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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTTCGTCGTTTGGCGTCCTCCTGAGTTTGCGAGAGATCTCTTGCCGAACTACTTCAAGCACAACAATTTTTCCAGCTTCGTGCGGCAACTAAACACCTATgtaagctccgcatttctacacaaccttgactattgtgatggaacgcctctctgttaacttaccagcatgtaaatgagacaaccgatcagataaaggagga...

Basic information

species Physcomitrella patens
transcript PP1S85_27V6.1
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S85_27V6.1 (Physcomitrella patens), 5'ss of exon 1
lower sequence: LOC_Os07g44690.1 (Oryza sativa), 5'ss of exon 1
CTTCGTCGTTTGGCGTCCTCCTGAGTTTGCGAGAGATCTCTTGCCGAACTACTTCAAGCACAACAATTTTTCCAGCTTCGTGCGGCAACTAAACACCTATgtaagct-ccgc-atttctacacaaccttgactattgtgatggaacgcctctctgttaacttaccagcatgtaaatgagacaaccgatcagataaaggagga----
||||||||| ||||| || || ||||| ||  | || ||| | || |||||||||||||||||||| || |||||||||||  |||| || |||||||||||||||| | || |    | ||||   ||| |   |   ||  |  |   |||| | |   | ||   || |  |||   |   | |  | || | || ||     
CTTCGTCGTGTGGCGGCCGCCGGAGTTCGCCCGCGACCTCCTCCCCAACTACTTCAAGCACAACAACTTCTCCAGCTTCGTCAGGCAGCTCAACACCTATgtaagctgctgctaccattgcacatttttgccacat---atatattgttgctctataagaat-ccgtaattttcatgt--cggtcaaaaacatgacggtggttgtg

upper sequence: PP1S85_27V6.1 (Physcomitrella patens), 5'ss of exon 1
lower sequence: LOC_Os03g25120.1 (Oryza sativa), 5'ss of exon 1
CTTCGTCGTTTGGCGTCCTCCTGAGTTTGCGAGAGATCTCTTGCCGAACTACTTCAAGCACAACAATTTTTCCAGCTTCGTGCGGCAACTAAACACCTATgtaagc-tccgcatttc-tacacaaccttgactattgtgatggaacgcctctctgttaacttaccagcatgtaaatgagacaaccgatcagataaaggagga
|||||| || ||||| || || ||||| || || || ||| | || |||||||||||||||||||| || |||||||||||  |||| || ||||||||||||||| |    |  || | ||      |   |||    ||    |||   |   || ||| |  |   | ||     |        |  | ||        
CTTCGTGGTGTGGCGGCCGCCGGAGTTCGCCAGGGACCTCCTCCCAAACTACTTCAAGCACAACAACTTCTCCAGCTTCGTCAGGCAGCTCAACACCTATgtaagcatatatacatcatgcatgtatatatatatatatatatgccgcaattaatttcactcattatgttatatgcatgctgtttttttcgctagctctt--

upper sequence: PP1S85_27V6.1 (Physcomitrella patens), 5'ss of exon 1
lower sequence: GRMZM2G025685_T01 (Zea mays), 5'ss of exon 1
CTTCGTCGTTTGGCGTCCTCCTGAGTTTGCGAGAGATCTCTTGCCGAACTACTTCAAGCACAACAATTTTTCCAGCTTCGTGCGGCAACTAAACACCTATgtaagctcc--gcatttctacacaaccttgac-tattgtgatggaacgcctctctgttaacttaccagcatgtaaatgagacaaccgatcagataaaggagga
||||||||| ||||| || || ||||| ||  | || ||| | || |||||||||||||||||||| || |||||||||||  |||| || |||||||||||| |  |   | | |  ||||  || |  || || ||   || |  || |  |  ||    | |  |||||    | ||    |      |||   |   | 
CTTCGTCGTGTGGCGCCCGCCCGAGTTCGCCCGCGACCTCCTCCCAAACTACTTCAAGCACAACAACTTCTCCAGCTTCGTCAGGCAGCTCAACACCTATgtacgtacgtagtagtattacattacatacacataatgcattgcattgcattgc-attgtactgcatgcatg-gtttcagttcccttgctcgatcttgtttg-

