAGTTGGGGTCATTTCTTGCTGGTGTTATGATATCAACCACAGATTTTGCTCATCATACTATGGAGCAGgtggtattct ... ttattttaagGTTGAAGCCATTCGCAATCTATTTGCAGCACTCTTCCTTGCAAGCATTGGAATGCTCATACATGTTAAGTTCTTGTGGAATCATGTTGACATATTACTTG


Block sizes: 48 (upstream exon), 45 (downstream exon)
Score: 43

TGCAGTGACTATTGTGGATTGAGTCTTGAGTTGGGGTCATTTCTTGCTGGTGTTATGATATCAACCACAGATTTTGCTCATCATACTATGGAGCAGgtggtattct ... ttattttaagGTTGAAGCCATTCGCAATCTATTTGCAGCACTCTTCCTTGCAAGCATTGGAATGCTCATACATGTTAAGTTCTTGTGGAATCATGTTGACATATTACTTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggacatttcatttagtaaagctgcactctctaacgacttttctttttattttaagGTTGAAGCCATTCGCAATCTATTTGCAGCACTCTTCCTTGCAAGCATTGGAATGCTCATACATGTTAAGTTCTTGTGGAATCATGTTGACATATTACTTG
                           ctctaac  putative branch site (score: 43)
                                    cttttctttttatttt  putative PPT
                                   acttttctttttattt  TA-rich tract