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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagccaacatggacttactttattgtgtttatacattttttaaaaactgctcactttgattttttaagatcttcgccttctttgttatctgatgttcctgttgtaatgttcttttagATGTGCATCATCTTCATTAAATGGAGAAGAACTTATAAGGGATGGTGGTATCCCCTTGTTGGCAACACTTCTTTCTCGCTGTATGTGCATTGTTCAGCCC

Basic information

species Zea mays
transcript GRMZM2G001895_T01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G001895_T01 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os10g42439.1 (Oryza sativa), 3'ss of exon 12
gtaagccaacatggacttactttattgtgtttatacattttttaaaaactgctcactttgattttttaagatcttcgccttctttgttatctgatgttcctgttgtaatgttcttttagATGTGCATCATCTTCATTAAATGGAGAAGAACTTATAAGGGATGGTGGTATCCCCTTGTTGGCAACACTTCTTTCTCGCTGTATGTGCATTGTTCAGCCC
|||||  || |   ||| ||||||       |||   ||||| | | | || | |||||||||      ||   ||  ||   || |       || | |       ||| | | ||||||| |||||||||||||||||||| ||||| || ||| |||||||||||||||| ||||||||||||||||||||||| || ||||||||||||||||||
gtaagtgaagacaaactgactttacc-----tatgtttttttaagataatgtttactttgatt------gaatatcaactggattat------gtgcttc-------atgctttgttagATGCGCATCATCTTCATTAAATGGCGAAGAGCTCATACGGGATGGTGGTATCCCATTGTTGGCAACACTTCTTTCTCGTTGCATGTGCATTGTTCAGCCC

upper sequence: GRMZM2G001895_T01 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA17G12950.1 (Glycine max), 3'ss of exon 12
gtaagccaacatggacttactttattgtgtttatacattttttaaaaactgctcactttgattttttaagatcttcgccttctttgttatctgatgttcct-gttgtaatgttctt----ttagATGTGCATCATCTTCATTAAATGGAGAAGAACTTATAAGGGATGGTGGTATCCCCTTGTTGGCAACACTTCTTTCTCGCTGTATGTGCATTGTTCAGCCC
|||||  |   |  | || |||| ||  | |||| ||  |   ||          |||| || |  |    |     | || | || || ||  || ||||   |  ||| ||| |    ||||||||||||| |||||||| ||||| ||||| ||  |||||||||| ||  | |   |  | ||||| |||||||| || || ||| |  |||||||||| 
gtaag--agtttcaagtt-ctttcttaggattatgcaaat---aagtttcatgttctttcatgtcctt--gttgcaacattttgtggtaacttttgatccttaattgaattttcatatggttagATGTGCATCTTCTTCATTGAATGGTGAAGAGCTGGTAAGGGATGGAGGAGTACATCTTCTTGCAACTCTTCTTTCCCGTTGCATGGGTGTTGTTCAGCCA

upper sequence: GRMZM2G001895_T01 (Zea mays), 3'ss of exon 6
lower sequence: Vv11s0016g04420.t01 (Vitis vinifera), 3'ss of exon 12
gtaa--gccaacatggacttactttattgtgtttatacattttttaaaaactgctcactttgattttttaagatcttcgccttctttgttatctgatgttcctgttgtaatgttcttttagATGTGCATCATCTTCATTAAATGGAGAAGAACTTATAAGGGATGGTGGTATCCCCTTGTTGGCAACACTTCTTTCTCGCTGTATGTGCATTGTTCAGCCC
||||  ||  |  ||   ||| ||| || |||| |   ||||  | | |  |  | |     ||||   | |    | | |   |||    |   || || ||  |||       |||||||||||| || || ||||||||||| ||||||||| ||||||||||||| ||||   |  | ||||| |||||||| || || |||||  | ||||| || 
gtaaatgctcatctgccattattttcttttgttaa---atttcattatagattttga----aatttgggagggagattgacaaattt-cacttcaatctttcttatgtg------ttttagATGTGCGTCTTCCTCATTAAATGGTGAAGAACTTGTAAGGGATGGTGGGATCCAACTTCTTGCAACTCTTCTTTCCCGTTGCATGTGTGTAGTTCAACCA

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: 88

TGTTGCTAAATGCAGTTACTGTAGATAAGGATGACAGCAATTTTCTTTCATCTGATAGGGCCCCTCTTCTTATAGCTGCTTCAGAGCTGATTTGGCTGACgtaagccaac ... gttcttttagATGTGCATCATCTTCATTAAATGGAGAAGAACTTATAAGGGATGGTGGTATCCCCTTGTTGGCAACACTTCTTTCTCGCTGTATGTGCATTGTTCAGCCC


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 60

TGTTGCTAAATGCAGTTACTGTAGATAAGGATGACAGCAATTTTCTTTCATCTGATAGGGCCCCTCTTCTTATAGCTGCTTCAGAGCTGATTTGGCTGACgtaagccaac ... gttcttttagATGTGCATCATCTTCATTAAATGGAGAAGAACTTATAAGGGATGGTGGTATCCCCTTGTTGGCAACACTTCTTTCTCGCTGTATGTGCATTGTTCAGCCC


Block sizes: 45 (upstream exon), 45 (downstream exon)
Score: 71

TGTTGCTAAATGCAGTTACTGTAGATAAGGATGACAGCAATTTTCTTTCATCTGATAGGGCCCCTCTTCTTATAGCTGCTTCAGAGCTGATTTGGCTGACgtaagccaac ... gttcttttagATGTGCATCATCTTCATTAAATGGAGAAGAACTTATAAGGGATGGTGGTATCCCCTTGTTGGCAACACTTCTTTCTCGCTGTATGTGCATTGTTCAGCCC


Block sizes: 45 (upstream exon), 45 (downstream exon)
Score: 97

TGTTGCTAAATGCAGTTACTGTAGATAAGGATGACAGCAATTTTCTTTCATCTGATAGGGCCCCTCTTCTTATAGCTGCTTCAGAGCTGATTTGGCTGACgtaagccaac ... gttcttttagATGTGCATCATCTTCATTAAATGGAGAAGAACTTATAAGGGATGGTGGTATCCCCTTGTTGGCAACACTTCTTTCTCGCTGTATGTGCATTGTTCAGCCC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttaagatcttcgccttctttgttatctgatgttcctgttgtaatgttcttttagATGTGCATCATCTTCATTAAATGGAGAAGAACTTATAAGGGATGGTGGTATCCCCTTGTTGGCAACACTTCTTTCTCGCTGTATGTGCATTGTTCAGCCC
                        atctgat  putative branch site (score: 97)
                                            tgttctttt  putative PPT
                  tttgttat  TA-rich tract