upper sequence: PP1S85_27V6.1 (Physcomitrella patens), 5'ss of exon 1
lower sequence: AC216247.3_FGT001 (Zea mays), 5'ss of exon 1
CTTCGTCGTTTGGCGTCCTCCTGAGTTTGCGAGAGATCTCTTGCCGAACTACTTCAAGCACAACAATTTTTCCAGCTTCGTGCGGCAACTAAACACCTATgtaagctccgcatttctacacaaccttgactattgtgatggaacgcctctctgttaacttaccagcatgtaaatgagaca-accgatcagataaaggagga
|||||| || ||||| || || ||||| ||  | || ||| | || | |||||||||||||||||| || |||||||||||  |||| || |||||||| || ||  |   || | || | |    |   |||    ||  |     | | | |  |  ||  |    |      |  ||  | ||    || |  |||  
CTTCGTGGTGTGGCGGCCGCCGGAGTTCGCCCGGGACCTCCTCCCCAGCTACTTCAAGCACAACAACTTCTCCAGCTTCGTCAGGCAGCTCAACACCTACgtgagtgcaatatatgtatatatatatatatatatatatata-tatatatatatatatatattaattagcggcgcatgcatgctgaggttatgatcgagtg

upper sequence: PP1S85_27V6.1 (Physcomitrella patens), 5'ss of exon 1
lower sequence: GRMZM2G088242_T01 (Zea mays), 5'ss of exon 1
CTTCGTCGTTTGGCGTCCTCCTGAGTTTGCGAGAGATCTCTTGCCGAACTACTTCAAGCACAACAATTTTTCCAGCTTCGTGCGGCAACTAAACACCTATgtaagctccgcatttctacacaaccttgactattgtga---tggaacgcctctctgttaacttaccagcatgtaaatga-gacaac--cgatcagataaaggagga--------
|||||| || ||||| || || ||||| ||| | ||  || | || |||||||||||||||||||| || |||  |||||| || || ||||||||||| || ||   ||| ||   ||    |||||  |    | |   | | | ||| | | |    |  ||      || |  |  |   ||  | ||     || ||   |        
CTTCGTGGTCTGGCGCCCGCCGGAGTTCGCGCGCGACATCCTCCCCAACTACTTCAAGCACAACAACTTCTCCTCCTTCGTTCGACAGCTAAACACCTACgtgagt--cgccttcgcacttggccttggtttagctaagccttggaggccgcgcggagcgcggacggatg-gtgaccgccggtgacggcaatgctgcaacgggcaataatgcag

upper sequence: PP1S85_27V6.1 (Physcomitrella patens), 5'ss of exon 1
lower sequence: GLYMA04G04200.1 (Glycine max), 5'ss of exon 1
CTTCGTCGTTTGGCGTCCTCCTGAGTTTGCGAGAGATCTCTTGCCGAACTACTTCAAGCACAACAATTTTTCCAGCTTCGTGCGGCAACTAAACACCTATgtaagctccgcatttctacacaaccttgactattgtgatggaacgcctctctgttaacttaccagcatgtaaa-tgagacaaccgatcagataaaggagga
|||||||||||||||||||||||| || || ||||| ||  | || ||||||||||| |||||||| || ||||||||||| || ||||| ||||||||||||   |    | ||  ||||            | |  |    |   | | ||||  |||  |    | ||   ||| |      |   ||| ||  ||  
CTTCGTCGTTTGGCGTCCTCCTGAATTCGCCAGAGACCTTCTTCCTAACTACTTCAAACACAACAACTTCTCCAGCTTCGTTCGCCAACTCAACACCTATgtattatatttacttacacactgatacactatctctagttcttcaattat-tgttttcttttctttttatattctgacagttttaaatggatgaactag--

