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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatcatattttttaaatgtccagaaaacatagcttctgaatttctcataaaatgtgtttttttctttggcttgcaacacatctgactgataatctatctcctaccagGTTAGTGCACTCTCAAGAATAGCACAAGGGTCTCAAATTGCTGATACTAACTCCATTGTGTCATCCCAGACAGTTTCTGTAAAAGGCTCGTCTCTCCAG

Basic information

species Zea mays
transcript GRMZM2G335287_T01
intron # 14
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G335287_T01 (Zea mays), 3'ss of exon 14
lower sequence: LOC_Os07g37750.1 (Oryza sativa), 3'ss of exon 13
gtaatcatattttttaaatgtccagaaaacatagcttctgaatttctca--taaaatgtgtttttttctttggcttgcaacacatctgactgataatctatctcctaccagGTTAGTGCACTCTCAAGAATAGCACAAGGGTCTCAAATTGCTGATACTAACTCCATTGTGTCATCCCAGACAGTTTCTGTAAAAGGCTCGTCTCTCCAG
                   |  ||   ||  |   || |  | |    |  ||  || | || |     |   |     | | |||||| |||  || |||| | || ||||| |||||||||||||| || |||||||| ||||||| ||| ||||| ||| |    |  || || || ||||||||||| |||||||| ||||| |||
---------------gtgagcacaatgaattttatttttacactagaaaactagtatctcttctaactatctccacatgatatatctgattgaacatgtatcac-tatcagGTCAGTGCACTCTCAAGGATTGCACAAGGATCTCAAAATGCGGATACAAACACTGCCGCATCTTCTCAAACAGTTTCTGTGAAAGGCTCATCTCTTCAG
















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), 49 (downstream exon)
Score: 340

GATGTTGGAGAAAGTTTGCAAAGATCCCCAAATGCTTGCAGATGTGTTTGTGAACTATGACTGTGATCTTGAGGGACCAAATCTTTTTGAACGCACGgtaatcatat ... ctcctaccagGTTAGTGCACTCTCAAGAATAGCACAAGGGTCTCAAATTGCTGATACTAACTCCATTGTGTCATCCCAGACAGTTTCTGTAAAAGGCTCGTCTCTCCAG


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 208

GATGTTGGAGAAAGTTTGCAAAGATCCCCAAATGCTTGCAGATGTGTTTGTGAACTATGACTGTGATCTTGAGGGACCAAATCTTTTTGAACGCACGgtaatcatat ... ctcctaccagGTTAGTGCACTCTCAAGAATAGCACAAGGGTCTCAAATTGCTGATACTAACTCCATTGTGTCATCCCAGACAGTTTCTGTAAAAGGCTCGTCTCTCCAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 200

GATGTTGGAGAAAGTTTGCAAAGATCCCCAAATGCTTGCAGATGTGTTTGTGAACTATGACTGTGATCTTGAGGGACCAAATCTTTTTGAACGCACGgtaatcatat ... ctcctaccagGTTAGTGCACTCTCAAGAATAGCACAAGGGTCTCAAATTGCTGATACTAACTCCATTGTGTCATCCCAGACAGTTTCTGTAAAAGGCTCGTCTCTCCAG


Block sizes: 48 (upstream exon), 46 (downstream exon)
Score: 261

GATGTTGGAGAAAGTTTGCAAAGATCCCCAAATGCTTGCAGATGTGTTTGTGAACTATGACTGTGATCTTGAGGGACCAAATCTTTTTGAACGCACGgtaatcatat ... ctcctaccagGTTAGTGCACTCTCAAGAATAGCACAAGGGTCTCAAATTGCTGATACTAACTCCATTGTGTCATCCCAGACAGTTTCTGTAAAAGGCTCGTCTCTCCAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtgtttttttctttggcttgcaacacatctgactgataatctatctcctaccagGTTAGTGCACTCTCAAGAATAGCACAAGGGTCTCAAATTGCTGATACTAACTCCATTGTGTCATCCCAGACAGTTTCTGTAAAAGGCTCGTCTCTCCAG
                               gactgat  putative branch site (score: 261)
                                        tctatctcct  putative PPT
     ttttttcttt  TA-rich tract