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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagcccgcctgtgcatggatgcatatgagattatggttggattggtcaccgactccagttccgttgcgttgatatggtgtattggatcgatggtgtgtgcagTGTTCAAGAGCTGCACTGCTCTCCGGCCCTACATCGCGCACCTGGATGATATCTACAAGGACTTCAACAACTACAAGTTTCGTGTGCCTGTGTCCGGTGC

Basic information

species Zea mays
transcript GRMZM2G051756_T01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G051756_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os02g56210.1 (Oryza sativa), 3'ss of exon 2
gtaagc-ccgcctgtgcatggatgcatatgagattatggttggattggtcaccgactccagttccgttgcgttgatatggtgtattggatcgatg-gtgtgtgcagTGTTCAAGAGCTGCACTGCTCTCCGGCCCTACATCGCGCACCTGGATGATATCTACAAGGACTTCAACAACTACAAGTTTCGTGTGCCTGTGTCCGGTGC
|||||| ||| | |  |          ||       |||  |  |  | |   |  |  |   | |   |   | ||| || | |||    | ||  |||||||||||||||| |||||  |||| ||| |||| |||  ||||||||| ||||| || |||||||| ||||   |||| ||||| ||||| ||||| | ||| ||
gtaagctccggccgaactccaccttggattcatcggtggc-gcttccgccgttggtttgatcgctg--acaccgttattgt-tgttgtggtggtgtatgtgtgcagTGTTCAATAGCTGTGCTGCGCTCAGGCCATACCGCGCGCACCTTGATGACATTTACAAGGATTTCACTCACTATAAGTTCCGTGTCCCTGTCTGCGGCGC
















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: 28 (upstream exon), 48 (downstream exon)
Score: 443

CTGTTCCTGCTAGAGCAGGCGCACTGGTTCTATGAGGACAACTCCGTTGAGCACAACCCCAACCTCAAGTCTCTCTCCTTCAAGGACTTCACTTCCCTCAgtaagcccgc ... gtgtgtgcagTGTTCAAGAGCTGCACTGCTCTCCGGCCCTACATCGCGCACCTGGATGATATCTACAAGGACTTCAACAACTACAAGTTTCGTGTGCCTGTGTCCGGTGC


Block sizes: 28 (upstream exon), 48 (downstream exon)
Score: 367

CTGTTCCTGCTAGAGCAGGCGCACTGGTTCTATGAGGACAACTCCGTTGAGCACAACCCCAACCTCAAGTCTCTCTCCTTCAAGGACTTCACTTCCCTCAgtaagcccgc ... gtgtgtgcagTGTTCAAGAGCTGCACTGCTCTCCGGCCCTACATCGCGCACCTGGATGATATCTACAAGGACTTCAACAACTACAAGTTTCGTGTGCCTGTGTCCGGTGC


Block sizes: 28 (upstream exon), 48 (downstream exon)
Score: 283

CTGTTCCTGCTAGAGCAGGCGCACTGGTTCTATGAGGACAACTCCGTTGAGCACAACCCCAACCTCAAGTCTCTCTCCTTCAAGGACTTCACTTCCCTCAgtaagcccgc ... gtgtgtgcagTGTTCAAGAGCTGCACTGCTCTCCGGCCCTACATCGCGCACCTGGATGATATCTACAAGGACTTCAACAACTACAAGTTTCGTGTGCCTGTGTCCGGTGC


Block sizes: 28 (upstream exon), 48 (downstream exon)
Score: 273

CTGTTCCTGCTAGAGCAGGCGCACTGGTTCTATGAGGACAACTCCGTTGAGCACAACCCCAACCTCAAGTCTCTCTCCTTCAAGGACTTCACTTCCCTCAgtaagcccgc ... gtgtgtgcagTGTTCAAGAGCTGCACTGCTCTCCGGCCCTACATCGCGCACCTGGATGATATCTACAAGGACTTCAACAACTACAAGTTTCGTGTGCCTGTGTCCGGTGC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

accgactccagttccgttgcgttgatatggtgtattggatcgatggtgtgtgcagTGTTCAAGAGCTGCACTGCTCTCCGGCCCTACATCGCGCACCTGGATGATATCTACAAGGACTTCAACAACTACAAGTTTCGTGTGCCTGTGTCCGGTGC
                   cgttgat  putative branch site (score: 273)
                     ttgatat  TA-rich tract