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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTTTACGATTTATACGAAAATGACTCTATTTTCGACAAGTTTGAGTGTTGTCTTAGTGGCGATGGCATGCGTGTAGCTACTGGTTCCTACAGgtattgtgttagctacacagtttgatggattcaagtccttgaatgaagtgaatgaaacatacatgacaggactttttttgcgttgtatcacagtattcttgtatgctatgttttatggaggagtatgactgaagtattctctgtgtcgcag

Basic information

species Physcomitrella patens
transcript PP1S301_53V6.1
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S301_53V6.1 (Physcomitrella patens), 5'ss of exon 11
lower sequence: LOC_Os01g41630.1 (Oryza sativa), 5'ss of exon 11
CTTTACGATTTATACGAAAATGACTCTATTTTCGACAAGTTTGAGTGTTGTCTTAGTGGCGATGGCATGCGTGTAGCTACTGGTTCCTACAGgtattgtgttagcta--cacagtt-tgatggattcaagtccttgaatgaagtgaatgaaacatacatgacaggactttttttgcgttgtatcacagtattcttgtatgctatgttttatggaggagtatgactgaagtattctctgtgtcgcag
|| |  |||||||| |||||||| || ||||| || ||||||||||| ||||  || || |||||  |||| ||||| |||||||| ||||||| |||  || |||   | ||||| || |        |||      | | |||||  ||   |   |    | |   | |||  |                                                                     
CTATGTGATTTATATGAAAATGATTCCATTTTTGATAAGTTTGAGTGCTGTCAAAGCGGAGATGGATTGCGAGTAGCAACTGGTTCTTACAGgtgttgcttttgctcatctcagttatggtactgctcggtctcct--tcatgtgaactaattgttagttgatgtatgctctttcag---------------------------------------------------------------------

upper sequence: PP1S301_53V6.1 (Physcomitrella patens), 5'ss of exon 11
lower sequence: GRMZM2G142334_T02 (Zea mays), 5'ss of exon 11
CTTTACGATTTATACGAAAATGACTCTATTTTCGACAAGTTTGAGTGTTGTCTTAGTGGCGATGGCATGCGTGTAGCTACTGGTTCCTACAGgtattgtgttagctacacagtttgatggattcaagtccttgaatgaagtgaatgaaacatacatgacaggactttttttgcgttgtatcacagtattcttgtatgctatgttttatggaggagtatgactgaagtattctctgtgtcgcag
 | |  |||||||| ||||||||||| ||||||||||| |||||||||||||  ||||| |||||  |  | ||||| |||||||||||||||||  || | |  | | |     | || | |  ||  ||||  |  | | |  | |||     | ||  | || ||| ||   |  |                                                                
TTATGTGATTTATATGAAAATGACTCAATTTTCGACAAATTTGAGTGTTGTCAAAGTGGTGATGGATTAAGAGTAGCAACTGGTTCCTACAGgta--gtctcatatgctcgtccagttgtaatacag--cttggctccattaacaggaac-----taactag-ctgtttgtgatcttcag---------------------------------------------------------------

upper sequence: PP1S301_53V6.1 (Physcomitrella patens), 5'ss of exon 11
lower sequence: GRMZM2G165418_T01 (Zea mays), 5'ss of exon 11
CTTTACGATTTATACGAAAATGACTCTATTTTCGACAAGTTTGAGTGTTGTCTTAGTGGCGATGGCATGCGTGTAGCTACTGGTTCCTACAGgtattgtgttagctacacagtttgatggattcaagtccttgaatgaagtgaatgaaacatacatgacaggactttttttgcgttgtatcacagtattcttgtatgctatgttttatggaggagtatgactgaagtattctctgtgtcgcag
|| |  ||| | ||||| |||||||| |||||||||||||||||||| ||||||||||| |||||  | ||||| || |||||||| ||  ||||||   ||     ||   ||   || |  |  ||| ||        | ||  || | |   |   |  ||||   ||   | || ||     | |   |                                                  
CTCTGTGATCTGTACGAGAATGACTCAATTTTCGACAAGTTTGAGTGCTGTCTTAGTGGGGATGGACTTCGTGTTGCAACTGGTTCTTATGGgtatttctttcatc-cattattgactgta--cgtgtcattt-------taaagaaatcctctctattaacacttccattttctggtgtcttcaaactgcag--------------------------------------------------

