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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...actttctcactaaacatgcagctgattatttcattttcccatgtgcttttctatagaaattattcatctgaatctgattaagtctttctttacactttagATGTAAATACTGCCGCTGTAGCGAAGGAAGCATTGGAAGGGCATTGCATCTACGATGGCGGCTACTGTAAGCTTCACCTGTCATACTCCCGTCATACTGA

Basic information

species Zea mays
transcript GRMZM5G883601_T01
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G883601_T01 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os03g25980.1 (Oryza sativa), 3'ss of exon 8
----actttctcactaaacatgcagctgattatttcattttcccatgtgcttttctatagaaattattcatctgaatctgattaagtctttctttacactttagATGTAAATACTGCCGCTGTAGCGAAGGAAGCATTGGAAGGGCATTGCATCTACGATGGCGGCTACTGTAAGCTTCACCTGTCATACTCCCGTCATACTGA
    || |  | || |||||||    || |   || ||  |  ||||||||||   ||  | |   ||  ||   |||||| |   |  | | ||||  || |||||||| ||| ||  | || |||||||||||||||||||||||||||||||||||||| |||||||||||||| ||||||||||| || |||||||||||
ctttacatcgtaac-aaacatgtgcttgttctgtttatgatttcatgtgctttaa-attcagacattttttcatgatctgacttcat--tacattaccattcagATGTAACTACAGCTTCAGTTGCGAAGGAAGCATTGGAAGGGCATTGCATCTACGATGGTGGCTACTGTAAGCTCCACCTGTCATATTCTCGTCATACTGA

upper sequence: GRMZM5G883601_T01 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA09G37080.1 (Glycine max), 3'ss of exon 9
actttctcactaaacatgcagctgattatttcattttcccatg-tgcttttctatagaaattattcatctgaatctgattaagtcttt-ctttacactttagATGTAAATACTGCCGCTGTAGCGAAGGAAGCATTGGAAGGGCATTGCATCTACGATGGCGGCTACTGTAAGCTTCACCTGTCATACTCCCGTCATACTGA
    |   || |   |      | | ||   |   | |   |  || || |  ||  |   | ||  | ||    |||| | |  |   | ||    |  |||| | |  || ||  | |  || |  |||||  | || ||||||||||| || ||||| ||||| ||||||||||| || |||||||| |||||||||||
--aatggaaccaggtagcagatttactagcccccctcctgttcctggttcttgatgaagcatttttttttgttcttgatcatgagtaaacatttttttgcagATATCATAACGGCATCAGCTGCTAGAGAAGCTCTAGAGGGGCATTGCATATATGATGGTGGCTATTGTAAGCTTCATCTATCATACTCTCGTCATACTGA

upper sequence: GRMZM5G883601_T01 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA18G49580.1 (Glycine max), 3'ss of exon 8
actttctcactaaac-atgcagctgattatttcattttcccatgtgcttttctatagaaattattcatctgaatc--tgattaagtcttt-ctttacactttagATGTAAATACTGCCGCTGTAGCGAAGGAAGCATTGGAAGGGCATTGCATCTACGATGGCGGCTACTGTAAGCTTCACCTGTCATACTCCCGTCATACTGA-
        |   |||   | ||| ||||   |     |||  || |  |||||  |  ||  |||  | |   |   |||| | || |   | ||    |  |||| | |  || ||  | |  || |  |||||  | || ||||||||||| || ||||| ||||| ||||||||||| || |||||||| ||||||||||| 
-----ggaatggaactgggtagcagatttactagccctcctgtgcgtgtttcttgatgaaacatttgtttttgttcttgatcatgtgtaaacatttttttgcagaTATCATAACGGCATCAGCTGCTAGAGAAGCTCTAGAGGGGCATTGCATATATGATGGTGGCTATTGTAAGCTTCATCTATCATACTCTCGTCATACTGAT

upper sequence: GRMZM5G883601_T01 (Zea mays), 3'ss of exon 8
lower sequence: AT3G01150.2 (Arabidopsis thaliana), 3'ss of exon 6
-------------------------actttctcactaaacatgcagctgattatttcattt-tcccatgtgcttttctatagaaat-tattcatctg-aatctgattaagtctttctttacactttagATGTAAATACTGCCGCTGTAGCGAAGGAAGCATTGGAAGGGCATTGCATCTACGATGGCGGCTACTGTAAGCTTCACCTGTCATACTCCCGTCATACTGA
                         | | | | | |        |    |   ||| ||   | |       || | | |     |  | ||||||  | | |  |    ||| | |   | || ||||| ||   || || ||  | || || |||||| ||||||| || ||||| || || || ||||||||||||||||  || |||||||| |||||||||||
gtacatccgactgctgatctgcactaatgtttgattgtgacccgattcaaccgttttataaattctgaacatttatttgttactgtacaatcatcttcagtttcgtgctttctatttcgtctctgtagATATACCAACAGCAGCAATGGCCAAAGAAGCACTGGAAGGACACTGCATTTATGACGGTGGCTACTGTAAGCTTCGACTATCATACTCTCGTCATACTGA

