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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgcattgtgttccaccacatcctcgcttcctgtatgtttcatcagctgtttaagccaatcctaatgctgtcttctttgctcagGTTCCATTTTCTCGTTCATCGTTGAACCATGATGATGTCTTTATCTTGGATACTGAGAACAAAATATATCAATTCAACGGTGCAAACTCCAACATCCAAG

Basic information

species Zea mays
transcript GRMZM2G081322_T01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G081322_T01 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os03g24220.2 (Oryza sativa), 3'ss of exon 5
gtgcattgtgttccaccacatcctcgcttcctgtatgtttcatcagctgtttaagccaatcctaatgctgtcttctttgctcagGTTCCATTTTCTCGTTCATCGTTGAACCATGATGATGTCTTTATCTTGGATACTGAGAACAAAATATATCAATTCAACGGTGCAAACTCCAACATCCAAG
|||  |  | || ||||   |||  | ||| |  |   | | | | ||  | | |  |     | |    | | || |  ||||||||||||| |||| || || ||||| ||||||||||| |||||||||||||| || || ||||||||||||||||| |||||||||||||| || ||||
gtgactactatttcacc---tccctgtttcttagac--tactttatctcctcatgttatatacactaa-atgtcctatattcagGTTCCATTTGCTCGCTCGTCATTGAATCATGATGATGTATTTATCTTGGATACGGAAAAGAAAATATATCAATTCAATGGTGCAAACTCCAATATTCAAG

upper sequence: GRMZM2G081322_T01 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA03G29280.1 (Glycine max), 3'ss of exon 4
gtgcattgtgttccac-cacatcctcgcttcctgtatgtttcatcagctgtttaagccaatcctaatgctgtcttctttgctcagGTTCCATTTTCTCGTTCATCGTTGAACCATGATGATGTCTTTATCTTGGATACTGAGAACAAAATATATCAATTCAACGGTGCAAACTCCAACATCCAAG
|   | |||  || |  ||  | ||       || |     |||    ||  |||     |  ||     || ||| ||   |||||||| ||| | || || ||  |||| ||||||||||| || ||| | || ||| |||| || || ||||||||||| |||||||||||||| ||||| |
gcatagtgttctctattcatgtacttttcaaatgcagtgcacattcattgactaaaaatgtgata-caaagttttccttatgcagGTTCCTTTTGCACGGTCTTCACTGAATCATGATGATGTATTCATCCTAGACACTCAGAATAAGATTTATCAATTCAATGGTGCAAACTCCAATATCCAGG

upper sequence: GRMZM2G081322_T01 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA19G32010.1 (Glycine max), 3'ss of exon 5
---------------gtgcattgtgttccac-cacatcctcgcttcctgtatgtttcatcagctgtttaagccaatcctaatgctgtcttctttgctcagGTTCCATTTTCTCGTTCATCGTTGAACCATGATGATGTCTTTATCTTGGATACTGAGAACAAAATATATCAATTCAACGGTGCAAACTCCAACATCCAAG
               |  || |||  || |  ||  | ||       |  |     |||  | ||  |||     |  ||     || ||  ||   ||||| || ||| | || || || ||||| ||||||||||| || ||| | || ||| |||| || || ||||||||||| |||||||||||||| ||||| |
gtcagaataaaacaggcacaatgttctctattcatgtacttttcaaattcagtgcacattcgttgcctaaaaatgtgata-caaagttttgcttatgcagGTCCCTTTTGCACGGTCTTCATTGAATCATGATGATGTATTCATCCTAGACACTCAGAATAAGATTTATCAATTCAATGGTGCAAACTCCAATATCCAGG

upper sequence: GRMZM2G081322_T01 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA10G21350.2 (Glycine max), 3'ss of exon 4
gtgcattgtgttccaccacatcctcgcttcctgtatgtttcatcagctgtttaagccaatcctaatgctgtcttctttgctcagGTTCCATTTTCTCGTTCATCGTTGAACCATGATGATGTCTTTATCTTGGATACTGAGAACAAAATATATCAATTCAACGGTGCAAACTCCAACATCCAAG
         ||     |   ||   | |     |    ||||| |  |   || ||      |  ||   | ||  ||   ||||| || ||| |  | || |||||||||||||| ||||| || ||  | |||||||||||||| || ||||||||||| |||||||| ||||| || || |
---------gtatagtct--tctctgttattcatgaacttcattaattcagtacgcatgaagtt-tgacattttgctttgacagGTCCCTTTTGCAAGGTCTTCGTTGAACCATGAAGATGTATTCATACTAGATACTGAGAACAAGATTTATCAATTCAATGGTGCAAATTCCAATATTCAGG

