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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaactttgtgttggtctgttcttgcacaagcaaacaatggaagagtaggtgtgcatgtaacaccactttatggaactcgaaacagATTCCTCCAAAGCATACAATGATTACCCCGTCTCAGTGCAAGTCACTGTGGAAACAATTTAAAGCAGAAACTGAGTTCACGATTACAAGCAGTATCCACA

Basic information

species Zea mays
transcript GRMZM2G439169_T01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AC193355.3_FGT005 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os12g41170.1 (Oryza sativa), 3'ss of exon 18
gtaactttgtgttggtctgttcttgcacaagcaaacaatggaagagtaggtgtgcatgtaac-accact-ttatggaactcg-aaacagATTCCTCCAAAGCATACAATGATTACCCCGTCTCAGTGCAAGTCACTGTGGAAACAATTTAAAGCAGAAACTGAGTTCACGATTAC--AAGCAGTATCCACA
||||  |||||||  | | |||  ||    | ||| | | |||| | |    | |||| ||| | |||  |||| ||||||   | ||| || |||||||| ||||  | || || || ||||| ||||||||||||||||| || || |||||||||||||||||| | |||||  |||| || ||||  
gtaagcttgtgttaattt-ttcgcgctgctgtaaatattagaagtgcataaat-catggaaccatcacgattattgaactcttgagcagGTTTCTCCAAAGTATACCCTCATCACTCCTTCTCAATGCAAGTCACTGTGGAAGCAGTTCAAAGCAGAAACTGAGTTCGCCATTACACAAGCGGTTTCCA--
















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: 46 (upstream exon), 47 (downstream exon)
Score: 128

TGAAAGCATCCTCACTTCAACACTTCTGGAAGGCTCTGTTGTATCAAAGATTGCAAGTGCTGCTTCTGCTGATCCACTTGCTTCTACCACTTGGGAAGAGgtaactttgt ... ctcgaaacagATTCCTCCAAAGCATACAATGATTACCCCGTCTCAGTGCAAGTCACTGTGGAAACAATTTAAAGCAGAAACTGAGTTCACGATTACAAGCAGTATCCACA


Block sizes: 38 (upstream exon), 45 (downstream exon)
Score: 16

TGAAAGCATCCTCACTTCAACACTTCTGGAAGGCTCTGTTGTATCAAAGATTGCAAGTGCTGCTTCTGCTGATCCACTTGCTTCTACCACTTGGGAAGAGgtaactttgt ... ctcgaaacagATTCCTCCAAAGCATACAATGATTACCCCGTCTCAGTGCAAGTCACTGTGGAAACAATTTAAAGCAGAAACTGAGTTCACGATTACAAGCAGTATCCACA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 70

TGAAAGCATCCTCACTTCAACACTTCTGGAAGGCTCTGTTGTATCAAAGATTGCAAGTGCTGCTTCTGCTGATCCACTTGCTTCTACCACTTGGGAAGAGgtaactttgt ... ctcgaaacagATTCCTCCAAAGCATACAATGATTACCCCGTCTCAGTGCAAGTCACTGTGGAAACAATTTAAAGCAGAAACTGAGTTCACGATTACAAGCAGTATCCACA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 172

TGAAAGCATCCTCACTTCAACACTTCTGGAAGGCTCTGTTGTATCAAAGATTGCAAGTGCTGCTTCTGCTGATCCACTTGCTTCTACCACTTGGGAAGAGgtaactttgt ... ctcgaaacagATTCCTCCAAAGCATACAATGATTACCCCGTCTCAGTGCAAGTCACTGTGGAAACAATTTAAAGCAGAAACTGAGTTCACGATTACAAGCAGTATCCACA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caaacaatggaagagtaggtgtgcatgtaacaccactttatggaactcgaaacagATTCCTCCAAAGCATACAATGATTACCCCGTCTCAGTGCAAGTCACTGTGGAAACAATTTAAAGCAGAAACTGAGTTCACGATTACAAGCAGTATCCACA
                        atgtaac  putative branch site (score: 172)
                                  actttat  TA-rich tract