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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CATCGGAACCTTGTGAGGTTAATTGGTATCTGCACCGAGCAAATTCGATGCTTGGTTTATGAACTCATAACGAATGGGAGTGTGGAATCTCATTTGCATGgtatgtaattctgttcactgaataacttgtcagaatcttcttcgatgattagagtcaagtgtgagtccgaaccgtctgaaataccaagaaattctgtaca...

Basic information

species Physcomitrella patens
transcript PP1S43_35V6.1
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S43_35V6.1 (Physcomitrella patens), 5'ss of exon 1
lower sequence: LOC_Os01g09860.1 (Oryza sativa), 5'ss of exon 12
CATCGGAACCTTGTGAGGTTAATTGGTATCTGCACCGAGCAAA---TTCGATGCTTGGTTTATGAACTCATAACGAATGGGAGTGTGGAATCTCATTTGCATGgtatgtaattctgttcactgaataacttgtcagaatcttcttcgatgattagagtcaagtgtgagtccgaaccgtctgaaataccaagaaattctgtaca
   || ||  | || | |||  | || || ||    ||| | |      ||||  ||||||||||||| ||  ||||||| ||||| ||||| ||||||||||||| ||| ||              ||  | | | |   | ||     ||| || | ||   |  | |     | | || |                    
---CGAAATTTGGTCAAGTTGTTAGGCATATGTGTAGAGGAGAACGCAAGATGTCTGGTTTATGAACTTATTCCGAATGGCAGTGTAGAATCCCATTTGCATGgtaagtacttgaagaattaaggccaccagcctgtaaagt-ttaagcaatt-gactgaaagatctgcctttgacttttgtag-------------------

upper sequence: PP1S43_35V6.1 (Physcomitrella patens), 5'ss of exon 1
lower sequence: GRMZM2G330298_T01 (Zea mays), 5'ss of exon 5
CATCGGAACCTTGTGAGGTTAATTGGTATCTGCACCGAG---CAAATTCGATGCTTGGTTTATGAACTCATAACGAATGGGAGTGTGGAATCTCATTTGCATGgta--tgtaattctgttcactgaata-acttgtcagaatcttcttcgatgattagagtcaagtgtgagtccgaacc--gtc--tgaaataccaagaaattctgtaca
    ||||| | || | | | || ||||| ||||| |||   || |  ||||| ||||||||||| ||  |  ||||||| |||||||||||||| ||||||||||  | |  |||||| |  | | |  ||||   |     ||||||  |   |    | |  | |   ||  ||    |||  |  | |  |||||  |        
---AGGAACTTGGTTAAGCTGATAGGTATATGCACAGAGGGGCATAGCCGATGTTTGGTTTATGAGCTTGTTCCGAATGGCAGTGTGGAATCTCACTTGCATGgtaaatttccttctgtgccgtaacttcactttctaaggctttcttcatttcatcatataacttctctttcttaatttagtcattttattggcaagaggtg-------

upper sequence: PP1S43_35V6.1 (Physcomitrella patens), 5'ss of exon 1
lower sequence: GLYMA09G07140.1 (Glycine max), 5'ss of exon 8
CATCGGAACCTTGTGAGGTTAATTGGTATCTGCACCGAG--CAAATTC-GATGCTTGGTTTATGAACTCATAACGAATGGGAGTGTGGAATCTCATTTGCATGgtatgtaattctgttcactgaataacttgtcagaatcttcttcgatgattagagtcaagtgtgagtccgaaccgtctgaaataccaagaaattctgtaca
    | ||| | || | ||| |||||||| ||| | |||  ||  ||| | ||  | ||||||||||||||  | ||||| ||||||||||| ||||| |||||||  ||| | |  |   ||| | | |    || | |    |   || ||||     |  |  | |  |     ||| |  ||    |   |   |||  
---AGAAACTTGGTTAAGTTGATTGGTATATGCGCAGAGGTCAGCTTCCGCTGTCTAGTTTATGAACTCATTCCAAATGGCAGTGTGGAATCCCATTTACATGgtacttaacttttct---tgattcagtctgaagtaccactctgattgtttagttcttaaagataat--ggtttttctta--tatttggtcttctggtag-

upper sequence: PP1S43_35V6.1 (Physcomitrella patens), 5'ss of exon 1
lower sequence: GLYMA15G18470.1 (Glycine max), 5'ss of exon 7
CATCGGAACCTTGTGAGGTTAATTGGTATCTGCACCGAG--CAAATTC-GATGCTTGGTTTATGAACTCATAACGAATGGGAGTGTGGAATCTCATTTGCATGgtatgtaattctgttcactgaataacttgtcagaatcttcttcgatgattagagtcaagtgtgagtccgaaccgtctgaaataccaagaaattctgtaca
    | ||| | || | ||| |||||||| ||| | |||  ||  ||| | || || ||||||||||||||  | ||||| ||||||||||| ||||| |||||||  ||| | |  |   ||| | | |    || | | |      || |||| |      |  | |        ||| |  ||    |   |   |||  
---AGAAACTTGGTTAAGTTGATTGGTATATGCGCAGAGGTCAGCTTCCGCTGTTTAGTTTATGAACTCATTCCAAATGGCAGTGTGGAATCCCATTTACATGgtacctaacttttct---tgattcagtctcgagtaccattccaattgtttagtgctttaagataat---ggttttctta--tatttggtcttctggtag-

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: 32 (upstream exon), 13 (downstream exon)
Score: 3

CATCGGAACCTTGTGAGGTTAATTGGTATCTGCACCGAGCAAATTCGATGCTTGGTTTATGAACTCATAACGAATGGGAGTGTGGAATCTCATTTGCATGgtatgtaatt ... taatctgcagGTTTAGACAAATACACAGCTCCTCTCAACTGGGAGGCACGTGTCAAAATTGCTCTGGGATCTGCACGCGGGCTGGCATACCTACATGAGGATTCCCAGCC




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