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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttttctcataactttgctttaattgattgtacctttttctgtatatggcacctttttattgaagtattctcttacagagttaaaatgtccttttttatagGCAAATTTTGCATGGAACTGTTGGTGGCTTATCAGGCACTCTGCAACAAGTTCAGGCCAGGAGCCCCCAACTTCCTGGGCCTGCTCAG

Basic information

species Zea mays
transcript GRMZM2G022383_T01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G022383_T01 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os01g42260.4 (Oryza sativa), 3'ss of exon 5
ttttctcataactttgctttaattgattgtacctttttctgtatatggcacctttttattg----aagta--ttctcttacagagttaaaatgtccttttttatagGCAAATTTTGCATGGAACTGTTGGTGGCTTATCAGGCACTCTGCAACAAGTTCAGGCCAGGAGCCCCCAACTTCCTGGGCCTGCTCAG
       | |    |  |  |  | |   |   || |  ||   ||   |    |    ||    | |||  || ||| | | |||| |  | |  |  ||| |||||||||||||||||| |||||||||||  | ||||||| |||||||||||||||| ||||||| || ||  |||||||||| ||||||
-----gtagatgcctattgaacatcaccatgttttatattgaccataatatacatgcgctgcaagaggtaacttttctcagatagtttacttctt-tcctttgtagGCAAATTTTGCATGGTACTGTTGGTGGTCTGTCAGGCAGTCTGCAACAAGTTCAGTCCAGGAGTCCACAGATTCCTGGGCCAGCTCAG
















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), 47 (downstream exon)
Score: 142

TATGGTTGCAGCAAAGATACGGAGAGAACGCTGGGCAACTACTTGATTCAAATGAAGCATCATTGTTGAAAGCAGCTTCAAGTGCACAATCCTCAGGgtacttgctg ... ttttttatagGCAAATTTTGCATGGAACTGTTGGTGGCTTATCAGGCACTCTGCAACAAGTTCAGGCCAGGAGCCCCCAACTTCCTGGGCCTGCTCAG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 122

TATGGTTGCAGCAAAGATACGGAGAGAACGCTGGGCAACTACTTGATTCAAATGAAGCATCATTGTTGAAAGCAGCTTCAAGTGCACAATCCTCAGGgtacttgctg ... ttttttatagGCAAATTTTGCATGGAACTGTTGGTGGCTTATCAGGCACTCTGCAACAAGTTCAGGCCAGGAGCCCCCAACTTCCTGGGCCTGCTCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 133

TATGGTTGCAGCAAAGATACGGAGAGAACGCTGGGCAACTACTTGATTCAAATGAAGCATCATTGTTGAAAGCAGCTTCAAGTGCACAATCCTCAGGgtacttgctg ... ttttttatagGCAAATTTTGCATGGAACTGTTGGTGGCTTATCAGGCACTCTGCAACAAGTTCAGGCCAGGAGCCCCCAACTTCCTGGGCCTGCTCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 125

TATGGTTGCAGCAAAGATACGGAGAGAACGCTGGGCAACTACTTGATTCAAATGAAGCATCATTGTTGAAAGCAGCTTCAAGTGCACAATCCTCAGGgtacttgctg ... ttttttatagGCAAATTTTGCATGGAACTGTTGGTGGCTTATCAGGCACTCTGCAACAAGTTCAGGCCAGGAGCCCCCAACTTCCTGGGCCTGCTCAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tggcacctttttattgaagtattctcttacagagttaaaatgtccttttttatagGCAAATTTTGCATGGAACTGTTGGTGGCTTATCAGGCACTCTGCAACAAGTTCAGGCCAGGAGCCCCCAACTTCCTGGGCCTGCTCAG
                       ctcttac  putative branch site (score: 125)
                                        tgtcctttttt  putative PPT
       tttttattgaagtatt  TA-rich tract