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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtcaatcatcactcagggctgtgcctgcaatgttcatcaccatacaattttcagaccagaatgcagaaatgaaccgagttatgatttcttgcagGGCAATAGGGCTATAGTTGTTGATGAACCTGGTGTGACAAGGGACCGCTTATATGGACGATCTTATTGGGGTGATCATGAGTTTATGGTTATTGATACTG

Basic information

species Zea mays
transcript GRMZM2G302233_T01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G302233_T01 (Zea mays), 3'ss of exon 3
lower sequence: AT3G12080.1 (Arabidopsis thaliana), 3'ss of exon 3
gtatgtcaatcatcactcagggctgtgcctgcaatgttcatcaccatacaattttcagaccagaatgcagaaatgaaccgagttatgatttcttgcagGGCAATAGGGCTATAGTTGTTGATGAACCTGGTGTGACAAGGGACCGCTTATATGGACGATCTTATTGGGGTGATCATGAGTTTATGGTTATTGATACTG
            | | |   |        || ||| ||  |   | |    |||||  ||||   |    || |   |    |||  ||   || ||||  ||||| ||||| || || ||||||||||| || || ||||| || || |||||  |||| |||||||||||||| |||||| ||||  | || || |
-----------gtaagttttgctaacatttg-aattttttttttcttttttttttcctaccattttatgtaagttgtct---ttacaatgcatttcagGAGAATAGAGCTATTGTAGTGGATGAACCTGGAGTTACTAGGGATCGATTGTATGGTAGATCATATTGGGGTGATCAAGAGTTTGTGGTGGTAGACACCG
















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: 107

ATTCCAGATAATCTTCTTCCAAAGGTGGCAATTATTGGTAGGCCGAATGTTGGTAAATCTGCACTCTTCAATCGTCTTGTCGGAgtatgtcaat ... tttcttgcagGGCAATAGGGCTATAGTTGTTGATGAACCTGGTGTGACAAGGGACCGCTTATATGGACGATCTTATTGGGGTGATCATGAGTTTATGGTTATTGATACTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 301

ATTCCAGATAATCTTCTTCCAAAGGTGGCAATTATTGGTAGGCCGAATGTTGGTAAATCTGCACTCTTCAATCGTCTTGTCGGAgtatgtcaat ... tttcttgcagGGCAATAGGGCTATAGTTGTTGATGAACCTGGTGTGACAAGGGACCGCTTATATGGACGATCTTATTGGGGTGATCATGAGTTTATGGTTATTGATACTG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 54

ATTCCAGATAATCTTCTTCCAAAGGTGGCAATTATTGGTAGGCCGAATGTTGGTAAATCTGCACTCTTCAATCGTCTTGTCGGAgtatgtcaat ... tttcttgcagGGCAATAGGGCTATAGTTGTTGATGAACCTGGTGTGACAAGGGACCGCTTATATGGACGATCTTATTGGGGTGATCATGAGTTTATGGTTATTGATACTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 134

ATTCCAGATAATCTTCTTCCAAAGGTGGCAATTATTGGTAGGCCGAATGTTGGTAAATCTGCACTCTTCAATCGTCTTGTCGGAgtatgtcaat ... tttcttgcagGGCAATAGGGCTATAGTTGTTGATGAACCTGGTGTGACAAGGGACCGCTTATATGGACGATCTTATTGGGGTGATCATGAGTTTATGGTTATTGATACTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccatacaattttcagaccagaatgcagaaatgaaccgagttatgatttcttgcagGGCAATAGGGCTATAGTTGTTGATGAACCTGGTGTGACAAGGGACCGCTTATATGGACGATCTTATTGGGGTGATCATGAGTTTATGGTTATTGATACTG
                                             tttcttgc  CT-rich tract
                                       ttatgattt  TA-rich tract