upper sequence: PP1S301_53V6.1 (Physcomitrella patens), 5'ss of exon 11
lower sequence: GRMZM2G164185_T02 (Zea mays), 5'ss of exon 11
CTTTACGATTTATACGAAAATGACTCTATTTTCGACAAGTTTGAGTGTTGTCTTAGTGGCGATGGCATGCGTGTAGCTACTGGTTCCTACAGgtattgtgttagctacacagtttgatggattcaagtccttgaatgaagtgaatgaaacatacatgacaggactttttttgcgttgtatcacagtattcttgtatgctatgttttatggaggagtatgactgaagtattctctgtgtcgcag
 | |  |||||||| ||||||||||| ||||| ||||| |||||||||||||  ||||| |||||  |  | ||||| ||||||||||||||||| | || ||  | |    |  | || | |   |  ||||     | |||  | |||     ||||  |   ||| |    ||                                                                   
TTATGTGATTTATATGAAAATGACTCAATTTTTGACAAATTTGAGTGTTGTCAAAGTGGTGATGGATTAAGAGTAGCAACTGGTTCCTACAGgtagtctgata--ttcttgttcagttgtaatacgg--cttggcctcattgacaggaac-----tgactagctatttgtcatcttcag----------------------------------------------------------------

upper sequence: PP1S301_53V6.1 (Physcomitrella patens), 5'ss of exon 11
lower sequence: GRMZM2G452572_T01 (Zea mays), 5'ss of exon 1
CTTTACGATTTATACGAAAATGACTCTATTTTCGACAAGTTTGAGTGTTGTCTTAGTGGCGATGGCATGCGTGTAGCTACTGGTTCCTACAGgtattgtgttagctacacagtttgatggattcaagtccttgaatgaagtgaatgaaacatacatgacaggactttttttgcgttgtatcacagtattcttgtatgctatgttttatggaggagtatgactgaagtattctctgtgtcgcag
           |  |||||||||||| ||||||||||| |||||||||||||  ||||| |||||  |  | ||||  |||||||||||||||||  || | |  | |  |    | || | |  ||  ||||  |  | | |  | |||     | ||  | || ||| ||   |  |                                                                
---------ACACGCGAAAATGACTCAATTTTCGACAAATTTGAGTGTTGTCAAAGTGGTGATGGATTAAGAGTAGAAACTGGTTCCTACAGgta--gtctcatatgctaatccagttgtaatacag--cttggctccattaacaggaac-----taactag-ctgtttgtgatcttcag---------------------------------------------------------------

upper sequence: PP1S301_53V6.1 (Physcomitrella patens), 5'ss of exon 11
lower sequence: GLYMA07G01440.1 (Glycine max), 5'ss of exon 11
CTTTACGATTTATACGAAAATGACTCTATTTTCGACAAGTTTGAGTGTTGTCTTAGTGGCGATGGCATGCGTGTAGCTACTGGTTCCTACAGgtattgtgttagctacacagtttgatggattcaagtccttgaatgaagtgaatgaaacatacatgacaggactttttttgcgttgtatcacagtattcttgtatgctatgttttatggaggagtatgactgaagtattctctgtgtcgcag
||||  |||||||| |||||||| || ||||| || ||||||||||||||||| ||||| |||||  |||||||  | |||||||| |||||||||       | |||| |  || ||  ||    |    ||       ||| |      | | |   |  | ||| ||| | ||  ||  |||                                                          
CTTTGTGATTTATATGAAAATGATTCAATTTTTGATAAGTTTGAGTGTTGTCTAAGTGGTGATGGATTGCGTGTTTCAACTGGTTCTTACAGgtat------ggataca-aacttaatctatctgtggttctgtcattcttgagtc-----tgcttcttactattttgttt-catttgataccag----------------------------------------------------------

