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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagctactaagcaaagagatacctcccctgcagctgcaatacttgtttgtcacgcacatttattagattcttagagtatctgttacatttttgtttacagGCATCCGAGATTATAAAAAATCCATACCTCCAACCTTATGTGAATCAATACCGTCCATTTGCTAATATATTACATCCTGGTCGATCACCAGAGAAACCTG

Basic information

species Zea mays
transcript GRMZM2G074262_T01
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G074262_T01 (Zea mays), 3'ss of exon 13
lower sequence: LOC_Os01g64490.1 (Oryza sativa), 3'ss of exon 13
gtaagctactaagcaaagagatacctcccctgcagctgcaatacttgtttgtcacgcacatttattagattcttagagtatctgttacatttttgtttacagGCATCCGAGATTATAAAAAATCCATACCTCCAACCTTATGTGAATCAATACCGTCCATTTGCTAATATATTACATCCTGGTCGATCACCAGAGAAACCTG
|| ||||| || ||| | ||| |||||||       ||||||||||||||||  |    ||||| |||||| | | | |||||||      |||||  ||||||||| |||||| | ||||  |||||||| ||||||||||| ||||||||||| ||||||||| |||||| ||||||   ||  ||||  ||||||||  
gttagctattatgcacacagaaacctccc-------tgcaatacttgtttgttgc----atttagtagattttgacaatatctgtacacactttgtaaacagGCATCTGAGATTCTTAAAAGCCCATACCTTCAACCTTATGTTAATCAATACCGCCCATTTGCTGATATATCACATCCCATTCACTCACTGGAGAAACCCA
















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), 49 (downstream exon)
Score: 52

GAAAACACTTATCAAAAGCATGTTGAGGAAGAGTCCTGAACATCGACCTACTgtaagctact ... ttgtttacagGCATCCGAGATTATAAAAAATCCATACCTCCAACCTTATGTGAATCAATACCGTCCATTTGCTAATATATTACATCCTGGTCGATCACCAGAGAAACCTG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 58

GAAAACACTTATCAAAAGCATGTTGAGGAAGAGTCCTGAACATCGACCTACTgtaagctact ... ttgtttacagGCATCCGAGATTATAAAAAATCCATACCTCCAACCTTATGTGAATCAATACCGTCCATTTGCTAATATATTACATCCTGGTCGATCACCAGAGAAACCTG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 106

GAAAACACTTATCAAAAGCATGTTGAGGAAGAGTCCTGAACATCGACCTACTgtaagctact ... ttgtttacagGCATCCGAGATTATAAAAAATCCATACCTCCAACCTTATGTGAATCAATACCGTCCATTTGCTAATATATTACATCCTGGTCGATCACCAGAGAAACCTG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 183

GAAAACACTTATCAAAAGCATGTTGAGGAAGAGTCCTGAACATCGACCTACTgtaagctact ... ttgtttacagGCATCCGAGATTATAAAAAATCCATACCTCCAACCTTATGTGAATCAATACCGTCCATTTGCTAATATATTACATCCTGGTCGATCACCAGAGAAACCTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttgtcacgcacatttattagattcttagagtatctgttacatttttgtttacagGCATCCGAGATTATAAAAAATCCATACCTCCAACCTTATGTGAATCAATACCGTCCATTTGCTAATATATTACATCCTGGTCGATCACCAGAGAAACCTG
                                          tttttgttt  CT-rich tract
            atttattagattctta  TA-rich tract