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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGATAAAAGCTTGGCTCTATGATCTCCTTGGATCTAGAGTTGACTACGATGCACCTGGTCATTGGTGCACTACAATGGCTTACAGTGCTGACGGCACTAGgtattccaaactttaatctcctttcttacgttttgaagttatttggtgtgcacaactaaacgctctatccaagatcaatgtgcgtggttttcttgtagca...

Basic information

species Physcomitrella patens
transcript PP1S316_34V6.1
intron # 14
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S316_34V6.1 (Physcomitrella patens), 5'ss of exon 14
lower sequence: LOC_Os08g06480.1 (Oryza sativa), 5'ss of exon 14
AGATAAAAGCTTGGCTCTATGATCTCCTTGGATCTAGAGTTGACTACGATGCACCTGGTCATTGGTGCACTACAATGGCTTACAGTGCTGACGGCACTAGgtatt------ccaaactttaatctcctttcttacgttttgaagttatttggtgtgcacaactaaacgctctatccaagatcaatgtgcgtggttttcttgtagca
| || || || ||| | |||||     | || || || |||||||| ||||| ||||| |||||||| ||||| ||||||||||||||||| || || ||||  |      |   |  | ||| ||   |  ||  | || |||  | |   | |      ||||||  ||    |||  | | ||    |  |       |||  
AAATTAAGGCATGGTTATATGACTGTTTGGGCTCAAGGGTTGACTATGATGCTCCTGGACATTGGTGTACTACCATGGCTTACAGTGCTGATGGAACAAGgtgatgagacactgcaaatgaatatcagctgctaattgttcaagacaat-aatata-gtttctaaaccttca---caaattaagtgaatatattgaataaatagt-

upper sequence: PP1S316_34V6.1 (Physcomitrella patens), 5'ss of exon 14
lower sequence: LOC_Os03g14980.1 (Oryza sativa), 5'ss of exon 15
AGATAAAAGCTTGGCTCTATGATCTCCTTGGATCTAGAGTTGACTACGATGCACCTGGTCATTGGTGCACTACAATGGCTTACAGTGCTGACGGCACTAGgtattccaaactttaatctcctttcttacgttttgaagttatttggtgtgcacaactaaacgctctatccaagatcaatgtgcgtggttttctt-gtagca
||||||| |||||||| ||||||    | ||||| ||||||||||| ||||| || || ||||||||||| |||||||| || ||||| || ||  | ||||  ||  || |   || || ||  |  | |     | | || |||    |     |     || | |      | | | |   ||   || |  ||||  
AGATAAAGGCTTGGCTATATGATAATTTGGGATCCAGAGTTGACTATGATGCGCCAGGACATTGGTGCACAACAATGGCATATAGTGCAGATGGTTCAAGgt--tcataatt---atttctttgttagcat----gattcatgtgggtaactgggtttttgtctttgttttcactgattctttttgcccttgtgagtag--

upper sequence: PP1S316_34V6.1 (Physcomitrella patens), 5'ss of exon 14
lower sequence: GRMZM2G030422_T01 (Zea mays), 5'ss of exon 15
AGATAAAAGCTTGGCTCTATGATCTCCTTGGATCTAGAGTTGACTACGATGCACCTGGTCATTGGTGCACTACAATGGCTTACAGTGCTGACGGCACTAGgtattccaaactttaatctcctttcttacgttttgaagttatttggtgtgcacaactaaacgctctatccaagatcaatgtgcgtggttttcttgtagca
|||| || || ||||| ||||||    | ||||||||||||||||| |||||||| ||||||||||||||||||||||| || ||||| || ||  | |||| | |     |    | ||  |||||     | | |||   | || ||    || |  |  ||    | ||     || || ||  |||     |||  
AGATCAAGGCATGGCTATATGATAATTTGGGATCTAGAGTTGACTATGATGCACCAGGTCATTGGTGCACTACAATGGCATATAGTGCAGATGGTTCAAGgt-tcctgctttcctttttctgttcttgaaggtagtagtatgtgggcgtttttaattccagccttccgctaa-----atttgtgtcttttatgcatag--