upper sequence: PP1S301_53V6.1 (Physcomitrella patens), 5'ss of exon 11
lower sequence: GLYMA08G20830.4 (Glycine max), 5'ss of exon 11
CTTTACGATTTATACGAAAATGACTCTATTTTCGACAAGTTTGAGTGTTGTCTTAGTGGCGATGGCATGCGTGTAGCTACTGGTTCCTACAGgtattgtgttagctacacagtttgatggattcaagtccttgaatgaagtgaatgaaacatacatgacaggactttttttgcgttgtatcacagtattcttgtatgctatgttttatggaggagtatgactgaagtattctctgtgtcgcag
||||  |||||||| |||||||| || ||||| || ||||||||||||||||| ||||| |||||  |||||||  | ||||| || ||||||||| |  |||       |  || ||  ||    |    ||  | |      |  | | | |||   |  | ||| ||| | ||  ||  |||                                                          
CTTTGTGATTTATATGAAAATGATTCAATTTTTGATAAGTTTGAGTGTTGTCTAAGTGGTGATGGATTGCGTGTTTCAACTGGCTCTTACAGgtatgggattaa------aacttaatctatatgtggttctg--ttattc---ttgagcctgcatcttactattttgttt-catttgattccag----------------------------------------------------------

upper sequence: PP1S301_53V6.1 (Physcomitrella patens), 5'ss of exon 11
lower sequence: GLYMA13G42800.1 (Glycine max), 5'ss of exon 11
CTTTACGATTTATACGAAAATGACTCTATTTTCGACAAGTTTGAGTGTTGTCTTAGTGGCGATGGCATGCGTGTAGCTACTGGTTCCTACAGgtattgtgttagctacacagtttgatggattcaagtccttgaatgaagtgaatgaaacatacatgacaggactttttttgcgttgtatcacagtattcttgtatgctatgttttatggaggagtatgactgaagtattctctgtgtcgcag
|||| ||||||||| ||||||||||| || || || ||||| || |||||||| ||||| |||||  ||||  |||| |||||||| ||||||| |  || ||   ||  | |  |   | |||| ||  | |   ||| ||  |  | | | |||   | || ||| ||| |  | | | ||||                                                          
CTTTGCGATTTATATGAAAATGACTCAATCTTTGATAAGTTCGAATGTTGTCTAAGTGGTGATGGATTGCGCTTAGCAACTGGTTCTTACAGgtctc-tgatacaaacttaatccgt--ggttca-gttgtcgttggaattgttt--atcctgcatcttacgattttgttt-cactttttgacag----------------------------------------------------------

upper sequence: PP1S301_53V6.1 (Physcomitrella patens), 5'ss of exon 11
lower sequence: AT1G17720.1 (Arabidopsis thaliana), 5'ss of exon 11
CTTTACGATTTATACGAAAATGACTCTATTTTCGACAAGTTTGAGTGTTGTCTTAGTGGCGATGGCATGCGTGTAGCTACTGGTTCCTACAGgt-attgtgttagctacacagtttgatggattcaagtccttgaatgaagtgaatgaaacatacatgacaggactttttttgcgttgtatcacagtattcttgtatgctatgttttatggaggagtatgactgaagtattctctgtgtcgcag
|| | |||| |||| ||||||||||| || || || || |||||||||||||| |||||||||||  || | ||||| || ||||| |||||||     || | |       ||   || | |  |  |   ||  |    | |   | | |   |||||   | || || | | |  | || | ||   |  |                                                  
CTATGCGATCTATATGAAAATGACTCCATCTTTGATAAATTTGAGTGTTGTCTGAGTGGCGATGGATTGAGGGTAGCAACAGGTTCTTACAGgttgacttgcttgtcttctggtc--attgctgtacttttctgtcttgtataaggaataaactaatgacca-atttattatacttaatctc-cggtgaaccag--------------------------------------------------

