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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagttaagttttcaacacatgcatctctgttccaacttgagcttaatgattattgggttcttttccctcagctaagcttatatttgttacattttagGTGAGAATCATGTCAAGGCTAAGGCATCCCAATGTTGTTCTTTTCTTGGGATATGTGACACAATCGCCTAATCTCTCTATATTAACTGAGTACCTCCCAA

Basic information

species Zea mays
transcript GRMZM2G413069_T01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G413069_T01 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os02g12810.3 (Oryza sativa), 3'ss of exon 5
gtaagttaagtt------ttcaacacat-gcatctctgttccaacttgagcttaatgattattgggttcttttccctcagctaagcttatatttgttacattttagGTGAGAATCATGTCAAGGCTAAGGCATCCCAATGTTGTTCTTTTCTTGGGATATGTGACACAATCGCCTAATCTCTCTATATTAACTGAGTACCTCCCAA
|| ||| | || || || ||| |||||||| || | ||| | ||| ||||| | || ||||| ||| || || | ||| || || |||| | |||||||||||||| |||||||| ||||| ||||| ||||||||||||||||||||| | || ||||| || ||||||||||| ||||| ||||
gtgagtccacttttaagatttaatgcattgcatctcttttggagtttgtgtataaatattatcgactttatttcc-tcaactgagtgtgcattccttctcttcaagGTTGGGATCATGTCAAGGCTGAGGCATCCAAATGTAGTTCTGTTCTTGGGATATGTGACACAACCACCAAATCTTTCGATATTAACTGAATACCTTCCAA
















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: 48 (upstream exon), 49 (downstream exon)
Score: 34

GAGGTTGCAGTGAAGAAATTTCTTGACCAGGATTTATCAGGTGTTTCACTAGAGCAATTTAAATGTGAAgtaagttaag ... tacattttagGTGAGAATCATGTCAAGGCTAAGGCATCCCAATGTTGTTCTTTTCTTGGGATATGTGACACAATCGCCTAATCTCTCTATATTAACTGAGTACCTCCCAA


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 110

GAGGTTGCAGTGAAGAAATTTCTTGACCAGGATTTATCAGGTGTTTCACTAGAGCAATTTAAATGTGAAgtaagttaag ... tacattttagGTGAGAATCATGTCAAGGCTAAGGCATCCCAATGTTGTTCTTTTCTTGGGATATGTGACACAATCGCCTAATCTCTCTATATTAACTGAGTACCTCCCAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 123

GAGGTTGCAGTGAAGAAATTTCTTGACCAGGATTTATCAGGTGTTTCACTAGAGCAATTTAAATGTGAAgtaagttaag ... tacattttagGTGAGAATCATGTCAAGGCTAAGGCATCCCAATGTTGTTCTTTTCTTGGGATATGTGACACAATCGCCTAATCTCTCTATATTAACTGAGTACCTCCCAA


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 91

GAGGTTGCAGTGAAGAAATTTCTTGACCAGGATTTATCAGGTGTTTCACTAGAGCAATTTAAATGTGAAgtaagttaag ... tacattttagGTGAGAATCATGTCAAGGCTAAGGCATCCCAATGTTGTTCTTTTCTTGGGATATGTGACACAATCGCCTAATCTCTCTATATTAACTGAGTACCTCCCAA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttaatgattattgggttcttttccctcagctaagcttatatttgttacattttagGTGAGAATCATGTCAAGGCTAAGGCATCCCAATGTTGTTCTTTTCTTGGGATATGTGACACAATCGCCTAATCTCTCTATATTAACTGAGTACCTCCCAA
 gcttaat  putative branch site (score: 91)
 ttatatttgttacatt  TA-rich tract