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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacctgcacacatctgtccactttaattctttttagatgaatgccttttaaactcaatgcattctgtcatttgcacttttagGAGTTGAAATTGTCATTGCAACTCCTGGCCGGTTGATTGATATGCTGGAAGCTGGTCACACAAACCTACGTAGAGTGACGTACCTTGTGTTGGATGAGGC

Basic information

species Zea mays
transcript AC209019.3_FGT003
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AC209019.3_FGT003 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os01g68320.3 (Oryza sativa), 3'ss of exon 4
gtacctgcacacatctgtccactttaattctttttagatg-aatgccttttaaactcaatgcattctgtcatttgcacttttagGAGTTGAAATTGTCATTGCAACTCCTGGCCGGTTGATTGATATGCTGGAAGCTGGTCACACAAACCTACGTAGAGTGACGTACCTTGTGTTGGATGAGGC
|||  ||  | |||||    ||   || |  |||| ||   || |  || ||  || | |   ||  |||      ||||  ||| ||||| |||||||||||||| ||||| |||||||| ||||||||||||| ||||||||| ||||| || ||||| || ||||| ||  ||||||||||
gtatttgtcc-catct---taccgaaaataattttggacataaggttttgtaggctaagtctcttgcgtc-----tacttccagGGGTTGAGATTGTCATTGCAACACCTGGTCGGTTGATCGATATGCTGGAAGGTGGTCACACTAACCTGCGAAGAGTAACATACCTCGTCCTGGATGAGGC

upper sequence: AC209019.3_FGT003 (Zea mays), 3'ss of exon 2
lower sequence: Vv17s0000g09130.t01 (Vitis vinifera), 3'ss of exon 4
gtacctgcacacatctgtccactttaattcttt-ttagatgaatgccttttaaactcaatgca------ttctgtcatttgcactt---ttagGAGTTGAAATTGTCATTGCAACTCCTGGCCGGTTGATTGATATGCTGGAAGCTGGTCACACAAACCTACGTAGAGTGACGTACCTTGTGTTGGATGAGGC
      | ||  || | ||  || |   | |||  || ||   |     || |  |   ||||      |  | ||  |||| |||    |||| ||||| ||||||||||| || ||||| || || || ||||||||||| |||   || |||||||| || |||||||| |||||||| || ||||||||
------gtacttatgtttcttctatggctatttgctaaatccctataaatttaggttggtgcacgaaaatcttatctattgcccttatgctagGTGTTGAGATTGTCATTGCTACACCTGGACGATTAATAGATATGCTGGAGGCTCAACATACAAACCTGCGAAGAGTGACTTACCTTGTATTAGATGAGGC
















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), 22 (downstream exon)
Score: 131

CAGGAAGAATCTACAAAATTTGGATCATATTCAAGAACTAGAAGCACATGTGTCTATGGTGGTGCACCTAAGGGTCCACAAATACGGGGCCTTAGAAGAGgtacctgcac ... gcacttttagGAGTTGAAATTGTCATTGCAACTCCTGGCCGGTTGATTGATATGCTGGAAGCTGGTCACACAAACCTACGTAGAGTGACGTACCTTGTGTTGGATGAGGC


Block sizes: 49 (upstream exon), 25 (downstream exon)
Score: 85

CAGGAAGAATCTACAAAATTTGGATCATATTCAAGAACTAGAAGCACATGTGTCTATGGTGGTGCACCTAAGGGTCCACAAATACGGGGCCTTAGAAGAGgtacctgcac ... gcacttttagGAGTTGAAATTGTCATTGCAACTCCTGGCCGGTTGATTGATATGCTGGAAGCTGGTCACACAAACCTACGTAGAGTGACGTACCTTGTGTTGGATGAGGC


Block sizes: 49 (upstream exon), 34 (downstream exon)
Score: 155

CAGGAAGAATCTACAAAATTTGGATCATATTCAAGAACTAGAAGCACATGTGTCTATGGTGGTGCACCTAAGGGTCCACAAATACGGGGCCTTAGAAGAGgtacctgcac ... gcacttttagGAGTTGAAATTGTCATTGCAACTCCTGGCCGGTTGATTGATATGCTGGAAGCTGGTCACACAAACCTACGTAGAGTGACGTACCTTGTGTTGGATGAGGC


Block sizes: 49 (upstream exon), 16 (downstream exon)
Score: 162

CAGGAAGAATCTACAAAATTTGGATCATATTCAAGAACTAGAAGCACATGTGTCTATGGTGGTGCACCTAAGGGTCCACAAATACGGGGCCTTAGAAGAGgtacctgcac ... gcacttttagGAGTTGAAATTGTCATTGCAACTCCTGGCCGGTTGATTGATATGCTGGAAGCTGGTCACACAAACCTACGTAGAGTGACGTACCTTGTGTTGGATGAGGC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctttttagatgaatgccttttaaactcaatgcattctgtcatttgcacttttagGAGTTGAAATTGTCATTGCAACTCCTGGCCGGTTGATTGATATGCTGGAAGCTGGTCACACAAACCTACGTAGAGTGACGTACCTTGTGTTGGATGAGGC
                                              cactttt  CT-rich tract
                  ttttaaact  TA-rich tract