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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gcacaaagccaaagtaggtaaatagttctgaacagagggagtatcattcttatggcatcttatgtctttcgtctaactggtttatctgtcattttcccagCGAAGGATCGACAAAGGTGGCATCTGAGGCAGCAGATATAGGAAGATCAGCCTTGTTTCCAGCTTCTGCTTTATCAAACACTTTTGGGTTCAAGATTCAG

Basic information

species Zea mays
transcript GRMZM2G133621_T02
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G133621_T01 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os01g69900.1 (Oryza sativa), 3'ss of exon 10
gcacaaagccaaagtaggtaaatagttctgaacagagggagtatcattcttatggcatcttatgtctttcgtctaactggtttatctgtcattttcccagCGAAGGATCGACAAAGGTGGCATCTGAGGCAGCAGATATAGGAAGATCAGCCTTGTTTCCAGCTTCTGCTTTATCAAACACTTTTGGGTTCAAGATTCAG
       |  |   |   |   ||  ||| | ||    ||     | ||| |||||||  |       |  | ||  |  || |  || ||| ||  ||| |||||||| || || ||||| ||||||||| ||||| ||||||||||||| || | ||| ||||||| ||| || ||||| || |||||||||||||| 
-------gttagtatctttgcttatatcttatcattttga----taatctgatggcatggttctgtcatgattta--taattcacttggcatattatcagTGAAGGATCAACTAAAGTGGCGTCTGAGGCAACAGATGTAGGAAGATCAGCTTTTTATCCGGCTTCTGGTTTGTCCAACACATTCGGGTTCAAGATTCAA
















Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|71426714|gb|DR807764.1|DR807764
EST:     TCAGCAATGTCCATTGGACCTCTTGATGATGATGATGACTCCACCAGAAG                         CGAAGGATCGACAAAGGTGGCATCTGAGGCAGCAGATATAGGAAGATCAGC
genomic: TCAGCAATGTCCATTGGACCTCTTGATGATGATGATGACTCCACCAGAAGgttagtttgc ... attttcccagCGAAGGATCGACAAAGGTGGCATCTGAGGCAGCAGATATAGGAAGATCAGC
EST: gi|60359150|gb|DN226123.1|DN226123
EST:     GATGATGATGACTCCACCAGAAG                         CGAAGGATCGACAAAGGTGGCATCTGAGGCAGCAGATATAGGAAGATCAGC
genomic: GATGATGATGACTCCACCAGAAGgttagtttgc ... attttcccagCGAAGGATCGACAAAGGTGGCATCTGAGGCAGCAGATATAGGAAGATCAGC

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), 45 (downstream exon)
Score: 60

GGGCAGCTGGATCTGAGTCAACGTCTGCCATGATGCAGAGGTTCTGGGATTCAGCAATGTCCATTGGACCTCTTGATGATGATGATGACTCCACCAGAAGgttagtttgc ... attttcccagCGAAGGATCGACAAAGGTGGCATCTGAGGCAGCAGATATAGGAAGATCAGCCTTGTTTCCAGCTTCTGCTTTATCAAACACTTTTGGGTTCAAGATTCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 111

GGGCAGCTGGATCTGAGTCAACGTCTGCCATGATGCAGAGGTTCTGGGATTCAGCAATGTCCATTGGACCTCTTGATGATGATGATGACTCCACCAGAAGgttagtttgc ... attttcccagCGAAGGATCGACAAAGGTGGCATCTGAGGCAGCAGATATAGGAAGATCAGCCTTGTTTCCAGCTTCTGCTTTATCAAACACTTTTGGGTTCAAGATTCAG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 143

GGGCAGCTGGATCTGAGTCAACGTCTGCCATGATGCAGAGGTTCTGGGATTCAGCAATGTCCATTGGACCTCTTGATGATGATGATGACTCCACCAGAAGgttagtttgc ... attttcccagCGAAGGATCGACAAAGGTGGCATCTGAGGCAGCAGATATAGGAAGATCAGCCTTGTTTCCAGCTTCTGCTTTATCAAACACTTTTGGGTTCAAGATTCAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 129

GGGCAGCTGGATCTGAGTCAACGTCTGCCATGATGCAGAGGTTCTGGGATTCAGCAATGTCCATTGGACCTCTTGATGATGATGATGACTCCACCAGAAGgttagtttgc ... attttcccagCGAAGGATCGACAAAGGTGGCATCTGAGGCAGCAGATATAGGAAGATCAGCCTTGTTTCCAGCTTCTGCTTTATCAAACACTTTTGGGTTCAAGATTCAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attcttatggcatcttatgtctttcgtctaactggtttatctgtcattttcccagCGAAGGATCGACAAAGGTGGCATCTGAGGCAGCAGATATAGGAAGATCAGCCTTGTTTCCAGCTTCTGCTTTATCAAACACTTTTGGGTTCAAGATTCAG
                         gtctaac  putative branch site (score: 129)
                                       tctgtcattttccc  putative PPT
           atcttat  TA-rich tract