upper sequence: PP1S85_27V6.1 (Physcomitrella patens), 5'ss of exon 1
lower sequence: GLYMA06G04390.1 (Glycine max), 5'ss of exon 1
CTTCGTCGTTTGGCGTCCTCCTGAGTTTGCGAGAGATCTCTTGCCGAACTACTTCAAGCACAACAATTTTTCCAGCTTCGTGCGGCAACTAAACACCTATgtaagctccgcatttctacacaaccttgactattgtgatggaacgcctctctgttaacttaccagcatgtaaatgagacaaccgatcagataaaggagga
||||||||||||||||||||||||||| || ||||| ||  | || ||||||||||| |||||||| || || |||||||| || || || ||||||||||||   |   || ||  |||| |  |  | |  |    |       ||     ||||| |       | ||||||    ||                   
CTTCGTCGTTTGGCGTCCTCCTGAGTTCGCAAGAGACCTTCTTCCTAACTACTTCAAACACAACAACTTCTCAAGCTTCGTTCGCCAGCTCAACACCTATgtattatattcacttacacactatatctagttcttcagttat---tcttataattaacatggttaattttaaatgcatgaattag---------------

upper sequence: PP1S85_27V6.1 (Physcomitrella patens), 5'ss of exon 1
lower sequence: GLYMA07G36370.1 (Glycine max), 5'ss of exon 1
CTTCGTCGTTTGGCGTCCTCCTGAGTTTGCGAGAGATCTCTTGCCGAACTACTTCAAGCACAACAATTTTTCCAGCTTCGTGCGGCAACTAAACACCTATgtaagctccgcatttctacacaaccttgactattgtgatggaacgcctctctgttaacttaccagcatgtaaatgagacaaccgatcagataaaggagga-----
 || || || |||   || ||||||||||| ||||||||  | || ||||| ||||| |||||||| || || ||||| ||  ||||||| |||||||||||||||     ||   ||      |||   || |    |  ||  ||| |   | | |||  |  ||| | | |      |      || |||||          
ATTTGTTGTGTGGAAGCCCCCTGAGTTTGCCAGAGATCTTCTTCCCAACTATTTCAAACACAACAACTTCTCAAGCTTTGTTAGGCAACTCAACACCTATgtaagc-----atccttatcttttcttatgtacttctctacaatccctattcttcatctttgcttcatttcacttcattgagtttgaaggtaaagctctttccat

upper sequence: PP1S85_27V6.1 (Physcomitrella patens), 5'ss of exon 1
lower sequence: GLYMA14G09190.1 (Glycine max), 5'ss of exon 1
CTTCGTCGTTTGGCGTCCTCCTGAGTTTGCGAGAGATCTCTTGCCGAACTACTTCAAGCACAACAATTTTTCCAGCTTCGTGCGGCAACTAAACACCTATgtaagctccgcatttctacacaaccttgactattgtgatggaacgcctctct--gttaacttacc---agcatgtaaatgagacaaccgatcagataaaggagga
||||||||||||| | || || ||||| || || || ||  | || ||||| ||||| |||||||| || ||||||||||| || ||||| |||||||||||| |   | ||   | |    | ||    | || |  |        | | |  |||   ||| |    |||   |  |  || |    ||||   ||       
CTTCGTCGTTTGGAGACCCCCCGAGTTCGCTAGGGACCTTCTCCCCAACTATTTCAAACACAACAACTTCTCCAGCTTCGTTCGCCAACTCAACACCTATgtatgtatcacacacccatcatatctctcttctttttttcttttttttttttaagttcttttatcgaaggcaatcatgtttgaaacattatcaatcaata-----

upper sequence: PP1S85_27V6.1 (Physcomitrella patens), 5'ss of exon 1
lower sequence: GLYMA17G35980.1 (Glycine max), 5'ss of exon 1
CTTCGTCGTTTGGCGTCCTCCTGAGTTTGCGAGAGATCTCTTGCCGAACTACTTCAAGCACAACAATTTTTCCAGCTTCGTGCGGCAACTAAACACCTATgtaagctccgcatttctacacaaccttgactattgtgatggaacgcctctctgttaacttaccagcatgtaaatgagacaaccgatcagataaaggagga-
||||||||||||| | || || || || || || || ||  | || ||||| ||||| |||||||| || ||||||||||| || ||||| |||||||||||| |   |  |   | |      ||    | || |  |  |   |  |||        | ||   |   |  | |  |||   || |   ||      | 
CTTCGTCGTTTGGAGACCCCCCGAATTCGCTAGGGACCTTCTCCCCAACTATTTCAAACACAACAACTTCTCCAGCTTCGTTCGCCAACTCAACACCTATgtatgtatcatacacccatcatgtctctcttctttttcttaatttctactcatacgttcttccgagaca-atcttattcaatacattatgaaacactaaat