upper sequence: PP1S301_53V6.1 (Physcomitrella patens), 5'ss of exon 11
lower sequence: Vv04s0008g00840.t01 (Vitis vinifera), 5'ss of exon 11
CTTTACGATTTATACGAAAATGACTCTATTTTCGACAAGTTTGAGTGTTGTCTTAGTGGCGATGGCATGCGTGTAGCTACTGGTTCCTACAGgta----ttgtgttagctacacagtttgatggat---tcaagtccttgaatgaagtgaatgaaac---atacatgacaggactttttttgcgttgtatcacagtattcttgtatgctatgttttatggaggagtatgactgaagtattctctgtgtcgcag
|| |  |||||||| |||||||| ||||| |||||||| |||||||||||||| ||||| |||||  | || || || ||||||||||||||||     || || | | | || | ||  |  |||   | || |||| |    |  ||  |    |   |||  |||    |  |  |||   |  | | |  | |                                                        
CTGTGTGATTTATATGAAAATGATTCTATCTTCGACAAATTTGAGTGTTGTCTGAGTGGAGATGGACTACGAGTGGCGACTGGTTCCTACAGgtgtgatttatgcttgatccataattatagtgatcaataaaatcctgggccaagatgccttcgcctgaatatttgatgtaatgtggtttttttcatgtgattgcag-------------------------------------------------------

upper sequence: PP1S301_53V6.1 (Physcomitrella patens), 5'ss of exon 11
lower sequence: Vv09s0002g02470.t01 (Vitis vinifera), 5'ss of exon 11
CTTTACGATTTATACGAAAATGACTCTATTTTCGACAAGTTTGAGTGTTGTCTTAGTGGCGATGGCATGCGTGTAGCTACTGGTTCCTACAGgtattgtgttagctacacagtttgatggattcaagtccttgaatgaagtgaatgaaacatacatgacaggactttttttgcgttgtatcacagtattcttgtatgctatgttttatggaggagtatgactgaagtattctctgtgtcgcag
 | |  |||||||| |||||||| || || || || || ||||| |||||||| ||||| ||||| |||||||||||||| ||||| |||||||   || ||    |     |||            | ||||||     |      | |||   |   |  |     ||   ||  |  ||                                                             
TTGTGTGATTTATATGAAAATGATTCAATCTTTGATAAATTTGAATGTTGTCTGAGTGGTGATGGAATGCGTGTAGCTACAGGTTCTTACAGgt-ccgttttttaaattttctttatccaccattgtttcttgaaccctct------accatgagtactaacataaaattgatgtgatcccag------------------------------------------------------------

upper sequence: PP1S301_53V6.1 (Physcomitrella patens), 5'ss of exon 11
lower sequence: Vv11s0016g02550.t01 (Vitis vinifera), 5'ss of exon 11
CTTTACGATTTATACGAAAATGACTCTATTTTCGACAAGTTTGAGTGTTGTCTTAGTGGCGATGGCATGCGTGTAGCTACTGGTTCCTACAGgtattgtgttagctacacagtttgatggattcaagtccttgaatgaagtgaatgaaacatacatgacaggactttttttgcgttgtatcacagtattcttgtatgctatgttttatggaggagtatgactga-agtattctctgtgtcgcag
 | | |||||| || |||||||| || || || |||||||||||||||||||| ||||| ||||| |  || || || |||||||| |||||||||    ||   |  | | |||    ||  |   | | |   |        |    | | | |   |||   |  ||   |||| |    | | |  |||| ||  |   |||  | | | | |  ||| | | | ||  |   ||| |||
TTGTGCGATTTGTATGAAAATGATTCAATCTTTGACAAGTTTGAGTGTTGTCTGAGTGGAGATGGAACTCGAGTTGCAACTGGTTCATACAGgtatgccttt---tttaaatttttgcagaacc---ttccttttttttcccccttcttctttccttttaggttgtcattaaggttggaaggga-tctggttgt-tgaaaccctttg-gaatgtgcaatactaatactgtttccatggtcccag