upper sequence: PP1S316_34V6.1 (Physcomitrella patens), 5'ss of exon 14
lower sequence: GRMZM2G042992_T01 (Zea mays), 5'ss of exon 14
AGATAAAAGCTTGGCTCTATGATCTCCTTGGATCTAGAGTTGACTACGATGCACCTGGTCATTGGTGCACTACAATGGCTTACAGTGCTGACGGCACTAGgtattccaaactttaatctcctttcttacgttttgaagttatttggtgtgcacaactaaacgctctatccaagatcaatgtgcgtggttttcttgtagca
| || || || ||| | ||||||  | | || || ||||||||||| ||||| ||||| |||||||| ||||| ||||||||||||||||| || || ||||    || |    |   |  |    ||   ||| |  |    || || | |       ||   ||||  ||| ||    | | |  |||||||| ||  
AAATCAAGGCATGGTTGTATGATTGCTTGGGCTCAAGAGTTGACTATGATGCTCCTGGACATTGGTGTACTACCATGGCTTACAGTGCTGATGGGACAAGgtgaaacatagcaaa---tgttaatataaagtttaatatctgctgatgagta-------acaaactatataagttcttgatccatt-ttttcttgcag--

upper sequence: PP1S316_34V6.1 (Physcomitrella patens), 5'ss of exon 14
lower sequence: GLYMA10G29090.1 (Glycine max), 5'ss of exon 15
AGATAAAAGCTTGGCTCTATGATCTCCTTGGATCTAGAGTTGACTACGATGCACCTGGTCATTGGTGCACTACAATGGCTTACAGTGCTGACGGCACTAGgtattccaaactttaatctcctttcttacgttttgaagttatttggtgtgcacaactaaacgctctatccaagat-caatgtgcgtggttttcttgtagca----------------------
| ||||| || ||||| || |||  | | || ||||| |||||||| ||||| |||||||| |||||||||||||||  |||||||||||| || ||||||||      |  |  ||     |  |||    || |   |||    ||       ||    |  |  |  |||||  | | |       |||||| |  ||                      
AAATAAAGGCATGGCTATACGATAACATGGGTTCTAGGGTTGACTATGATGCCCCTGGTCACTGGTGCACTACAATGCTTTACAGTGCTGATGGAACTAGgtaagttggatatggatgagggtaattattcctttacagtatc--atgcttggtgcttggtggac-gtttaagatgtattatattaaagtttcttatgacattttccaaaatattttctccag

upper sequence: PP1S316_34V6.1 (Physcomitrella patens), 5'ss of exon 14
lower sequence: GLYMA20G38230.1 (Glycine max), 5'ss of exon 15
AGATAAAAGCTTGGCTCTATGATCTCCTTGGATCTAGAGTTGACTACGATGCACCTGGTCATTGGTGCACTACAATGGCTTACAGTGCTGACGGCACTAGgtattccaaactttaatct---cctttcttacgttttgaagttatttggtgtgcacaactaa-acgctctatccaagatcaatgtgcgtggttttcttgtagca----------
| ||||| || ||| | || |||  | | || ||||| |||||||| ||||| |||||||| |||||||||||||||  ||||||||| || || ||||||||      | ||  ||        || ||  |||      | ||      || | || ||| | |   |||   | |      |  |    ||||    |  |          
AAATAAAGGCATGGTTATACGATAACATGGGTTCTAGGGTTGACTATGATGCCCCTGGTCACTGGTGCACTACAATGCTTTACAGTGCAGATGGAACTAGgtaagatggatttggatgagggtaattattcggttacagtatcatgctcaatggataattaagatgtattatattaaagtttcttatgacactttccaa-aatattttctccag

upper sequence: PP1S316_34V6.1 (Physcomitrella patens), 5'ss of exon 14
lower sequence: GLYMA17G12110.1 (Glycine max), 5'ss of exon 15
AGATAAAAGCTTGGCTCTATGATCTCCTTGGATCTAGAGTTGACTACGATGCACCTGGTCATTGGTGCACTACAATGGCTTACAGTGCTGACGGCACTAGgt--attccaaactttaatctcctttcttacgttttgaagttatttggtgtgcac-aactaaacgctctatccaagatcaatgtgcgtggttttcttgtagca
| |||||||| ||| | ||||||  | | || ||||| |||||||| ||||||||||||||||  |  ||||||||||| || |||||||| || || ||||  |     || | |  |  |  ||||||  ||     | | | |    ||||  || ||     | |||         || ||  |||||||         
AAATAAAAGCATGGTTGTATGATAACATGGGTTCTAGGGTTGACTATGATGCACCTGGTCATTCTTCTACTACAATGGCATATAGTGCTGATGGAACAAGgttaagagataaatgtttttcctcttcttatcttcccttgctctgtttgatgcatgaattagtttatttattttcttattatatgtctggtttttag------