upper sequence: PP1S85_27V6.1 (Physcomitrella patens), 5'ss of exon 1
lower sequence: GLYMA20G08250.1 (Glycine max), 5'ss of exon 1
CTTCGTCGTTTGGCGTCCTCCTGAGTTTGCGAGAGATCTCTTGCCGAACTACTTCAAGCACAACAATTTTTCCAGCTTCGTGCGGCAACTAAACACCTATgtaagc-tccgcatttctacacaaccttgactattgtgatggaacgcctctctgttaacttaccagcatgtaaatgagacaaccgatcagataaaggagga
 || || || ||| | || ||||||||||| ||||||||  | || ||||| || || |||||||| || || ||||| ||  ||||||| ||||||||||||||| |||  || | | |  |       || ||    |       ||   | || ||||    |  | | || |  |  |  ||||   | | |     
ATTTGTTGTCTGGAGGCCCCCTGAGTTTGCAAGAGATCTTCTTCCCAACTATTTTAAACACAACAACTTCTCAAGCTTTGTTAGGCAACTCAACACCTATgtaagcatccttatcttttcttatgtacttct-ttacactccctactcttcatcttcacttcattgagtttgaaggtaattaaagatcttttcatgtgaac

upper sequence: PP1S85_27V6.1 (Physcomitrella patens), 5'ss of exon 1
lower sequence: Vv06s0009g02730.t01 (Vitis vinifera), 5'ss of exon 1
CTTCGTCGTTTGGCGTCCTCCTGAGTTTGCGAGAGATCTCTTGCCGAACTACTTCAAGCACAACAATTTTTCCAGCTTCGTGCGGCAACTAAACACCTATgtaagctccgcatttctacacaaccttgactattgtgatggaacgcctctctgttaacttaccagcatgtaaa-tgagacaaccgatcagataaaggagga-
||| || |||||| | || ||||||||||| || |||||| | || |||||||||||||||||||| || |||||||| ||  |||| || || |||||||| ||    ||||   ||  |  |  |  || |     |    |  |||||| |     | |          | || |        |||  | |  | ||  
CTTTGTTGTTTGGAGACCCCCTGAGTTTGCCAGGGATCTCCTCCCCAACTACTTCAAGCACAACAACTTCTCCAGCTTTGTTAGGCAGCTCAATACCTATgtgagagt-gcatcattaaccctctctctctctctctctctctc-tctctctctctctctcctgattcaagcactgtgtttcattttcacttcattgggggt

upper sequence: PP1S85_27V6.1 (Physcomitrella patens), 5'ss of exon 1
lower sequence: Vv18s0001g10380.t01 (Vitis vinifera), 5'ss of exon 1
CTTCGTCGTTTGGCGTCCTCCTGAGTTTGCGAGAGATCTCTTGCCGAACTACTTCAAGCACAACAATTTTTCCAGCTTCGTGCGGCAACTAAACACCTATgtaagctccgcatttctacacaaccttgact-------attgtgatggaacgcctctctgttaacttaccagcatgtaaatgagacaaccgatcagataaaggagga------------------------------------
|||||| || ||||||||||||||||| ||  | |||||| | || || |||||||| |||||||| || || ||||||||  | || || |||||||||||| ||      | ||| | |   |||  ||       || ||    | |    |  ||| | |  ||     || | ||  |  |  |  ||    |  |                                          
CTTCGTGGTGTGGCGTCCTCCTGAGTTCGCTCGCGATCTCCTTCCCAATTACTTCAAACACAACAACTTCTCAAGCTTCGTCAGACAGCTCAACACCTATgtatgccttctctctcttcccccacttcccttcttcaaatcgtttctggagatgtaactggttatatatatatatatgaaacaagcttcttattgtttttactgatttagattttgttttgcttgcttgcttccggaaactag

