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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgctccattcccctctctagcactcaaatgcatgtttatttgttactcctaagtggctgaagttacaagatttttcatttcagGTTGCTACTGACAAATGCATTATGGCGTTCCTGTTTCTGATTGTCTGTGGCGTTATTGCAATAATTGTTGTTAAG

Basic information

species Zea mays
transcript GRMZM2G170191_T01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G170191_T01 (Zea mays), 3'ss of exon 2
lower sequence: AT1G48240.1 (Arabidopsis thaliana), 3'ss of exon 8
---------------------gtgctccattccc---ctctctagcactcaaatgcatgtttatttgttactcctaagtggctgaagttacaagatttt-tcatttcagGTTGCTACTGACAAATGCATTATGGCGTTCCTGTTTCTGATTGTCTGTGGCGTTATTGCAATAATTGTTGTTAAG
                            ||||     | ||  |  |   |||    ||| ||  | |||   |    |   |  |    |||   ||| |  |  ||||| ||||| || |||||||| ||||||||||||||||||||||||||||| ||||| || |||||  |||| |||
gtttgtatgatctctcacaggacataagattctaagacactgcaaaagctaaaattgtgtctaactattatcaccgtttcctttcaacctcaattctttcttgtcacagGTAGCTACAGATAAATGCATAATGGCGTTCCTGTTTCTGATTGTCTGTGGTGTTATAGCTATAATCATTGTGAAG

upper sequence: GRMZM2G170191_T01 (Zea mays), 3'ss of exon 2
lower sequence: AT3G17440.2 (Arabidopsis thaliana), 3'ss of exon 8
gtgctccattcccctctcta-gcactcaaatgcatgtttatttgttactcctaagtggctgaagttacaagatttttcatttcagGTTGCTACTGACAAATGCATTATGGCGTTCCTGTTTCTGATTGTCTGTGGCGTTATTGCAATAATTGTTGTTAAG
       |  | | | |  |   |   | ||  ||  || || | |   ||| |    |||||     | |  |  | ||||||||| ||||| || |||||||| |||| |||||||||||| ||||| || || ||  | || |||||  | || |||
-----gtaacctcatatggacatatgtagatttatcctttttggcttgacctcaaaacctgaatgcttatgtctacttatttcagGTGGCTACCGATAAATGCATAATGGGGTTCCTGTTTCTCATTGTATGCGGTGTAGTAGCCATAATCATAGTGAAG

upper sequence: GRMZM2G170191_T01 (Zea mays), 3'ss of exon 2
lower sequence: AT3G17440.1 (Arabidopsis thaliana), 3'ss of exon 8
gtgctccattcccctctctagcactcaaatgcatgtttatttgttactcctaagtggctgaagttacaagatttttcatttcagGTTGCTACTGACAAATGCATTATGGCGTTCCTGTTTCTGATTGTCTGTGGCGTTATTGCAATAATTGTTGTTAAG
|||    |   |          |   | ||  ||  || || | |   ||| |    |||||     | |  |  | ||||||||| ||||| || |||||||| |||| |||||||||||| ||||| || || ||  | || |||||  | || |||
gtgtgtaacctcatatggacatatgtagatttatcctttttggcttgacctcaaaacctgaatgcttatgtctacttatttcagGTGGCTACCGATAAATGCATAATGGGGTTCCTGTTTCTCATTGTATGCGGTGTAGTAGCCATAATCATAGTGAAG

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: 38 (upstream exon), 49 (downstream exon)
Score: 221

ACAGAGCAAATGAAGAGAATCGGCAATGAGTTAGATTCTGTTCACTTCTCACTGAAGAAGGCCAGTCAAATGGTGAAAGAGATTGGCCGTCAGgtgctccatt ... ttcatttcagGTTGCTACTGACAAATGCATTATGGCGTTCCTGTTTCTGATTGTCTGTGGCGTTATTGCAATAATTGTTGTTAAG


Block sizes: 44 (upstream exon), 49 (downstream exon)
Score: 226

ACAGAGCAAATGAAGAGAATCGGCAATGAGTTAGATTCTGTTCACTTCTCACTGAAGAAGGCCAGTCAAATGGTGAAAGAGATTGGCCGTCAGgtgctccatt ... ttcatttcagGTTGCTACTGACAAATGCATTATGGCGTTCCTGTTTCTGATTGTCTGTGGCGTTATTGCAATAATTGTTGTTAAG


Block sizes: 38 (upstream exon), 49 (downstream exon)
Score: 121

ACAGAGCAAATGAAGAGAATCGGCAATGAGTTAGATTCTGTTCACTTCTCACTGAAGAAGGCCAGTCAAATGGTGAAAGAGATTGGCCGTCAGgtgctccatt ... ttcatttcagGTTGCTACTGACAAATGCATTATGGCGTTCCTGTTTCTGATTGTCTGTGGCGTTATTGCAATAATTGTTGTTAAG


Block sizes: 42 (upstream exon), 49 (downstream exon)
Score: 179

ACAGAGCAAATGAAGAGAATCGGCAATGAGTTAGATTCTGTTCACTTCTCACTGAAGAAGGCCAGTCAAATGGTGAAAGAGATTGGCCGTCAGgtgctccatt ... ttcatttcagGTTGCTACTGACAAATGCATTATGGCGTTCCTGTTTCTGATTGTCTGTGGCGTTATTGCAATAATTGTTGTTAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgcatgtttatttgttactcctaagtggctgaagttacaagatttttcatttcagGTTGCTACTGACAAATGCATTATGGCGTTCCTGTTTCTGATTGTCTGTGGCGTTATTGCAATAATTGTTGTTAAG
                                          tttttcatttc  CT-rich tract
                                      aagatttttcattt  TA-rich tract