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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagttaatgaataggattatgcagtgtgtgtctcattatttacatactgttgcatcttatgttatattgcttgtatagGAGTATAATGCAAAACTCTCCGATTTTGGGCTTGCAAAAGACGGACCTGTAGGTGATAAAACTCATGTCTCTACTCGAGTAATGGGAACCTATGGATATG

Basic information

species Zea mays
transcript GRMZM2G150806_T01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G150806_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os09g19700.1 (Oryza sativa), 3'ss of exon 4
-------gtaagttaatgaataggattatgcagtgtgtgtctcattatttacatactgttgcatcttatgttatattgcttgtatagGAGTATAATGCAAAACTCTCCGATTTTGGGCTTGCAAAAGACGGACCTGTAGGTGATAAAACTCATGTCTCTACTCGAGTAATGGGAACCTATGGATATG
        |||||   ||||| |||||| | | ||     | ||  ||| ||||  |||    |  ||| ||||  | ||  |  |||| || |||||||||||||| |||||||||||||| ||||| || ||||||||||| |||||||| || |||||||||||||||||||| ||||| ||||
gtaagttttaagtccttgaattggattacgtattgcacaccacacgattcacatcttgtaattttgtatattatgctactcttgcagGATTACAATGCAAAACTCTCAGATTTTGGGCTTGCCAAAGATGGCCCTGTAGGTGACAAAACTCACGTGTCTACTCGAGTAATGGGAACATATGGTTATG

upper sequence: GRMZM2G150806_T01 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA02G02570.1 (Glycine max), 3'ss of exon 4
gtaagttaatgaataggattatgcagtgtgtgtctcattatttacatactgttgcatcttatgttatattgcttgtatagGAGTATAATGCAAAACTCTCCGATTTTGGGCTTGCAAAAGACGGACCTGTAGGTGATAAAACTCATGTCTCTACTCGAGTAATGGGAACCTATGGATATG
    || | ||   |  | ||  || |  |  |  ||||     | |  | |    ||| || || ||  | ||    ||||||| ||||| || ||||| |||||||| ||||| ||||| || || | |||||||||||| ||||| ||||||||||| |||||||||||||| ||||
----gtaagtgtcaaaaacta--caataag-attgcatttccccctttttatca-gtctaatattgtaccgatt---cagGAGTACAATGCCAAGCTCTCAGATTTTGGTCTTGCCAAAGATGGTCCAGAAGGTGATAAAACCCATGTGTCTACTCGAGTGATGGGAACCTATGGTTATG

upper sequence: GRMZM2G150806_T01 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA19G02480.1 (Glycine max), 3'ss of exon 3
---gtaagttaatgaataggattat-gcagtg-tgtgtctcattatttacatactgttgc--atcttatgttatattgcttgtatagGAGTATAATGCAAAACTCTCCGATTTTGGGCTTGCAAAAGACGGACCTGTAGGTGATAAAACTCATGTCTCTACTCGAGTAATGGGAACCTATGGATATG
    ||  || |  | |    || |  |  || |   | |||  || || ||||  |     |  |  |  ||   | ||  |  || | || || |||||||| ||||||||||||||||||||||| |  || || || |||||||  ||||| || ||   ||| ||||||||  | || ||||
gtaatagcttgaacattgcatttcttactatgataattttcaacatatatataccttcattgacatcttaataccattctgtttcagAACTACAACGCAAAACTTTCCGATTTTGGGCTTGCAAAAGATGCTCCAGTGGGAGATAAAAGCCATGTATCAACAAAAGTGATGGGAACAAAAGGGTATG

upper sequence: GRMZM2G150806_T01 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA18G16300.1 (Glycine max), 3'ss of exon 5
gtaagt-taatgaataggattatgcagtgtgtgtctcattatttacatactgttgcatcttatgttatattgcttgtatagGAGTATAATGCAAAACTCTCCGATTTTGGGCTTGCAAAAGACGGACCTGTAGGTGATAAAACTCATGTCTCTACTCGAGTAATGGGAACCTATGGATATG
||||||   |    |   |||||  |   | | |||  | |||     | |  ||  |  ||| ||||  |   | |  |||| || ||||| || ||||| || ||||| ||||||||||| || || |  ||||||||||||||||| ||||||||||| |||||||||||||| ||||
gtaagtgccaaattttaaattat-taccatttttcttttcattccttgatt--tgatttatatattattataactattcagGAATACAATGCTAAGCTCTCAGACTTTGGACTTGCAAAAGATGGTCCAGAGGGTGATAAAACTCATGTGTCTACTCGAGTGATGGGAACCTATGGTTATG

