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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agcttaacgtactattttcaagtgatttcactgctagatttctctcagatttcattcagtctaaaggaattgagtgaatcgattggatgtttttgagcagATCATTGCCTCAAATGGAGAAACTGTGAAGTGGACTACTCCTCTTGGACTTCCCGTTGTGCAACCTTACCGCAAGCCTGGCAGACATTTG

Basic information

species Physcomitrella patens
transcript PP1S256_41V6.1
intron # 15
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S256_41V6.1 (Physcomitrella patens), 3'ss of exon 15
lower sequence: GLYMA18G51160.1 (Glycine max), 3'ss of exon 14
-----------agcttaacgtact-attttcaagtg-atttcactgctagatt------tctctcagatttcat-tcagtctaaag---gaattgagtgaat-cgattggatgtttttgagcagATCATTGCCTCAAATGGAGAAACTGTGAAGTGGACTACTCCTCTTGGACTTCCCGTTGTGCAACCTTACCGCAAGCCTGGCAGACATTTG
             || |  ||||| |  | |  |||  |||   |   | |||       |   |||   | |  ||||| ||| |    | ||   ||| |  || |       ||||| ||| | ||||| ||  |     || | |||   ||||| ||||||||||||||||| || |||||||||||||| || |  || |  ||| | 
gtatgttgcattactcattgtactgacatgcgtgtgtgtttggatagaaaattggttaagccgacagtgatgacatcagtataaggtgtcacttatatgattatgactaagacaatttgaacagGTAATTGCTTCTGAAAATCAACCAGTGCGCTGGACCACTCCTCTTGGACTTCCTGTGGTGCAACCTTACCGTAAACTAGGAAAGCATATT

upper sequence: PP1S256_41V6.1 (Physcomitrella patens), 3'ss of exon 15
lower sequence: Vv14s0083g00790.t01 (Vitis vinifera), 3'ss of exon 14
agcttaacgtactattttcaagtgatttcactgctagatttctctcagat-ttcattcagtctaaaggaattgagtgaatcgattggatgtttttgagcagATCATTGCCTCAAATGGAGAAACTGTGAAGTGGACTACTCCTCTTGGACTTCCCGTTGTGCAACCTTACCGCAAGCCTGGCAGACATTTG
    |  |   || | |     |   |      ||  || | | | |  | |  ||  | |        | | | ||| |  |  |  ||    ||| ||||| ||||| ||  |     |  ||||||  |||||||| || ||||||||||| || |||||||||||||||||    || || ||||||
tctctctctctctctctctctctctctctctctctccatgtgtgtgaattatgtatataattgttgttgactaa-tgactgtagagtttgaacatgaacagATAATTGCATCGGAAAATCAGCCTGTGAGATGGACTACACCACTTGGACTTCCTGTAGTGCAACCTTACCGCAAATTAGGGAGGCATTTG

upper sequence: PP1S256_41V6.1 (Physcomitrella patens), 3'ss of exon 15
lower sequence: Vv01s0010g00690.t01 (Vitis vinifera), 3'ss of exon 14
----agcttaacgtactattttcaagtg-atttcactgctagatttctctcagatttcattcagtctaaaggaattgagtgaatcgattggatgtttttgagcagATCATTGCCTCAAATGGAGAAACTGTGAAGTGGACTACTCCTCTTGGACTTCCCGTTGTGCAACCTTACCGCAAGCCTGGCAGACATTTG
     ||||||  | |    ||    || || | | |  |  |  |   || |      ||| ||  | ||  | |   | |   ||||  |   |||   |||| | || || ||  |     |  | |||  ||||| ||||||| | |||||||| ||||||||||| ||||||||    || || ||| | 
ttggtgcttaaaattcccccttattctgtatcttatttttcaaactaattctgtgacatttccgt--acagtcacttccttacatgattaaaatattt---gcagGTGATAGCTTCTGAGAATCATCCAGTGCGGTGGAATACTCCTTTGGGACTTCCTGTTGTGCAACCCTACCGCAAATTAGGAAGGCATCTT

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 1 RNA-Seqlibrary.


Block sizes: 19 (upstream exon), 17 (downstream exon)
Score: 1

ACAACGTTAAACGCATTGGGAGAGATGTTCAAAGAAGCTCGTTGCATTATGAGCTGGCTTGGAGACTGTGCGAAGgtgagatcta ... ttttgagcagATCATTGCCTCAAATGGAGAAACTGTGAAGTGGACTACTCCTCTTGGACTTCCCGTTGTGCAACCTTACCGCAAGCCTGGCAGACATTTG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cagatttcattcagtctaaaggaattgagtgaatcgattggatgtttttgagcagATCATTGCCTCAAATGGAGAAACTGTGAAGTGGACTACTCCTCTTGGACTTCCCGTTGTGCAACCTTACCGCAAGCCTGGCAGACATTTG
             gtctaaa  putative branch site (score: 1)
                                          tgttttt  putative PPT
                                         atgttttt  TA-rich tract