upper sequence: PP1S301_53V6.1 (Physcomitrella patens), 5'ss of exon 11
lower sequence: EFJ09063 (Selaginella moellendorffii), 5'ss of exon 11
CTTTACGATTTATACGAAAATGACTCTATTTTCGACAAGTTTGAGTGTTGTCTTAGTGGCGATGGCATGCGTGTAGCTACTGGTTCCTACAGgtattgtgttagctacacagtttgatggattcaagtccttgaatgaagtgaatgaaacatacatgacaggactttttttgcgttgtatcacagtattcttgtatgctatgttttatggaggagtatgactgaagtattctctgtgtcgcag
 | |  || || || || || || ||| | |||||||| || ||||| ||| | |||||||||||| | |||||||| || || |||||||||||| |          |   || || |  | |||||   ||  ||| | |  |    |||   |  |||                                                                                  
TTATGTGACTTGTATGAGAACGATTCTTTATTCGACAAATTCGAGTGCTGTTTAAGTGGCGATGGCCTCCGTGTAGCAACCGGATCCTACAGgtatgg----------atgattcga-gtttccaagtgtgtgtgtgacgagcttttt-catgttttgcag----------------------------------------------------------------------------------

upper sequence: PP1S301_53V6.1 (Physcomitrella patens), 5'ss of exon 11
lower sequence: EFJ08844 (Selaginella moellendorffii), 5'ss of exon 11
CTTTACGATTTATACGAAAATGACTCTATTTTCGACAAGTTTGAGTGTTGTCTTAGTGGCGATGGCATGCGTGTAGCTACTGGTTCCTACAGgtattgtgttagctacacagtttgatggattcaagtccttgaatgaagtgaatgaaacatacatgacaggactttttttgcgttgtatcacagtattcttgtatgctatgttttatggaggagtatgactgaagtattctctgtgtcgcag
 | |  || || || || || || ||| | |||||||| || ||||| ||| | |||||||||||| | |||||||| || || ||||||||||||                   |  |||||| |||     | ||              |   ||||  |     |||| | |||  |  |||                                                          
TTATGTGACTTGTATGAGAACGATTCTTTATTCGACAAATTCGAGTGCTGTTTAAGTGGCGATGGCCTCCGTGTAGCAACCGGATCCTACAGgtat-------------------ggaggattcgagtttccaagtg------------tgtgtgtgacgag----ctttttcattgctttccag----------------------------------------------------------

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|37828516|gb|BJ586528.1|BJ586528
EST:     GAGTGTTGTCTTAGTGGCGATGGCATGCGTGTAGCTACTGGTTCCTACAG                         CAACTTGTTTCGGGTGTTCGGGGCAACCTCTGGAAGTGAAGAGGCGTCTAC
genomic: GAGTGTTGTCTTAGTGGCGATGGCATGCGTGTAGCTACTGGTTCCTACAGgtattgtgtt ... tgtgtcgcagCAACTTGTTTCGGGTGTTCGGGGCAACCTCTGGAAGTGAAGAGGCGTCTAC
EST: gi|37826792|gb|BJ584804.1|BJ584804
EST:     GAGTGTTGTCTTAGTGGCGATGGCATGCGTGTAGCTACTGGTTCCTACAG                         CAACTTGTTTCGGGTGTTCGGGGCAACCTCTGGAAGTGAAGAGGCGTCTAC
genomic: GAGTGTTGTCTTAGTGGCGATGGCATGCGTGTAGCTACTGGTTCCTACAGgtattgtgtt ... tgtgtcgcagCAACTTGTTTCGGGTGTTCGGGGCAACCTCTGGAAGTGAAGAGGCGTCTAC

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), 24 (downstream exon)
Score: 8

CTTTACGATTTATACGAAAATGACTCTATTTTCGACAAGTTTGAGTGTTGTCTTAGTGGCGATGGCATGCGTGTAGCTACTGGTTCCTACAGgtattgtgtt ... tgtgtcgcagCAACTTGTTTCGGGTGTTCGGGGCAACCTCTGGAAGTGAAGAGGCGTCTACGTTGGAAGCCAGCAAGACTCCAAACAG




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