upper sequence: GRMZM2G150806_T01 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA08G40770.1 (Glycine max), 3'ss of exon 4
gtaagttaatgaataggattatgcagtgtgtgtctcattatttacatactg--ttgcatcttatgttatattgcttgtatagGAGTATAATGCAAAACTCTCCGATTTTGGGCTTGCAAAAGACGGACCTGTAGGTGATAAAACTCATGTCTCTACTCGAGTAATGGGAACCTATGGATATG
||||||     |||    ||| |   |     |||   | || |     ||  |||    |||| ||||  |     |  |||| || ||| | || ||||| |||||||| ||||||||||| || || |  ||||||||||| ||||| ||||||||||| |||||||||||||| ||||
gtaagtggccaaatg---ttaagttattaccatctttcttttcattccttgatttgatctttatattattataacaattcagGAATACAATTCTAAGCTCTCAGATTTTGGACTTGCAAAAGATGGTCCAGAGGGTGATAAAACCCATGTGTCTACTCGAGTGATGGGAACCTATGGTTATG

upper sequence: GRMZM2G150806_T01 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA01G04930.1 (Glycine max), 3'ss of exon 4
gtaagttaatgaataggattatgcagtgtgtgtctcattatttacatactgttgcatcttatgttatattgcttgtatagGAGTATAATGCAAAACTCTCCGATTTTGGGCTTGCAAAAGACGGACCTGTAGGTGATAAAACTCATGTCTCTACTCGAGTAATGGGAACCTATGGATATG
    || | ||      | ||      |  || |  |||   | | |  ||||   ||| || ||       ||    |||| || ||||| || ||||| || ||||| ||||| ||||| || || | |||||||||||| ||||| |||||||| || |||||||||||||| || |
----gtaagtgcccgaaactacaataagattg-catatttcctcctttttgtta-gtctaatattgccccaatt---cagGACTACAATGCCAAGCTCTCAGACTTTGGTCTTGCCAAAGATGGTCCAGAAGGTGATAAAACCCATGTGTCTACTCGGGTGATGGGAACCTATGGTTACG

upper sequence: GRMZM2G150806_T01 (Zea mays), 3'ss of exon 4
lower sequence: AT3G28690.1 (Arabidopsis thaliana), 3'ss of exon 3
--------gtaagttaatgaataggattatgcagtgtgtgtctcattatttacatactgttgcatcttatgttatattgcttgtat---agGAGTATAATGCAAAACTCTCCGATTTTGGGCTTGCAAAAGACGGACCTGTAGGTGATAAAACTCATGTCTCTACTCGAGTAATGGGAACCTATGGATATG
        | |||  | | ||   ||| |       | ||||   || | |  ||  |  |  || |||    | | ||||   ||   |||| ||||||||||| ||||| |||||||||||||||||||| |  || |  |   | ||| | || || || || ||||| |||||||| ||||| ||||
gtatgtctgaaagccacttaacccgataacctcaactctgtcct-ttctctctatgtttataaattttagaaaaaaatgctcccattgcagGAATATAATGCAAAGCTCTCTGATTTTGGGCTTGCAAAAGATGCTCCAGACGAGAAAAAATCCCACGTATCAACCCGAGTCATGGGAACTTATGGTTATG

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: 112

TGCACTGGGAGCAGCAAAGGGTCTGGCTTTCCTTCATGAAGAAGCAGAAAGTCCAGTCATTTATCGTGATTTTAAAACATCTAATATACTACTGGATGCGgtaagttaat ... gcttgtatagGAGTATAATGCAAAACTCTCCGATTTTGGGCTTGCAAAAGACGGACCTGTAGGTGATAAAACTCATGTCTCTACTCGAGTAATGGGAACCTATGGATATG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 137

TGCACTGGGAGCAGCAAAGGGTCTGGCTTTCCTTCATGAAGAAGCAGAAAGTCCAGTCATTTATCGTGATTTTAAAACATCTAATATACTACTGGATGCGgtaagttaat ... gcttgtatagGAGTATAATGCAAAACTCTCCGATTTTGGGCTTGCAAAAGACGGACCTGTAGGTGATAAAACTCATGTCTCTACTCGAGTAATGGGAACCTATGGATATG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 151

TGCACTGGGAGCAGCAAAGGGTCTGGCTTTCCTTCATGAAGAAGCAGAAAGTCCAGTCATTTATCGTGATTTTAAAACATCTAATATACTACTGGATGCGgtaagttaat ... gcttgtatagGAGTATAATGCAAAACTCTCCGATTTTGGGCTTGCAAAAGACGGACCTGTAGGTGATAAAACTCATGTCTCTACTCGAGTAATGGGAACCTATGGATATG


Block sizes: 42 (upstream exon), 47 (downstream exon)
Score: 34

TGCACTGGGAGCAGCAAAGGGTCTGGCTTTCCTTCATGAAGAAGCAGAAAGTCCAGTCATTTATCGTGATTTTAAAACATCTAATATACTACTGGATGCGgtaagttaat ... gcttgtatagGAGTATAATGCAAAACTCTCCGATTTTGGGCTTGCAAAAGACGGACCTGTAGGTGATAAAACTCATGTCTCTACTCGAGTAATGGGAACCTATGGATATG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtgtgtgtctcattatttacatactgttgcatcttatgttatattgcttgtatagGAGTATAATGCAAAACTCTCCGATTTTGGGCTTGCAAAAGACGGACCTGTAGGTGATAAAACTCATGTCTCTACTCGAGTAATGGGAACCTATGGATATG
                              atcttatgttatatt  TA-rich tract