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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgcaaaaagtccctttgtagtagtttcagcctagatccttccatatgttgatctcttgctatcgctaatcgtggttgtcacatttctacagCTGGGTATGAAATTCAGTGAAACAAGATCGAAGTCATCTATTCTTCATGTATTTCCTTTCAACTCAGAGAAAAAGCGAGGCGGGGTTGCGGTGTACCTG

Basic information

species Zea mays
transcript GRMZM2G391042_T01
intron # 19
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G391042_T02 (Zea mays), 3'ss of exon 19
lower sequence: LOC_Os04g51610.3 (Oryza sativa), 3'ss of exon 19
--gtgcaaaaagtccctttgtagtagtttcagcctagatccttccatatgttgatctcttgctatcgctaatcgtggttgtcacatttctacagCTGGGTATGAAATTCAGTGAAACAAGATCGAAGTCATCTATTCTTCATGTATTTCCTTTCAACTCAGAGAAAAAGCGAGGCGGGGTTGCGGTGTACCTG
     || | | |||  || |||||| |  | |  |||| ||    | | |  ||  |||    | | | | | || |  ||| ||||| |||||| || |||| ||||| ||| |||||| | ||||| |||||||||||||| || || |||||||||||||||||  ||||||||||||| ||| | |||
gtacacatacaatcctattttagtagctgaatcacagattctagattttttgtatgccttctgtttggtgaccatgctcttcatatttccacagCTTGGCATGAGATTCAATGACACAAGAACAAAGTCCTCTATTCTTCATGTTTTCCCATTCAACTCAGAGAAAAAAAGAGGCGGGGTTGCAGTGCATCTG

upper sequence: GRMZM2G391042_T02 (Zea mays), 3'ss of exon 19
lower sequence: GLYMA17G06520.1 (Glycine max), 3'ss of exon 21
gtgcaaaaagtccctttgtagtagtttcagcctagatccttccatatgttgatctctt--gctatcgctaatcgtggttgtcacattt--ctacagCTGGGTATGAAATTCAGTGAAACAAGATCGAAGTCATCTATTCTTCATGTATTTCCTTTCAACTCAGAGAAAAAGCGAGGCGGGGTTGCGGTGTACCTG
         |||  ||| |   | ||  |   |  |        || |  | | | |     ||   ||| |  ||  ||| | ||     | ||||| || ||||| ||        | ||||| |||||||| ||| |||||||||| || ||||| ||||| ||||||||||| || |||||    |   ||
---------gtcttttt-tgaaacttaaaatttcaacttcattttaaggagttttatgcaattacaactagttatgagtgttagatcaaatttcagCTTGGGATGAATTTTGACACTGCCAGATCAAAGTCATCAATTATTCATGTATTCCCATTCAATTCAGACAAAAAGCGAGGAGGAGTTGCAACATGGGTG

upper sequence: GRMZM2G391042_T02 (Zea mays), 3'ss of exon 19
lower sequence: Vv09s0018g02130.t01 (Vitis vinifera), 3'ss of exon 20
gtgcaaaaagtccctttgtagtagtttcagcctagatccttcca-----tatgttgatctcttgctatcgctaatcgtggttgtcacatttctacagCTGGGTATGAAATTCAGTGAAACAAGATCGAAGTCATCTATTCTTCATGTATTTCCTTTCAACTCAGAGAAAAAGCGAGGCGGGGTTGCGGTGTACCTG
          |||| |  ||   |   ||   ||  |||||         || |  || ||  | |  |  || || |   | |  | ||  | ||| |||| ||||| ||   || || ||||    | || || ||||| ||||| || ||||||||||||||||||||| |||| || ||||| ||  |    
--------gttcccctactacctgaaacatattatctccttttggcatgcatatctatgtcaagttgactttagtcat--ctatatccttattgcagTTGGGGATGAAGTTTGATGTAATAAGAGAAGAATCCTCAATTCTCCATGTTTTCCCTTTCAACTCAGAGAAAAAGAGAGGTGGTGTTGCAGTACAG---

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: 43 (upstream exon), 49 (downstream exon)
Score: 64

CAGGGTGGTCAAGAACCAGAGGTGACTGGATCACCTACAGAAAAGGCTATCCTGTCTTGGGGACTAAAGgtgcaaaaag ... atttctacagCTGGGTATGAAATTCAGTGAAACAAGATCGAAGTCATCTATTCTTCATGTATTTCCTTTCAACTCAGAGAAAAAGCGAGGCGGGGTTGCGGTGTACCTG


Block sizes: 43 (upstream exon), 43 (downstream exon)
Score: 33

CAGGGTGGTCAAGAACCAGAGGTGACTGGATCACCTACAGAAAAGGCTATCCTGTCTTGGGGACTAAAGgtgcaaaaag ... atttctacagCTGGGTATGAAATTCAGTGAAACAAGATCGAAGTCATCTATTCTTCATGTATTTCCTTTCAACTCAGAGAAAAAGCGAGGCGGGGTTGCGGTGTACCTG


Block sizes: 43 (upstream exon), 47 (downstream exon)
Score: 27

CAGGGTGGTCAAGAACCAGAGGTGACTGGATCACCTACAGAAAAGGCTATCCTGTCTTGGGGACTAAAGgtgcaaaaag ... atttctacagCTGGGTATGAAATTCAGTGAAACAAGATCGAAGTCATCTATTCTTCATGTATTTCCTTTCAACTCAGAGAAAAAGCGAGGCGGGGTTGCGGTGTACCTG


Block sizes: 43 (upstream exon), 47 (downstream exon)
Score: 158

CAGGGTGGTCAAGAACCAGAGGTGACTGGATCACCTACAGAAAAGGCTATCCTGTCTTGGGGACTAAAGgtgcaaaaag ... atttctacagCTGGGTATGAAATTCAGTGAAACAAGATCGAAGTCATCTATTCTTCATGTATTTCCTTTCAACTCAGAGAAAAAGCGAGGCGGGGTTGCGGTGTACCTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccttccatatgttgatctcttgctatcgctaatcgtggttgtcacatttctacagCTGGGTATGAAATTCAGTGAAACAAGATCGAAGTCATCTATTCTTCATGTATTTCCTTTCAACTCAGAGAAAAAGCGAGGCGGGGTTGCGGTGTACCTG
                          cgctaat  putative branch site (score: 158)
                                            catttct  putative PPT
      atatgtt  TA-rich tract