upper sequence: PP1S316_34V6.1 (Physcomitrella patens), 5'ss of exon 14
lower sequence: GLYMA13G22720.1 (Glycine max), 5'ss of exon 15
AGATAAAAGCTTGGCTCTATGATCTCCTTGGATCTAGAGTTGACTACGATGCACCTGGTCATTGGTGCACTACAATGGCTTACAGTGCTGACGGCACTAGgtattccaaactttaatctcctttcttacgttttgaagttatttggtgtgcacaactaaacgctctatccaagatcaatgtgcgtggttttcttgtagca
| |||||||| ||| | ||||||  | | || ||||| |||||||| ||||||||||||||||  |  ||||||||||| || |||||||| || || ||||      |    |  | | | |  ||   | ||    ||  |  || ||    |  ||    | ||   |   ||    |   ||  |   || |||  
AAATAAAAGCATGGTTGTATGATAACATGGGTTCTAGGGTTGACTATGATGCACCTGGTCATTCTTCTACTACAATGGCATATAGTGCTGATGGAACAAGgttaaaagataaatgtttttcctctttttatcttccc-ttgctctgtttgatgcatgaattagtttaatgattttcttattatatgtctggtttatag--

upper sequence: PP1S316_34V6.1 (Physcomitrella patens), 5'ss of exon 14
lower sequence: GLYMA19G41840.2 (Glycine max), 5'ss of exon 14
AGATAAAAGCTTGGCTCTATGATCTCCTTGGATCTAGAGTTGACTACGATGCACCTGGTCATTGGTGCACTACAATGGCTTACAGTGCTGACGGCACTAGgtattccaaactttaatctcctttcttacgttttgaagttatttggt--gtgcacaactaa-acgctctatccaagatca-atgtgcgtggttttcttgtagca-----------------
| |||||||| ||| | ||||||    | || ||||| ||||| || ||||| || ||||||||||| |||||||||  |||||||||||| || | ||||||      | ||   |     |    | || || |||||   || |   || | || ||| | |   ||   || | |  ||   | ||  || ||  | |                   
AAATAAAAGCCTGGTTATATGATAATATGGGTTCTAGGGTTGATTATGATGCCCCAGGTCATTGGTGTACTACAATGCTTTACAGTGCTGATGGAAGTAGgtaagaaggatttgggtgcggat----aagtatttaagtttcatgttcaatggataattaagatgtattaaataaaaccgtattaacatgtcttcctatttgtcttccattatttctatag

upper sequence: PP1S316_34V6.1 (Physcomitrella patens), 5'ss of exon 14
lower sequence: GLYMA03G39290.1 (Glycine max), 5'ss of exon 15
AGATAAAAGCTTGGCTCTATGATCTCCTTGGATCTAGAGTTGACTACGATGCACCTGGTCATTGGTGCACTACAATGGCTTACAGTGCTGACGGCACTAGgtattccaaactttaatc----tcctttcttacgttttgaagttatttggtgtgcacaact-aaacgctctatccaagatca-atgtgcgtggttttct-tgtagca------------
| |||||||| ||| | || |||    | || ||||| ||||| || ||||| || ||||||||||| |||||||||  |||||||||||| || | ||||||      | ||   |     |   |  ||| ||||     | | | | |      |  | | | |   ||   || | |  ||   | ||  || || | || ||            
AAATAAAAGCCTGGTTATACGATAATATGGGTTCTAGGGTTGATTATGATGCCCCAGGTCATTGGTGTACTACAATGCTTTACAGTGCTGATGGAAGTAGgtaagaaggatttgggtgcggataagtatttaagtttcatgttcaatggataattgaatttgagatgtattaaataaaaccgtattaacatgtcttcctatttatcattatttctatag

