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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttattccgaccctcaattctgctgggacactaattacttccagctgtgacgtcgtgaatgacggtgtaaccattagagctgtaatcgctgcagttttttattttattattattattattattattttcaaaattactttttctgcagACTGCTGCGAGTTATCACGCTATCGCAATTGCGCTTTCCCTGATGGAGGCGTACTCCCTCAGTGTCCAGCATGAACAAACCACCTTACAGATTTTACAAG

Basic information

species Physcomitrella patens
transcript PP1S363_15V6.1
intron # 15
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S363_15V6.1 (Physcomitrella patens), 3'ss of exon 15
lower sequence: LOC_Os04g55230.1 (Oryza sativa), 3'ss of exon 19
gtttattccgaccctcaattctgctgggacactaattacttccagctgtgacgtcgtgaatgacggtgtaaccattagagctgtaatcgctgcagttttttattttattatt--attattattattattttcaaaattactttttctgcagACTGCTGCGAGTTATCACGCTATCGCAATTGCGCTTTCCCTGATGGAGGCGTACTCCCTCAGTGTCCAGCATGAACAAACCACCTTACAGATTTTACAAG
                                                | | |     ||  ||||   |||  | |  |  ||| | | |   |  | | ||    | |||   |||  || | | ||     | ||  ||   |  |||||||||||||| ||||| || || || || || || ||  ||||||| || |||||| | ||||| ||||||||||| ||||||||||||||  | || |
------------------------------------------------taatgcatgtaactacgg-acaact-tcaatggcgtatttgttat-gcatatgatcccgtgattcagttaacatgaattttcatgcatttctttgaacaacagACTGCTGCGAGCTATCATGCCATAGCCATAGCCCTCTCAATGATGGATGCATACTCCTTGAGTGTTCAGCATGAACAGACCACCTTACAGATACTTCAGG

upper sequence: PP1S363_15V6.1 (Physcomitrella patens), 3'ss of exon 15
lower sequence: GRMZM5G892758_T01 (Zea mays), 3'ss of exon 2
gtttattccgaccctcaattctgctgggacactaattacttccagctgtgacgtcgtgaatgacggtgtaaccattagagctgtaatcgctgcagttttttattttattattattattattattattttcaaaattactttttctgcagACTGCTGCGAGTTATCACGCTATCGCAATTGCGCTTTCCCTGATGGAGGCGTACTCCCTCAGTGTCCAGCATGAACAAACCACCTTACAGATTTTACAAG
                                     || |  |  | | |     ||||| |     | |  | | | |   |    | |  | ||  ||| | |    | |  |  | | || |||    ||| | |       ||||||||||| || || || ||||| || || || |||||  ||||||| ||||||||||| ||||| || ||||||||||| ||| | |||||  | || |
------------------------------------cacctg-atttataattcattgaataatatgatgaataattgggtcctg--tgatttaattacttactatgaactaacaagcaattttttttc---aatcaat-------cagACTGCTGCAAGCTACCATGCTATAGCCATAGCCCTTTCAATGATGGATGCGTACTCCCTAAGTGTGCAACATGAACAAACAACCATGCAGATACTTCAGG

upper sequence: PP1S363_15V6.1 (Physcomitrella patens), 3'ss of exon 15
lower sequence: GLYMA04G24430.1 (Glycine max), 3'ss of exon 19
gtttattccgaccctcaattctgctgggacactaattacttccagctgtgacgtcgtgaatgacggtgtaaccattagagctgtaatcgctgcagttttttattttattattattattattattattttcaaaattactt-tttctgcagACTGCTGCGAGTTATCACGCTATCGCAATTGCGCTTTCCCTGATGGAGGCGTACTCCCTCAGTGTCCAGCATGAACAAACCACCTTACAGATTTTACAAG
                                                                                                        |  ||   ||| |||  | |  ||| | ||||| ||  || | ||||||||||| || ||||| || || || ||||| |||||  ||||||| || ||||| || ||||| ||||||||||| |||||| | || ||  | || |
-------------------------------------------------------------------------------------------------------gtagttggcattttta--acttgttttataattatttactttttcagACTGCTGCAAGCTATCATGCAATAGCTATTGCTCTTTCTTTGATGGAAGCATACTCTCTAAGTGTTCAGCATGAACAGACCACCCTCCAAATCCTGCAGG

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: 31 (upstream exon), 34 (downstream exon)
Score: 6

GATGATGGAAGAGGGCCTGGGAAACATTCATGTTGCTCTGAGGTATTTACACGAGGCTCTGATCTGCAATCAGCGGCTTCTGGGAGCTGACCACATTCAGgtttattccg ... ttttctgcagACTGCTGCGAGTTATCACGCTATCGCAATTGCGCTTTCCCTGATGGAGGCGTACTCCCTCAGTGTCCAGCATGAACAAACCACCTTACAGATTTTACAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttttttattttattattattattattattattttcaaaattactttttctgcagACTGCTGCGAGTTATCACGCTATCGCAATTGCGCTTTCCCTGATGGAGGCGTACTCCCTCAGTGTCCAGCATGAACAAACCACCTTACAGATTTTACAAG
                                        ttactttttct  CT-rich tract
     ttattttattattatt  TA-rich tract