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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtctgttatctatatcctttatttttatttgtaaaaacatttgctctctagttttgatatttaaatatcattttaaattatttggttcaacttttttttggcagGTCCTGCAGCATCTCGGTGACTTTCCTCAGAAATTAGCACAGCATTGCCATTCGTTGTATGATTATGCTCCTATGCCACCCGTGACTTATCCGAATCTGA

Basic information

species Zea mays
transcript GRMZM2G001895_T01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G001895_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os10g42439.1 (Oryza sativa), 3'ss of exon 10
gtctgttatctatatcctttatttttatttgtaaaaacatttgctctctagttttgatatttaaatatcatttt-aaattatttggttca---acttttttttggcagGTCCTGCAGCATCTCGGTGACTTTCCTCAGAAATTAGCACAGCATTGCCATTCGTTGTATGATTATGCTCCTATGCCACCCGTGACTTATCCGAATCTGA
      ||| ||   || |  ||   |||||| ||||  ||| || |    |  |||  ||| ||| | ||||| ||||| ||  || ||      |   |||  |||||||||||||||||||||||||||||||||||||| || || ||||| ||||| |||||||||||||||||||||||||| ||||| || ||||||||||
-----gtatttaccaccctagtt---atttgttaaaatgtttactttgagatcatgagtttttaatctaattttcaaattgttctgtccatacgactggctttctcagGTCCTGCAGCATCTCGGTGACTTTCCTCAGAAATTGGCTCAACATTGTCATTCATTGTATGATTATGCTCCTATGCCACCTGTGACCTACCCGAATCTGA

upper sequence: GRMZM2G001895_T01 (Zea mays), 3'ss of exon 4
lower sequence: AT2G26890.1 (Arabidopsis thaliana), 3'ss of exon 10
gtctgttatctatatcctttatttttatttgtaaaaacatttgctctctagttttgatatttaaatatcattttaaattatttggttcaacttttt---------tttggcagGTCCTGCAGCATCTCGGTGACTTTCCTCAGAAATTAGCACAGCATTGCCATTCGTTGTATGATTATGCTCCTATGCCACCCGTGACTTATCCGAATCTGA
   | || |  |||| |  || |      | | |   |||||  |||  | |  |     | || ||||| ||| |||| ||  |||  | ||| |         ||   |||||  |||||||||| ||||| | ||||||||||||  ||||||| ||||||||  | |||||||||||||| |||||||| || || |||||  | || |
--gtatt-tacatattcgctactgagggct-ttaggtcattt--tcttgaatgctatctgtaaactatcactttcaattcttcagttttaatttctcgtttttatttcctcagGTTTTGCAGCATCTTGGTGATTATCCTCAGAAATTGTCACAGCACTGCCATTCTCTCTATGATTATGCTCCCATGCCACCTGTTACGTATCCAGAACTTA

upper sequence: GRMZM2G001895_T01 (Zea mays), 3'ss of exon 4
lower sequence: Vv11s0016g04420.t01 (Vitis vinifera), 3'ss of exon 10
------------gtctgttatctatatcctttatttttatttgtaaaaacatt-tgctctctagttttgatattta--aatatcattttaaattatttggttcaacttttttt-tggcagGTCCTGCAGCATCTCGGTGACTTTCCTCAGAAATTAGCACAGCATTGCCATTCGTTGTATGATTATGCTCCTATGCCACCCGTGACTTATCCGAATCTGA
             |   | |   | |      |||| | || ||  |     | || | | |  |||| | ||||   |  ||   |  || || |||  | || ||||  |   | |||||  |||||||||| ||||| ||||||||||||||  |||||||||| ||||| || |||||||||||||| |||||||| || || |||||  | || |
gtagttgaaaccttgaatgaggcacactgcagatttgttttggtttattttctatgatattttattttaagattttccatgattcctggaatttttttcatgcacctttcatcacgtcagGTGTTGCAGCATCTTGGTGATTTTCCTCAGAAATTGTCACAGCATTGTCATTCATTATATGATTATGCTCCAATGCCACCGGTAACATATCCAGAGCTAA

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: 48 (upstream exon), 47 (downstream exon)
Score: 73

CAGTGGCCCTTCTGCTTTTGCGGGTGCAATGGTGTCTGATTCTGACACACCAGAAATTATATGGACCCACAAGATGCGAGCAGAAAACCTTATTCGTCAGgtctgttatc ... tttttggcagGTCCTGCAGCATCTCGGTGACTTTCCTCAGAAATTAGCACAGCATTGCCATTCGTTGTATGATTATGCTCCTATGCCACCCGTGACTTATCCGAATCTGA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 82

CAGTGGCCCTTCTGCTTTTGCGGGTGCAATGGTGTCTGATTCTGACACACCAGAAATTATATGGACCCACAAGATGCGAGCAGAAAACCTTATTCGTCAGgtctgttatc ... tttttggcagGTCCTGCAGCATCTCGGTGACTTTCCTCAGAAATTAGCACAGCATTGCCATTCGTTGTATGATTATGCTCCTATGCCACCCGTGACTTATCCGAATCTGA


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 90

CAGTGGCCCTTCTGCTTTTGCGGGTGCAATGGTGTCTGATTCTGACACACCAGAAATTATATGGACCCACAAGATGCGAGCAGAAAACCTTATTCGTCAGgtctgttatc ... tttttggcagGTCCTGCAGCATCTCGGTGACTTTCCTCAGAAATTAGCACAGCATTGCCATTCGTTGTATGATTATGCTCCTATGCCACCCGTGACTTATCCGAATCTGA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 108

CAGTGGCCCTTCTGCTTTTGCGGGTGCAATGGTGTCTGATTCTGACACACCAGAAATTATATGGACCCACAAGATGCGAGCAGAAAACCTTATTCGTCAGgtctgttatc ... tttttggcagGTCCTGCAGCATCTCGGTGACTTTCCTCAGAAATTAGCACAGCATTGCCATTCGTTGTATGATTATGCTCCTATGCCACCCGTGACTTATCCGAATCTGA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agttttgatatttaaatatcattttaaattatttggttcaacttttttttggcagGTCCTGCAGCATCTCGGTGACTTTCCTCAGAAATTAGCACAGCATTGCCATTCGTTGTATGATTATGCTCCTATGCCACCCGTGACTTATCCGAATCTGA
  ttttgat  putative branch site (score: 108)
                                    ttcaactttttttt  putative PPT
       atatttaaatatcatt  TA-rich tract