upper sequence: PP1S316_34V6.1 (Physcomitrella patens), 5'ss of exon 14
lower sequence: Vv14s0060g01680.t01 (Vitis vinifera), 5'ss of exon 14
AGATAAAAGCTTGGCTCTATGATCTCCTTGGATCTAGAGTTGACTACGATGCACCTGGTCATTGGTGCACTACAATGGCTTACAGTGCTGACGGCACTAGgtattccaaactttaatctcctttcttacgttttgaagttatttggtgtgcacaactaaacgctctatccaagat--caa--tgtgcgtggttttcttgtagca-------------------------------------------------------------------------------------------------
| || ||||| ||| | |||||   | |||| || ||||||||||| ||||| ||||| |  |||||||||||||||  |||||||||||| || | ||||||        |  |||   |  |   |    |   |    |||  | |      ||    |||| ||  || ||  |||  | |  ||  | || || |||                                                                                                   
AAATTAAAGCCTGGTTGTATGACAACATTGGGTCCAGAGTTGACTATGATGCTCCTGGGCTATGGTGCACTACAATGCTTTACAGTGCTGATGGAAGTAGgtaagattgg-tgaaattcacaattccagacctaataaaattttattttatttttctttttgctcaatttaaaatttcaacttttctgtaatgttgttatagttgtcttttcataccatactgtgctacttttgatcaaatatatctgacagaacatttgtaactaatttgtgactttttttttcctcttcttcttttcag

upper sequence: PP1S316_34V6.1 (Physcomitrella patens), 5'ss of exon 14
lower sequence: Vv09s0002g08370.t01 (Vitis vinifera), 5'ss of exon 14
AGATAAAAGCTTGGCTCTATGATCTCCTTGGATCTAGAGTTGACTACGATGCACCTGGTCATTGGTGCACTACAATGGCTTACAGTGCTGACGGCACTAGgtattccaaactttaatctcctttcttacgttttgaa--------gttatttggtgtgcacaactaaacgctctatcca-agatcaatgtgcgtggttttcttgtagca--------------------
|||||||||| ||| | ||||||  | | |||||| ||||||| || ||||| || ||||  |||||||| ||||||||||||||||| || || || |||| |     ||| | | |   || ||   | |   |          ||  |||||||||  | |  ||   |  ||    |  |  ||||      |||  ||   |                      
AGATAAAAGCATGGTTATATGATAACTTGGGATCTCGAGTTGATTATGATGCTCCAGGTCGCTGGTGCACAACAATGGCTTACAGTGCAGATGGTACAAGgt-tggtttactcttacccatttgctagtgctacaagtcctcatcatttgttggtgtgccaatcagaattattgatgagtattttgatgtttaccttttctttcgggtggtgggttttcatatttacag

upper sequence: PP1S316_34V6.1 (Physcomitrella patens), 5'ss of exon 14
lower sequence: Vv16s0039g02410.t01 (Vitis vinifera), 5'ss of exon 14
AGATAAAAGCTTGGCTCTATGATCTCCTTGGATCTAGAGTTGACTACGATGCACCTGGTCATTGGTGCACTACAATGGCTTACAGTGCTGACGGCACTAGgta----ttccaaactttaatctcctttcttacgttttgaagttatttggtgtgcacaactaaacgctctatccaagatcaatgtgcgtggttttcttgtagca
|||| ||||||||||| ||||||  | | ||||||||||| ||||| ||||| ||||| |||||||| || |  ||||| || ||||| || || || ||||     ||   |||| |  ||      |    | | | || | | ||| | |    |   |||      ||   |  |   ||   ||  || | |  | | |
AGATTAAAGCTTGGCTATATGATTGCTTGGGATCTAGAGTAGACTATGATGCTCCTGGACATTGGTGTACCATGATGGCCTATAGTGCGGATGGAACAAGgtgaagctttttaactct--tcctgcccccagggatattaaatgaattgatttatgaag--aaatttgacatttgaattagttgattgtatttctatgtttgta

upper sequence: PP1S316_34V6.1 (Physcomitrella patens), 5'ss of exon 14
lower sequence: EFJ17248 (Selaginella moellendorffii), 5'ss of exon 14
AGATAAAAGCTTGGCTCTATGATCTCCTTGGATCTAGAGTTGACTACGATGCACCTGGTCATTGGTGCACTACAATGGCTTACAGTGCTGACGGCACTAGgtat--tccaaactttaatctcctttcttacgttttgaagttatttggtgtgcacaactaaacgctctatccaagatcaatgtgcgtggttttcttgtagca
| || ||||||||||| || |||   || || ||| |||| || || ||||| |||||||  |||||||| ||||||||||||||||| || || || |||| |  | ||| ||||  | |  |   | || |  |   ||| |   |                                                      
AAATCAAAGCTTGGCTTTACGATAATCTCGGTTCTCGAGTAGATTATGATGCTCCTGGTCGCTGGTGCACAACAATGGCTTACAGTGCGGATGGAACAAGgtttgcttcaacctttggtatt-tccatcacatccttt-gttttccag------------------------------------------------------

