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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...caagcttctccgtagtctgcttccgttgtcctacgaacttctcgactactttcgtaatatgtaaagaatgtcttaataacttttctaacctgttttgcagGTTCATCTGGATCACAAGCACATGGGCATCGGCGGTGACGACAGCTGGACACCATGTGTGCACCCCCAGTACCTTTTGCCTCCAGAATTATACCATTTCT

Basic information

species Physcomitrella patens
transcript PP1S130_43V6.1
intron # 17
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S130_43V6.1 (Physcomitrella patens), 3'ss of exon 17
lower sequence: LOC_Os01g72340.2 (Oryza sativa), 3'ss of exon 17
------------------------------caagcttctccgtagtctgc---ttccgttg------tcctacgaacttctcga---ctactttcg--taatatgtaaagaatgtcttaataacttttctaacctgttttgcagGTTCATCTGGATCACAAGCACATGGGCATCGGCGGTGACGACAGCTGGACACCATGTGTGCACCCCCAGTACCTTTTGCCTCCAGAATTATACCATTTCT
                               ||||||    | | ||  |   || | ||       |  ||  |   |  |||   | ||||| |  |   || |   ||   | | |   |    |      ||| |||||||| ||||| |||||||||||||||||  | || || |||||||||||| | || || ||||||   |||||| |  |||| || |    ||||   ||||
gttcgcatttgcactgtgtttagataaacaaaagctttattgaactcaacgaattacattaagatgatgatagaattgtaccgataacaacttttgattgtgatttggcgatgatttcagagagaaattgggtttgtgttgcagGTGCATCTTGATCACAAGCACATGGGGCTGGGAGGGGACGACAGCTGGTCGCCGTGCGTGCACGAGCAGTACTTGCTGCCGCCGGCGAGATACGCCTTCT

upper sequence: PP1S130_43V6.1 (Physcomitrella patens), 3'ss of exon 17
lower sequence: LOC_Os01g72340.1 (Oryza sativa), 3'ss of exon 17
----------------------------------caagcttctccgtagtctgc---ttccgttg------tcctacgaacttctcga---ctactttcg--taatatgtaaagaatgtcttaataacttttctaacctgttttgcagGTTCATCTGGATCACAAGCACATGGGCATCGGCGGTGACGACAGCTGGACACCATGTGTGCACCCCCAGTACCTTTTGCCTCCAGAATTATACCATTTCT
                                   ||||||    | | ||  |   || | ||       |  ||  |   |  |||   | ||||| |  |   || |   ||   | | |   |    |      ||| |||||||| ||||| |||||||||||||||||  | || || |||||||||||| | || || ||||||   |||||| |  |||| || |    ||||   ||||
gtgggttcgcatttgcactgtgtttagataaacaaaagctttattgaactcaacgaattacattaagatgatgatagaattgtaccgataacaacttttgattgtgatttggcgatgatttcagagagaaattgggtttgtgttgcagGTGCATCTTGATCACAAGCACATGGGGCTGGGAGGGGACGACAGCTGGTCGCCGTGCGTGCACGAGCAGTACTTGCTGCCGCCGGCGAGATACGCCTTCT

upper sequence: PP1S130_43V6.1 (Physcomitrella patens), 3'ss of exon 17
lower sequence: GLYMA15G37670.1 (Glycine max), 3'ss of exon 11
caagcttctccgtagtctgcttccgttgtcctacgaacttctcgactactttcgtaatatgtaaagaatgtcttaataacttttctaacctgt---tttgcagGTTCATCTGGATCACAAGCACATGGGCATCGGCGGTGACGACAGCTGGACACCATGTGTGCACCCCCAGTACCTTTTGCCTCCAGAATTATACCATTTCT
    | | |    ||          |     | | || || |       |||  | ||   ||  |      ||| ||  |||  |  | | |    |  ||| |||||||||||||||||||||||||  | || || || || || ||| |||||||||| |||   |||||  |  | ||||| |    ||||   ||||
---tcctatttacaggaactaaaaatatatttcccaaattattattattttttattattattattgtgcagtttattatgtttaatgtcttatgggatcacagATTCATCTGGATCACAAGCACATGGGATTGGGTGGAGATGATAGTTGGTCACCATGTGTCCACAAACAGTATTTGATTCCTCCTGTGCCATACTCATTCT

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: 29 (upstream exon), 23 (downstream exon)
Score: 5

AGACAGTCCACCAATGCAGATGAGTGCTAGCTTCTACACAAGCCAAGAGCTTGACCGAGCTACACATGAGGAGGAGCTCCAACAAGGGGATAAAATTGAGgtatgcattt ... tgttttgcagGTTCATCTGGATCACAAGCACATGGGCATCGGCGGTGACGACAGCTGGACACCATGTGTGCACCCCCAGTACCTTTTGCCTCCAGAATTATACCATTTCT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctactttcgtaatatgtaaagaatgtcttaataacttttctaacctgttttgcagGTTCATCTGGATCACAAGCACATGGGCATCGGCGGTGACGACAGCTGGACACCATGTGTGCACCCCCAGTACCTTTTGCCTCCAGAATTATACCATTTCT
                                     ttctaac  putative branch site (score: 5)
                                           cctgtttt  CT-rich tract
                           ttaataacttttctaa  TA-rich tract