upper sequence: PP1S85_27V6.1 (Physcomitrella patens), 5'ss of exon 1
lower sequence: EFJ15796 (Selaginella moellendorffii), 5'ss of exon 1
CTTCGTCGTTTGGCGTCCTCCTGAGTTTGCGAGAGATCTCTTGCCGAACTACTTCAAGCACAACAATTTTTCCAGCTTCGTGCGGCAACTAAACACCTATgtaagctccgcat---------ttctacacaaccttga----ctattgtgatggaacgcctctctgttaacttaccagcatgtaaatgagacaaccgatcagataaaggagga------------------------
 ||| |||| ||||| || || || || || |  ||| |||||||||| |||||||||||||| || || ||||| ||||| ||||| || |||||||| || ||   |||||         ||| ||||  |||       || | | | |    | | |   | || |||| | || |   |  |    |   | || |  |     |                           
GTTCATCGTCTGGCGACCCCCGGAATTCGCCAAGGATATCTTGCCGAATTACTTCAAGCACAATAACTTCTCCAGTTTCGTCCGGCAGCTCAACACCTACgtgagtctcgcatacgttttctttccacacctcctcatagttctttggagttcagtcccttagttcttcacttgc-agtactcagcttcagctgtcaatgatgttgcccactgaacttcgttcttgtcgactcgcag

upper sequence: PP1S85_27V6.1 (Physcomitrella patens), 5'ss of exon 1
lower sequence: EFJ31857 (Selaginella moellendorffii), 5'ss of exon 1
CTTCGTCGTTTGGCGTCCTCCTGAGTTTGCGAGAGATCTCTTGCCGAACTACTTCAAGCACAACAATTTTTCCAGCTTCGTGCGGCAACTAAACACCTATgtaagctccgcatttctacacaaccttgactattgtgatggaacgcctctctgttaacttaccagcatgtaaatgagacaaccgatcagataaagg-agga--------------------------------------------
 |||||||| |||   || || ||||| || |  ||| |  | || | |||||||||||||||||| || || |||||||| ||||| || ||||| ||||| || |||   |     | |    |||    ||     |    ||||  || |     |  |    |   |  ||| |    | |  |||    | | ||                                            
ATTCGTCGTGTGGAAGCCGCCCGAGTTCGCCACCGATTTGCTCCCCAGCTACTTCAAGCACAACAACTTCTCGAGCTTCGTCCGGCAGCTCAACACATATgtgagttccat-tccaagctcttgtttgttcgttcgctcgctttgccttcctatctttctctcgttcttccaccgag-cgtttgcttcgatccttgcaagagtctctctggcaactcactcacattgcaacaatgctgtgtgcag

upper sequence: PP1S85_27V6.1 (Physcomitrella patens), 5'ss of exon 1
lower sequence: EFJ28850 (Selaginella moellendorffii), 5'ss of exon 1
CTTCGTCGTTTGGCGTCCTCCTGAGTTTGCGAGAGATCTCTTGCCGAACTACTTCAAGCACAACAATTTTTCCAGCTTCGTGCGGCAACTAAACACCTATgtaagctccgcatttctacacaaccttgactattgtgatggaacgcctctctg-ttaacttaccagcatgtaaatgagacaaccgatcagataaaggagga
||||||||| ||| | || || ||||| ||  | ||  |  | || ||||||||||||||||||||||| ||||||||||||||||| || ||||||||||| ||   | |   ||      |||||||   |     | |  | ||  |||| | | |||| |  |  ||   ||                         
CTTCGTCGTGTGGAGGCCGCCAGAGTTCGCCCGCGACTTGCTCCCAAACTACTTCAAGCACAACAATTTCTCCAGCTTCGTGCGGCAGCTCAACACCTATgtgagtctctcgaatc------accttgaagctctcacttgttctccgatctgatcatcttatcgtcgcgttcttgcag----------------------

