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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgaggctctttccccccctcccctcccccttgtcttgatttgtagttgccattcctgttttggcggttgggagcgactgttttgcttttgagctatattttgattctgtgtaattttcgtacatgcagTGGAACTGTTCGCTATGCGAGTGTGCATGCACACATGGGAAGGACTGAGAGTAGGAAGGACGACTTGGGATCATTGGCTTATACTTTGATATTCCTTATG

Basic information

species Physcomitrella patens
transcript PP1S251_2V6.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S251_2V6.1 (Physcomitrella patens), 3'ss of exon 6
lower sequence: LOC_Os05g11140.1 (Oryza sativa), 3'ss of exon 8
gtgaggctctttccccccctcccctcccccttgtcttgatttgtagttgccattcctgttttggcggttgggagcgactgttttgcttttg--agctatattttgattctgtgtaattttcgtacatgcagTGGAACTGTTCGCTATGCGAGTGTGCATGCACACATGGGAAGGACTGAGAGTAGGAAGGACGACTTGGGATCATTGGCTTATACTTTGATATTCCTTATG
                                   |||    | || | |  |            |      |||    | ||| ||| ||  |   |||   ||| |     || |  |         || ||||||||||||||||| ||||||||||| ||| | ||||| ||||  || || |  || ||  | | |||  | || |||||  |  | || ||| | 
---------------------------------gtttgtgagggagatactttattgaaaactaagtcctaaagccctcgattttcttgtgttactaataaactgacttgtcatactgattacctgaaaagGGGAACTGTTCGCTATGCTAGTGTGCATGCTCACTTAGGAAGAACTGGAAGCAGAAGAGATGATCTTGAATCCCTTGCCTATACACTTGTTTTTCTTTTA

upper sequence: PP1S251_2V6.1 (Physcomitrella patens), 3'ss of exon 6
lower sequence: GRMZM2G158177_T01 (Zea mays), 3'ss of exon 1
gtgaggctctttccccccctcccctcccccttgtcttgatttgtagttgccattcctgttttggcggttgggagcgactgttttgcttttgagctatattttgattctgtgtaattttcgtacatgcagTGGAACTGTTCGCTATGCGAGTGTGCATGCACACATGGGAAGGACTGAGAGTAGGAAGGACGACTTGGGATCATTGGCTTATACTTTGATATTCCTTATG
                                       || ||  |||  | |  |  ||||  |      |         ||  ||    |  ||| |||     | |||| ||     | |  ||| ||||||||||||||||| ||||||||||| ||| ||||||| |||| ||||||||  || ||  | | |||  | || || ||  | || || ||| | 
--------------------------------------gttcgt--ttgggaatattagtttgatgtgctttactactcacattatttcattggaatacttttgacatttgtatttgcttcataaacagGGGAACTGTTCGCTATGCTAGTGTGCATGCTCACTTGGGAAGAACTGGGAGTAGGAGAGATGATCTTGAATCCCTTGCATACACGCTTATTTTTCTTCTA

upper sequence: PP1S251_2V6.1 (Physcomitrella patens), 3'ss of exon 6
lower sequence: GRMZM2G045259_T02 (Zea mays), 3'ss of exon 8
gtgaggctctttccccccctcccctcccccttgtcttgatttgtagttgccattcctgttttggcggttgggagcgactgttttgcttttgagctatattttgattctgtgtaattttcgtacatgcagTGGAACTGTTCGCTATGCGAGTGTGCATGCACACATGGGAAGGACTGAGAGTAGGAAGGACGACTTGGGATCATTGGCTTATACTTTGATATTCCTTATG
                                         |   ||||  | |  |  | ||         | |       ||  ||    |  ||| |||     | |||  ||     | |  ||| ||||||||||||||||| || |||||||| ||| ||||||| |||| ||||||||  || ||  | | |||  | || || ||| | || || ||| | 
----------------------------------------gttcggttgggaatattagtatgatatgctttaccactcacgttatttcattga-atacttttgacatttgtgtttgcttcataaacagGGGAACTGTTCGCTATGCTAGCGTGCATGCCCACTTGGGAAGAACTGGGAGTAGGAGAGATGATCTTGAATCCCTCGCATACACTCTTATTTTTCTTCTC

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: 34 (upstream exon), 15 (downstream exon)
Score: 13

CTACTCGATGGAGGGATGGTACAACCGGTCAGCATGTAGAATATGACCAAAGGCCTGATGTGTTCCGgtgaggctct ... gtacatgcagTGGAACTGTTCGCTATGCGAGTGTGCATGCACACATGGGAAGGACTGAGAGTAGGAAGGACGACTTGGGATCATTGGCTTATACTTTGATATTCCTTATG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cgactgttttgcttttgagctatattttgattctgtgtaattttcgtacatgcagTGGAACTGTTCGCTATGCGAGTGTGCATGCACACATGGGAAGGACTGAGAGTAGGAAGGACGACTTGGGATCATTGGCTTATACTTTGATATTCCTTATG
                        ttttgat  putative branch site (score: 13)
                                        ttttcgt  putative PPT
                    tatattttgattct  TA-rich tract