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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgcagcataaataaatactgttcattcttgctgagatactgtggtgcagtttatatgctattgcattgctggaattatacttgttccttttctgtaaacagGTTGCTCGTAAAATGAGAGAGGAGGATGGATTTTATTACCCTCACAATTTAGATTTCCGTGGGCGTGCATACCCTATGCATCCTCATTTGAGTCACCTAG

Basic information

species Zea mays
transcript GRMZM2G115564_T02
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G115564_T01 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os06g44230.1 (Oryza sativa), 3'ss of exon 8
gtatgcagcataaataaatactgttcattcttgctgagatactgtggtgcagtttatatgctattgcattgctggaattatacttgttccttttctgtaaacagGTTGCTCGTAAAATGAGAGAGGAGGATGGATTTTATTACCCTCACAATTTAGATTTCCGTGGGCGTGCATACCCTATGCATCCTCATTTGAGTCACCTAG
||| |   |||||||    | | ||  | | | |  ||||| |    | |||||| | |  |  |   ||  ||  | ||              |||||||||||||||||| ||||||||||||||||||||||||||||| || || ||| | ||||| ||||| |||||||||||||||||| | ||| | || |||||||
gtacgtgacataaattttcattctttgtaccttc--agatatttc--ttcagttttttttttcgtatgtta-tgacactac----------cacctgtaaacagGTTGCTCGGAAAATGAGAGAGGAGGATGGATTTTATTATCCCCATAATCTTGATTTTCGTGGCCGTGCATACCCTATGCATGCACATCTAAGCCACCTAG

upper sequence: GRMZM2G115564_T01 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA04G24350.1 (Glycine max), 3'ss of exon 3
---gtatgcagcataaataaatactgttcattcttgc-tgagatactgtggtgcagtttatatgctattgcattgctggaattatacttgttccttttctgtaaacagGTTGCTCGTAAAATGAGAGAGGAGGATGGATTTTATTACCCTCACAATTTAGATTTCCGTGGGCGTGCATACCCTATGCATCCTCATTTGAGTCACCTAG
         |   | ||  ||   |   |||| |    |   ||||| |       || |   | |     ||   |  ||  | |    ||| |       |||||||| || || ||||||| ||| ||||| || |||||||| ||||||||| | |||||||||||  | ||||| ||||||||||||||||||| |||  |||
taatcgcataatctgaactaa-gtttaccattatcatgttcaatactatcccatgtttcactagttgagcaataatttaaagaaaatacattctt-------aaacagGTGGCACGAAAAATGAAAGATGAGGAAGGCTTTTATTATCCTCACAATCTTGATTTCCGTGGTAGAGCATATCCTATGCATCCTCATTTGAATCATTTAG

upper sequence: GRMZM2G115564_T01 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA06G24890.1 (Glycine max), 3'ss of exon 1
---gtatgcagcataaataaatactgttcattcttgc-tgagatactgtggtgcagtttatatgctattgcattgctggaattatacttgttccttttctgtaaacagGTTGCTCGTAAAATGAGAGAGGAGGATGGATTTTATTACCCTCACAATTTAGATTTCCGTGGGCGTGCATACCCTATGCATCCTCATTTGAGTCACCTAG
    |    |   | ||  ||   |   |||| |  | |   ||||| |       || |   | |     ||   |  ||  | |    ||| |       |||||||| || || ||||||| ||| ||||| || |||||||| || |||||| | || ||||||||  | ||||| ||||||||||||||||||| |||  |||
taattgaataatctgaactaa-gtttaccattatcacattcaatactatcccatgtttcactagttgagcaataatttaaaggaaatacattctt-------aaacagGTGGCACGAAAAATGAAAGATGAGGAAGGCTTTTATTATCCACACAATCTTGACTTCCGTGGCAGAGCATATCCTATGCATCCTCATTTGAATCATTTAG

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), 46 (downstream exon)
Score: 188

TCCTGATGAAATGCAGAAATGGAAGTGGAGTTTAAAGAAGGCAAAGAAAACTAACCGTGAACTGCATGCTGAGAGATGTGACACTGAGCTCAAACTCTCGgtatgcagca ... ctgtaaacagGTTGCTCGTAAAATGAGAGAGGAGGATGGATTTTATTACCCTCACAATTTAGATTTCCGTGGGCGTGCATACCCTATGCATCCTCATTTGAGTCACCTAG


Block sizes: 46 (upstream exon), 45 (downstream exon)
Score: 131

TCCTGATGAAATGCAGAAATGGAAGTGGAGTTTAAAGAAGGCAAAGAAAACTAACCGTGAACTGCATGCTGAGAGATGTGACACTGAGCTCAAACTCTCGgtatgcagca ... ctgtaaacagGTTGCTCGTAAAATGAGAGAGGAGGATGGATTTTATTACCCTCACAATTTAGATTTCCGTGGGCGTGCATACCCTATGCATCCTCATTTGAGTCACCTAG


Block sizes: 46 (upstream exon), 41 (downstream exon)
Score: 44

TCCTGATGAAATGCAGAAATGGAAGTGGAGTTTAAAGAAGGCAAAGAAAACTAACCGTGAACTGCATGCTGAGAGATGTGACACTGAGCTCAAACTCTCGgtatgcagca ... ctgtaaacagGTTGCTCGTAAAATGAGAGAGGAGGATGGATTTTATTACCCTCACAATTTAGATTTCCGTGGGCGTGCATACCCTATGCATCCTCATTTGAGTCACCTAG


Block sizes: 49 (upstream exon), 41 (downstream exon)
Score: 93

TCCTGATGAAATGCAGAAATGGAAGTGGAGTTTAAAGAAGGCAAAGAAAACTAACCGTGAACTGCATGCTGAGAGATGTGACACTGAGCTCAAACTCTCGgtatgcagca ... ctgtaaacagGTTGCTCGTAAAATGAGAGAGGAGGATGGATTTTATTACCCTCACAATTTAGATTTCCGTGGGCGTGCATACCCTATGCATCCTCATTTGAGTCACCTAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cagtttatatgctattgcattgctggaattatacttgttccttttctgtaaacagGTTGCTCGTAAAATGAGAGAGGAGGATGGATTTTATTACCCTCACAATTTAGATTTCCGTGGGCGTGCATACCCTATGCATCCTCATTTGAGTCACCTAG
                               tacttgttccttttct  CT-rich tract
                          aattatactt  TA-rich tract