upper sequence: PP1S85_27V6.1 (Physcomitrella patens), 5'ss of exon 1
lower sequence: EFJ38003 (Selaginella moellendorffii), 5'ss of exon 1
CTTCGTCGTTTGGCGTCCTCCTGAGTTTGCGAGAGATCTCTTGCCGAACTACTTCAAGCACAACAATTTTTCCAGCTTCGTGCGGCAACTAAACACCTATgtaagctccgcatttctacacaaccttgactattgtgatggaacgcctctctgttaacttaccagcatgtaaatgagacaaccgatcagataaagg-agga--------------------------------------------
 |||||||| |||   || || ||||| || |  ||| |  | || | |||||||||||||||||| || || |||||||| ||||| || ||||| ||||| || |||   |     | |    |||    ||     |    ||||  || |     |  |    |   |  |||      | |  |||    | | ||                                            
ATTCGTCGTGTGGAAGCCGCCCGAGTTCGCCACCGATTTGCTCCCCAGCTACTTCAAGCACAACAACTTCTCGAGCTTCGTCCGGCAGCTCAACACATATgtgagttccat-tccaagctcttgtttgttcgttcgctcgctttgccttcctatctttctctcgttcttccaccgagcgttttgctttgatccttgcaagagtctctctggcaactcactcacattgcaacaatgctgtgtgcag

upper sequence: PP1S85_27V6.1 (Physcomitrella patens), 5'ss of exon 1
lower sequence: EFJ17520 (Selaginella moellendorffii), 5'ss of exon 1
CTTCGTCGTTTGGCGTCCTCCTGAGTTTGCGAGAGATCTCTTGCCGAACTACTTCAAGCACAACAATTTTTCCAGCTTCGTGCGGCAACTAAACACCTATgtaagctccgcatttctacacaaccttgactattgtgatggaacgcctctctg-ttaacttaccagcatgtaaatgagacaaccgatcagataaaggagga
||||||||| ||| | || || ||||| ||  | ||  |  | || ||||||||||||||||||||||| ||||||||||||||||| || ||||||||||||||  || |   ||      ||||||||  |     | |  | |   |||| | | |||| ||     |   ||                         
CTTCGTCGTGTGGAGGCCGCCAGAGTTCGCCCGCGACTTGCTCCCAAACTACTTCAAGCACAACAATTTCTCCAGCTTCGTGCGGCAGCTCAACACCTATgtaagtccctcgaatc------accttgacgctctcacttgttctctgatctgatcatcttatcattgctttcttgcag----------------------

upper sequence: PP1S85_27V6.1 (Physcomitrella patens), 5'ss of exon 1
lower sequence: EFJ32930 (Selaginella moellendorffii), 5'ss of exon 1
CTTCGTCGTTTGGCGTCCTCCTGAGTTTGCGAGAGATCTCTTGCCGAACTACTTCAAGCACAACAATTTTTCCAGCTTCGTGCGGCAACTAAACACCTATgtaagctccgcat-----ttctacaca-accttgactattgtgatg-gaacgcctctctgttaacttaccagca--tgtaaatgagaca-accgatcagataaaggagga---------------------------------------------
 |||||||| ||||| || || || || || |  ||| |||||||||| |||||||||||||| || || ||||| ||||| ||||| || |||||||| || ||   | |||     ||||   || ||||   | || ||  |  | |   |  ||  |||  |   |  ||  |||  || |     |    |||| |  || |                                                
GTTCGTCGTCTGGCGACCCCCGGAATTCGCCAAGGATATCTTGCCGAATTACTTCAAGCACAATAACTTCTCCAGTTTCGTCCGGCAGCTCAACACCTACgtgagtctcccatacgttttctttccacacctcctccatagttctttggagttcagtcccttagttcttcgccagttgtcgatcacttgcagtactcagcttcagcattttgtcaatgatgttgcgcactgaacttcgttcttgtcgactcgcag

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: 28 (upstream exon), 35 (downstream exon)
Score: 8

CTTCGTCGTTTGGCGTCCTCCTGAGTTTGCGAGAGATCTCTTGCCGAACTACTTCAAGCACAACAATTTTTCCAGCTTCGTGCGGCAACTAAACACCTATgtaagctccg ... gtgttgacagGGCTTCAGGAAGGTAGTTCCGGAACGGTGGGAGTTTGCAAACGATTATTTTCGGCGAGGAGAACGTCATCTTCTTTGCGAGATACACAGGCGGAAGGCAT




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