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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGTCCACTTGGTGGAGTTGCTTGGCACAGGTGAATACTTTGCCATGAAAGCTATGGATAAAAGTGTCATGCTTAACCGAAACAAGgtatgagtaacaaatttgatcacaaataacattttagttacttccatttttaatgattttttccacatctgatttgtctataatacctctag

Basic information

species Zea mays
transcript GRMZM2G001457_T02
intron # 13
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G001457_T02 (Zea mays), 5'ss of exon 13
lower sequence: LOC_Os12g01140.5 (Oryza sativa), 5'ss of exon 10
TGTCCACTTGGTGGAGTTGCTTGGCACAGGTGAATACTTTGCCATGAAAGCTATGGATAAAAGTGTCATGCTTAACCGAAACAAGgtatga-----gtaacaaatttgatcacaaataacattttagt-------------tacttccatttttaatgattttttccacatctgatttgt-------ctataatacctctag
||| |||||||| |||||| |    ||||| ||||||||||||||||||||||||||||||||  ||||||||||||| || ||||| |||     ||  ||  ||| |  |   |||   |||| ||             |  ||  | || || | || | |    |||   || | |        ||||||  ||||||
TGTACACTTGGTAGAGTTGTTGAATACAGGAGAATACTTTGCCATGAAAGCTATGGATAAAAGCATCATGCTTAACCGCAATAAGgtttgatgcttgtttcaccttttaaaatgtatacattttttgtgaataaaagacattgtttatacttctagttatgtctattgcattatatctctgagtacattataatgtctctag

upper sequence: GRMZM2G001457_T02 (Zea mays), 5'ss of exon 13
lower sequence: Vv06s0004g03700.t01 (Vitis vinifera), 5'ss of exon 14
TGTCCACTTGGTGGAGTTGCTTGGCACAGGTGAATACTTTGCCATGAAAGCTATGGATAAAAGTGTCATGCTTAACCGAAACAAGgtatgagtaacaaatttgatcacaaataacattttagttacttccatttttaatgattttttccacatctgatttgtctata-atacctctag----------
||| ||  ||||||| ||   ||| || |||||||||||||||||||||||||||||||||| ||||||||| ||||| ||||||||||    |  |||||    |     ||   || |||||| ||        |   |   | |    ||     |||| || |  ||   |||           
TGTGCATCTGGTGGAATTATGTGGAACTGGTGAATACTTTGCCATGAAAGCTATGGATAAAAATGTCATGCTCAACCGCAACAAGgtattcaaattaaatt---gctgggttacttttctagttaatttagcagccagataagctcttagaattcctattgtttacatgtatgactactacagctatg
















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), 48 (downstream exon)
Score: 31

TGTCCACTTGGTGGAGTTGCTTGGCACAGGTGAATACTTTGCCATGAAAGCTATGGATAAAAGTGTCATGCTTAACCGAAACAAGgtatgagtaa ... atacctctagGTCCATAGAGCTACCGCTGAACGACAAATCCTTGATATGTTGGACCACCCATTCCTTCCGACATTGTATGCATCATTTCAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 302

TGTCCACTTGGTGGAGTTGCTTGGCACAGGTGAATACTTTGCCATGAAAGCTATGGATAAAAGTGTCATGCTTAACCGAAACAAGgtatgagtaa ... atacctctagGTCCATAGAGCTACCGCTGAACGACAAATCCTTGATATGTTGGACCACCCATTCCTTCCGACATTGTATGCATCATTTCAG


Block sizes: 48 (upstream exon), 47 (downstream exon)
Score: 71

TGTCCACTTGGTGGAGTTGCTTGGCACAGGTGAATACTTTGCCATGAAAGCTATGGATAAAAGTGTCATGCTTAACCGAAACAAGgtatgagtaa ... atacctctagGTCCATAGAGCTACCGCTGAACGACAAATCCTTGATATGTTGGACCACCCATTCCTTCCGACATTGTATGCATCATTTCAG


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 116

TGTCCACTTGGTGGAGTTGCTTGGCACAGGTGAATACTTTGCCATGAAAGCTATGGATAAAAGTGTCATGCTTAACCGAAACAAGgtatgagtaa ... atacctctagGTCCATAGAGCTACCGCTGAACGACAAATCCTTGATATGTTGGACCACCCATTCCTTCCGACATTGTATGCATCATTTCAG