upper sequence: GRMZM2G081322_T01 (Zea mays), 3'ss of exon 5
lower sequence: AT2G41740.1 (Arabidopsis thaliana), 3'ss of exon 5
-----gtgcattgtgttccaccacatcctcgcttcctgtatgtttcatcagctgtttaagccaa-tcctaatgctgt--cttctttgctcagGTTCCATTTTCTCGTTCATCGTTGAACCATGATGATGTCTTTATCTTGGATACTGAGAACAAAATATATCAATTCAACGGTGCAAACTCCAACATCCAAG
        ||||||  ||  ||   |  | |        |    | || | |  | ||   ||| |  |  | ||||  ||  |||   |||||||| ||| | || |||||  |||| ||||||||||| ||||||||||| || ||| | || || ||||| ||||| |||||||| || ||||| || |
gttttaaccattgtactct-ccttgtattagaacgagtgaacggtgattaccaatgtacatcaactttttcttctgttcctcttttttgcagGTTCCTTTTGCCCGCTCATCACTGAATCATGATGATGTATTTATCTTGGACACCGAGGAAAAGATCTATCAGTTCAATGGTGCAAATTCAAACATTCAGG

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: 47 (upstream exon), 44 (downstream exon)
Score: 5

GGAGGGCGGCTTTGCTTCTGGGTTCAAAAAGCCAGAAGTGGACAAGTTTGAAACACGTCTATATATCTGCAAAGGGAAGAGAGCTATCAGAGTTAAAGAGgtgcattgtg ... ctttgctcagGTTCCATTTTCTCGTTCATCGTTGAACCATGATGATGTCTTTATCTTGGATACTGAGAACAAAATATATCAATTCAACGGTGCAAACTCCAACATCCAAG


Block sizes: 25 (upstream exon), 49 (downstream exon)
Score: 7

GGAGGGCGGCTTTGCTTCTGGGTTCAAAAAGCCAGAAGTGGACAAGTTTGAAACACGTCTATATATCTGCAAAGGGAAGAGAGCTATCAGAGTTAAAGAGgtgcattgtg ... ctttgctcagGTTCCATTTTCTCGTTCATCGTTGAACCATGATGATGTCTTTATCTTGGATACTGAGAACAAAATATATCAATTCAACGGTGCAAACTCCAACATCCAAG


Block sizes: 32 (upstream exon), 37 (downstream exon)
Score: 2

GGAGGGCGGCTTTGCTTCTGGGTTCAAAAAGCCAGAAGTGGACAAGTTTGAAACACGTCTATATATCTGCAAAGGGAAGAGAGCTATCAGAGTTAAAGAGgtgcattgtg ... ctttgctcagGTTCCATTTTCTCGTTCATCGTTGAACCATGATGATGTCTTTATCTTGGATACTGAGAACAAAATATATCAATTCAACGGTGCAAACTCCAACATCCAAG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 36

GGAGGGCGGCTTTGCTTCTGGGTTCAAAAAGCCAGAAGTGGACAAGTTTGAAACACGTCTATATATCTGCAAAGGGAAGAGAGCTATCAGAGTTAAAGAGgtgcattgtg ... ctttgctcagGTTCCATTTTCTCGTTCATCGTTGAACCATGATGATGTCTTTATCTTGGATACTGAGAACAAAATATATCAATTCAACGGTGCAAACTCCAACATCCAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cctgtatgtttcatcagctgtttaagccaatcctaatgctgtcttctttgctcagGTTCCATTTTCTCGTTCATCGTTGAACCATGATGATGTCTTTATCTTGGATACTGAGAACAAAATATATCAATTCAACGGTGCAAACTCCAACATCCAAG
                              tcctaat  putative branch site (score: 36)
                                      ctgtcttctttgctc  CT-rich tract
                  tgtttaa  TA-rich tract