upper sequence: GRMZM5G883601_T01 (Zea mays), 3'ss of exon 8
lower sequence: Vv14s0108g01030.t01 (Vitis vinifera), 3'ss of exon 8
---actttctcactaaacatgcagctgattattt-cattttcccatgtgcttttctatagaaattattcatctgaatctgattaagtctttctttacactttagATGTAAATACTGCCGCTGTAGCGAAGGAAGCATTGGAAGGGCATTGCATCTACGATGGCGGCTACTGTAAGCTTCACCTGTCATACTCCCGTCATACTGA
   | ||| |  |||       ||   ||  ||  || |||    | |  | |  |      | |  |   | ||     | | |    || ||| |  |  |||||| |  ||||| || || || || |||||  | || || || ||||| || ||||| ||||| ||||||||||| || |||||||| |||||||||||
tcaattttatttctaccaccatagggaatggttggcaattttatttata-tctcatccctccactgctgggcaga---caaatgatctgttgttttctttccagATGTCACAACTGCAGCAGTTGCCAAAGAAGCTCTAGAGGGACACTGCATATATGATGGTGGCTATTGTAAGCTTCATCTATCATACTCTCGTCATACTGA

upper sequence: GRMZM5G883601_T01 (Zea mays), 3'ss of exon 8
lower sequence: PP1S326_1V6.1 (Physcomitrella patens), 3'ss of exon 8
actttctcactaaacatgcagctg-attatttcattttcccatgtgcttttc-tatagaaattattcatctgaatctgattaagtctttctttacactttagATGTAAATACTGCCGCTGTAGCGAAGGAAGCATTGGAAGGGCATTGCATCTACGATGGCGGCTACTGTAAGCTTCACCTGTCATACTCCCGTCATACTGA
    | |||  |    ||    ||   |   |  |||      |  |||||  ||| |   |   |    |  | |   ||    |||| |||   ||  |||| |   |||||| | || ||| || |||||| | ||||| || ||||| ||||||||||| | ||| |||||||| || |||||||| || ||||||||
--agtgtcaagagctctgagattgtgctggatggtttattagcggccttttaatatggttctagctagcatccaacgagtttttgctttttttcttctacagATATTCCTACTGCAGTTGGAGCAAAAGAAGCACTCGAAGGTCACTGCATTTACGATGGCGGTTTCTGCAAGCTTCATCTATCATACTCTCGGCATACTGA

upper sequence: GRMZM5G883601_T01 (Zea mays), 3'ss of exon 8
lower sequence: PP1S81_184V6.1 (Physcomitrella patens), 3'ss of exon 8
actttctcactaaacatgcagctgattatttcattttcccatgtgcttttctatagaaattattcatctgaa--tctgattaagtctttctttacacttt---agATGTAAATACTGCCGCTGTAGCGAAGGAAGCATTGGAAGGGCATTGCATCTACGATGGCGGCTACTGTAAGCTTCACCTGTCATACTCCCGTCATACTGA
     |    |  |  |    ||||  |||     |  |  || |  ||   |   | |||||||   | |   ||| || |||| ||| |||   ||||   |||| |   |||||| | || ||| ||||| ||| | ||||| || ||||| |||||||| |||| ||| ||||||||||| || ||||| || ||||||||
-aacacgagttgcatgtaaccctgag-attgtgcgtagctttgggggttcgca---acattattctaataagcctctaatgaagtgttttttttttctttgttagATATTCCTACTGCAGTTGGAGCAAAGGAGGCACTTGAAGGTCACTGCATTTACGATGGAGGCTTCTGCAAGCTTCACCTATCTTACTCTCGGCATACTGA

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), 46 (downstream exon)
Score: 170

GTGTTCTCATCATTTGGTACAGTCCAGAAAATTGCTATTTTTGAGAAGAATGGGGGAACACAAGCTTTGATTCAGTACCCTGgtatgtgtct ... tacactttagATGTAAATACTGCCGCTGTAGCGAAGGAAGCATTGGAAGGGCATTGCATCTACGATGGCGGCTACTGTAAGCTTCACCTGTCATACTCCCGTCATACTGA


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 134

GTGTTCTCATCATTTGGTACAGTCCAGAAAATTGCTATTTTTGAGAAGAATGGGGGAACACAAGCTTTGATTCAGTACCCTGgtatgtgtct ... tacactttagATGTAAATACTGCCGCTGTAGCGAAGGAAGCATTGGAAGGGCATTGCATCTACGATGGCGGCTACTGTAAGCTTCACCTGTCATACTCCCGTCATACTGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 134

GTGTTCTCATCATTTGGTACAGTCCAGAAAATTGCTATTTTTGAGAAGAATGGGGGAACACAAGCTTTGATTCAGTACCCTGgtatgtgtct ... tacactttagATGTAAATACTGCCGCTGTAGCGAAGGAAGCATTGGAAGGGCATTGCATCTACGATGGCGGCTACTGTAAGCTTCACCTGTCATACTCCCGTCATACTGA


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 180

GTGTTCTCATCATTTGGTACAGTCCAGAAAATTGCTATTTTTGAGAAGAATGGGGGAACACAAGCTTTGATTCAGTACCCTGgtatgtgtct ... tacactttagATGTAAATACTGCCGCTGTAGCGAAGGAAGCATTGGAAGGGCATTGCATCTACGATGGCGGCTACTGTAAGCTTCACCTGTCATACTCCCGTCATACTGA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttttctatagaaattattcatctgaatctgattaagtctttctttacactttagATGTAAATACTGCCGCTGTAGCGAAGGAAGCATTGGAAGGGCATTGCATCTACGATGGCGGCTACTGTAAGCTTCACCTGTCATACTCCCGTCATACTGA
                          atctgat  putative branch site (score: 180)
                                     tctttctttacacttt  putative PPT
      tatagaaattattcat  TA-rich tract