upper sequence: PP1S316_34V6.1 (Physcomitrella patens), 5'ss of exon 14
lower sequence: EFJ37833 (Selaginella moellendorffii), 5'ss of exon 14
AGATAAAAGCTTGGCTCTATGATCTCCTTGGATCTAGAGTTGACTACGATGCACCTGGTCATTGGTGCACTACAATGGCTTACAGTGCTGACGGCACTAGgtattccaaactttaatctcctttcttacgttttgaagttatttggtgtgcacaactaaacgctctatccaagatcaatgtgcgtggttttcttgtagca
| || || || ||||| || |||  |||||| ||  | |||||||| ||||| |||||   ||||||||| |||||||| ||||||||||| ||||| |||| |  |   | ||  |||| |||||  |||    |||  |   | |   |    |||   | | | |                                
AAATCAAGGCGTGGCTGTACGATTGCCTTGGTTCACGGGTTGACTATGATGCGCCTGGAAGTTGGTGCACAACAATGGCCTACAGTGCTGATGGCACAAGgtttgtc--tcgttcgtctcgtttctatcgt----aagacacgcgctaaacgaggctatgtgttttgtag------------------------------

upper sequence: PP1S316_34V6.1 (Physcomitrella patens), 5'ss of exon 14
lower sequence: EFJ32018 (Selaginella moellendorffii), 5'ss of exon 14
AGATAAAAGCTTGGCTCTATGATCTCCTTGGATCTAGAGTTGACTACGATGCACCTGGTCATTGGTGCACTACAATGGCTTACAGTGCTGACGGCACTAGgtattccaaactttaatctcctttcttacgttttgaagttatttggtgtgcacaactaaacgctctatccaagatcaatgtgcgtggttttcttgtagca
| || || || ||||| || |||  |||||| ||  | |||||||| ||||| |||||   ||||||||| |||||||| ||||||||||| ||||| |||| |  |   | ||  |||| |||||  |||    |||  |   | |   |    |||   | | | |                                
AAATCAAGGCGTGGCTGTACGATTGCCTTGGTTCACGGGTTGACTATGATGCGCCTGGAAGTTGGTGCACAACAATGGCCTACAGTGCTGATGGCACAAGgtttgtc--tcgtttgtctcgtttctatcgt----aagacacgcgctaaacgaggctatgtgttttgtag------------------------------

upper sequence: PP1S316_34V6.1 (Physcomitrella patens), 5'ss of exon 14
lower sequence: EFJ30926 (Selaginella moellendorffii), 5'ss of exon 14
AGATAAAAGCTTGGCTCTATGATCTCCTTGGATCTAGAGTTGACTACGATGCACCTGGTCATTGGTGCACTACAATGGCTTACAGTGCTGACGGCACTAGgtat--tccaaactttaatctcctttcttacgttttgaagttatttggtgtgcacaactaaacgctctatccaagatcaatgtgcgtggttttcttgtagca
| || ||||||||||| || |||   || || ||| |||| || || ||||| |||||||  |||||||| ||||||||||||||||| || || || |||| |  | ||| ||||  | |  |   | || |  |    || |   |                                                      
AAATCAAAGCTTGGCTTTACGATAATCTCGGTTCTCGAGTAGATTATGATGCTCCTGGTCGCTGGTGCACAACAATGGCTTACAGTGCGGATGGAACAAGgtttgcttcaacctttggtatt-tccatcacatcctttgtttttccag------------------------------------------------------

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: 35 (upstream exon), 25 (downstream exon)
Score: 4

AGATAAAAGCTTGGCTCTATGATCTCCTTGGATCTAGAGTTGACTACGATGCACCTGGTCATTGGTGCACTACAATGGCTTACAGTGCTGACGGCACTAGgtattccaaa ... tggacgccagACTCTTTTCTTGTGGAACTAGCAAAGATGGAGAATCTTATCTGGTGGAATGGAATGAGAGCGAAGGCGCAATTAAGCGGACATACTCAGGTTTCCGCAAG




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