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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatgattaggcattttaaactatcacatgctaacctatttcatgttttaacaatccaataagttgtttgtagATATCCAACCTTGAACCGGTGGATACAGATGCAGTCTAATCTTCATCGAGTATCCGAGTCTTCTATAACAGATAAATCCGAAGTCTCTTTGCATCAATCC

Basic information

species Zea mays
transcript GRMZM2G327311_T01
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G327311_T02 (Zea mays), 3'ss of exon 9
lower sequence: LOC_Os01g40990.2 (Oryza sativa), 3'ss of exon 16
--------gtaatgattaggcattttaaactatcacatgctaacctatttcatgttttaacaatccaataagttgtttgtagATATCCAACCTTGAACCGGTGGATACAGATGCAGTCTAATCTTCATCGAGTATCCGAGTCTTCTATAACAGATAAATCCGA------AGTCTCTTTGCATCAATCC
         || ||||||| ||||| |||  || | ||  |||| |      |  |||   |||  | |||||| |||  || || ||||| |||||||| |||||||||||||||| ||| |||||||||||||| || ||| || || ||| | || | ||      |||| | ||||||      
gtactgaactactgattagtcattt-aaatgattatat-ttaactt------tacttttgtaattgactaagttctttacagGTACCCAACATTGAACCGTTGGATACAGATGCAGTGTAACCTTCATCGAGTATCTGAATCTGCTGTATCAGCTGAAACTGACAATGAAGTCACCTTGCAT------

upper sequence: GRMZM2G327311_T02 (Zea mays), 3'ss of exon 9
lower sequence: AT2G25730.2 (Arabidopsis thaliana), 3'ss of exon 15
----------------gtaatgattaggcattttaaact---atcacat--gctaacctatttcatgtt--ttaacaatccaataagttgttt--gtagATATCCAACCTTGAACCGGTGGATACAGATGCAGTCTAATCTTCATCGAGTATCCGAGTCTTCTATAACAGATAAATCCGAAGTCTCTT--TGCATCAATCC
                |   |  ||   | ||| ||  |   ||||  |  | |   || || ||| ||  | |   ||    ||  || | |   ||| ||||| || || ||||| ||||||||||||||| ||||||| |||||||| || || | |  | | |||    || |  ||  ||  |    ||   ||  
gtactgtcaagccaaagagttctttcctcctttcaatttgaaatcaactcggttcctcttttccatcttattcagtgatattttactttttcttcatagGTATCCCACTTTAAACCGATGGATACAGATGCAGACTAATCTGCATCGAGTTTCGGAATTTGTTGTGACAC-CGAAGCAAAAACCTGATGACACACGGATT-
















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), 43 (downstream exon)
Score: 36

CTGGGGACAATGAATCATCTTTTACTCATGTGAAAGATTCAACACAAGCTCCAGAAACTGAGAGATCATTTTTTGAATTTGCTCTTGAGCAATCAGAGAGgtaatgatta ... ttgtttgtagATATCCAACCTTGAACCGGTGGATACAGATGCAGTCTAATCTTCATCGAGTATCCGAGTCTTCTATAACAGATAAATCCGAAGTCTCTTTGCATCAATCC


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 44

CTGGGGACAATGAATCATCTTTTACTCATGTGAAAGATTCAACACAAGCTCCAGAAACTGAGAGATCATTTTTTGAATTTGCTCTTGAGCAATCAGAGAGgtaatgatta ... ttgtttgtagATATCCAACCTTGAACCGGTGGATACAGATGCAGTCTAATCTTCATCGAGTATCCGAGTCTTCTATAACAGATAAATCCGAAGTCTCTTTGCATCAATCC


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 37

CTGGGGACAATGAATCATCTTTTACTCATGTGAAAGATTCAACACAAGCTCCAGAAACTGAGAGATCATTTTTTGAATTTGCTCTTGAGCAATCAGAGAGgtaatgatta ... ttgtttgtagATATCCAACCTTGAACCGGTGGATACAGATGCAGTCTAATCTTCATCGAGTATCCGAGTCTTCTATAACAGATAAATCCGAAGTCTCTTTGCATCAATCC


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 42

CTGGGGACAATGAATCATCTTTTACTCATGTGAAAGATTCAACACAAGCTCCAGAAACTGAGAGATCATTTTTTGAATTTGCTCTTGAGCAATCAGAGAGgtaatgatta ... ttgtttgtagATATCCAACCTTGAACCGGTGGATACAGATGCAGTCTAATCTTCATCGAGTATCCGAGTCTTCTATAACAGATAAATCCGAAGTCTCTTTGCATCAATCC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aactatcacatgctaacctatttcatgttttaacaatccaataagttgtttgtagATATCCAACCTTGAACCGGTGGATACAGATGCAGTCTAATCTTCATCGAGTATCCGAGTCTTCTATAACAGATAAATCCGAAGTCTCTTTGCATCAATCC
                  tatttcatgttttaa  TA-rich tract