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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttcgtccggctgctgcttcggtttggtactttgattataatttcatgatgctggcttggatctgttaactttatctgctcttgtgatatgccttttgtagAAAAGTTCCCAGAGGCAGCTCGTAAATAGTGTGTTCCCCAAGCTTGCTGTGTACAATTCTGTGGATCCTTCGGTGGCTCCATCTCTTCTCATG

Basic information

species Zea mays
transcript GRMZM2G012319_T01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G012319_T01 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA05G36530.1 (Glycine max), 3'ss of exon 3
-----gttcgtccggctgctgcttcggtttggtactttgattataatttcatgatgctggcttggatctgttaactttatctgctcttgtgatatgccttttgtagAAAAGTTCCCAGAGGCAGCTCGTAAATAGTGTGTTCCCCAAGCTTGCTGTGTACAATTCTGTGGATCCTTCGGTGGCTCCATCTCTTCTCATG
     | | ||   |  | |  | |   |  |  |    | | |  |||| ||  |||||  |   |||  |   ||| | |    | || || ||  ||    |||||||||| ||  ||||  | ||  ||  |||||| || |||||||| ||||| ||||||||||| |||||| ||||||| ||||||||||||
taagtgcttgtggagaagtttatccacataagatccactaatgtgctttcgtg--gctggtctac-tcttatgtttttgtttttgatggtaatgtggtttc---agAAAAGTTCTCAACGGCAATTAGTGCATCATGTGTTTCCAAAGCTTGCAGTGTATAATTCTGTGGACCCTTCGTTGGCTCCCTCTCTTCTCATG

upper sequence: GRMZM2G012319_T01 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA08G03020.1 (Glycine max), 3'ss of exon 3
---gttcgtccggctgctgcttcggtttggtactttgattataatttcatgatgctggcttggatctgttaactttatctgctcttgtgatatgccttttgtagAAAAGTTCCCAGAGGCAGCTCGTAAATAGTGTGTTCCCCAAGCTTGCTGTGTACAATTCTGTGGATCCTTCGGTGGCTCCATCTCTTCTCATG
   | | |    |  | |  | |      |  |    | | |  |||| ||  | |||  |  || |  | |  || |    | |  || ||      ||  |||||||||| ||  ||||  | ||  ||  |||||| || |||||||| ||||| ||||| ||||| |||||  ||||||| ||||||||||||
agtgcttgcagagaagtttatccacacaagatccagtaatgtgctttcgtg--gttggtct--attttcttatgtttttgtttttgatggtaacatggtttcagAAAAGTTCTCAACGGCAATTAGTGCATCATGTGTTTCCAAAGCTTGCAGTGTATAATTCCGTGGACCCTTCATTGGCTCCCTCTCTTCTCATG

upper sequence: GRMZM2G012319_T01 (Zea mays), 3'ss of exon 2
lower sequence: AT2G07360.1 (Arabidopsis thaliana), 3'ss of exon 3
gttcgtccggctgctgcttcggtttggtactttgattataatttcatgatgctggcttggatctgttaactttatctgctcttgtgatatgccttttgtagAAAAGTTCCCAGAGGCAGCTCGTAAATAGTGTGTTCCCCAAGCTTGCTGTGTACAATTCTGTGGATCCTTCGGTGGCTCCATCTCTTCTCATG
|||        || |  |  | | ||    | |   | |  | |  || ||     | | |||||     ||  |||| | ||      ||      | |||||||||| ||||  || || || |||   |||||||| ||||||||||||||||| || || ||||||||  |||| ||||||||||| |||
gtttaagtttgtgttcttatgctctgcctttatacctctcttcttctgctga-aaatagtatctgactgtttcttctgtttttcgcgagtga-----gcagAAAAGTTCTCAGAAACAACTAGTGAATCACGTGTTCCCTAAGCTTGCTGTGTACAACTCAGTTGATCCTTCTCTGGCCCCATCTCTTCTTATG

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), 49 (downstream exon)
Score: 145

CCCGTCTCCTACGCACAGCTGGCCCGGAGCATCCACGAGCTCGCCGCGACGTGCGACCAGgttcgtccgg ... ccttttgtagAAAAGTTCCCAGAGGCAGCTCGTAAATAGTGTGTTCCCCAAGCTTGCTGTGTACAATTCTGTGGATCCTTCGGTGGCTCCATCTCTTCTCATG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 95

CCCGTCTCCTACGCACAGCTGGCCCGGAGCATCCACGAGCTCGCCGCGACGTGCGACCAGgttcgtccgg ... ccttttgtagAAAAGTTCCCAGAGGCAGCTCGTAAATAGTGTGTTCCCCAAGCTTGCTGTGTACAATTCTGTGGATCCTTCGGTGGCTCCATCTCTTCTCATG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 56

CCCGTCTCCTACGCACAGCTGGCCCGGAGCATCCACGAGCTCGCCGCGACGTGCGACCAGgttcgtccgg ... ccttttgtagAAAAGTTCCCAGAGGCAGCTCGTAAATAGTGTGTTCCCCAAGCTTGCTGTGTACAATTCTGTGGATCCTTCGGTGGCTCCATCTCTTCTCATG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 140

CCCGTCTCCTACGCACAGCTGGCCCGGAGCATCCACGAGCTCGCCGCGACGTGCGACCAGgttcgtccgg ... ccttttgtagAAAAGTTCCCAGAGGCAGCTCGTAAATAGTGTGTTCCCCAAGCTTGCTGTGTACAATTCTGTGGATCCTTCGGTGGCTCCATCTCTTCTCATG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgatgctggcttggatctgttaactttatctgctcttgtgatatgccttttgtagAAAAGTTCCCAGAGGCAGCTCGTAAATAGTGTGTTCCCCAAGCTTGCTGTGTACAATTCTGTGGATCCTTCGGTGGCTCCATCTCTTCTCATG
                 tgttaac  putative branch site (score: 140)
                                           tgcctttt  putative PPT
                   ttaactttat  TA-rich tract