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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATATTCTTTATGACTCTTGGTCACCAGCAATGACCGTGAGTTCTATCTGCATCAGCATCCTGTCCATGTTGTCTAGTTCAACTGTGAAGgtactttttaaagtttccacactagcctccacgtattgaattttcagtatatcgcatgtaaaaatggggactgttcttttagtgtcctgctttctaactt...

Basic information

species Physcomitrella patens
transcript PP1S211_21V6.1
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S211_21V6.1 (Physcomitrella patens), 5'ss of exon 5
lower sequence: LOC_Os12g44000.1 (Oryza sativa), 5'ss of exon 5
ATATTCTTTATGACTCTTGGTCACCAGCAATGACCGTGAGTTCTATCTGCATCAGCATCCTGTCCATGTTGTCTAGTTCAACTGTGAAGgt-actttttaaagtttccacactagcctccacgtattgaattttcagtatatcgcatgtaaaaatggggactgttcttttagtgtcctgctttctaactt
|||| || ||||| ||||||||||| |||||||| || |||||  |||||||||||||  |||| |||||||| |||||| | |  ||||| | | | || |  |  |||     ||| | | | ||    ||||  |  | |  |   |  ||  || |   ||  | || |||  || || |      
ATATACTGTATGATTCTTGGTCACCTGCAATGACTGTCAGTTCGGTCTGCATCAGCATTTTGTCAATGTTGTCAAGTTCACCAGCAAAGgttattatatataactaacac-----ccttcccatttt---ctttcgctg-accaaaaacattaaaaggtatc-ttgctataatgtggtgtttgcag----

upper sequence: PP1S211_21V6.1 (Physcomitrella patens), 5'ss of exon 5
lower sequence: LOC_Os03g47770.1 (Oryza sativa), 5'ss of exon 5
ATATTCTTTATGACTCTTGGTCACCAGCAATGACCGTGAGTTCTATCTGCATCAGCATCCTGTCCATGTTGTCTAGTTCAACTGTGAAGgtactttttaaagtttccacactagcctccacgtattgaattttcagtatatcgcatgtaaaaatggggactgttcttttagtgtcc-tgctttctaactt
||||  | |||||||| |||||||| || |||||||| |||||| | || ||||| ||| ||||||||||||| || ||| | |  |||||    | || || ||| ||  |  ||||  |   || |||    |  ||   |||| | |  ||      ||||  ||   |||   |||          
ATATATTGTATGACTCGTGGTCACCGGCGATGACCGTTAGTTCTGTTTGTATCAGTATCTTGTCCATGTTGTCAAGCTCACCAGCAAAGgt----tatagagcttc-actgtgtcctctcctgtttaaatggagatcat---gcatctgaccatattatatgtttattatatgttggtgcag--------

upper sequence: PP1S211_21V6.1 (Physcomitrella patens), 5'ss of exon 5
lower sequence: GRMZM2G007381_T01 (Zea mays), 5'ss of exon 5
ATATTCTTTATGACTCTTGGTCACCAGCAATGACCGTGAGTTCTATCTGCATCAGCATCCTGTCCATGTTGTCTAGTTCAACTGTGAAGgtactttttaaagtttccacactagcctccacgtattgaattttcagtatatcgcatgtaaaaatggggactgttcttttag--tgtcctgctttctaactt
||||||| |||||||| ||||||||||| ||||||||||| ||| |||| ||||| |||||||| ||||||||||||||  | |  |||||     |||  ||   || ||||  ||  |  |||| ||   || ||        |  | |    |   ||       |||  |||  || || |      
ATATTCTGTATGACTCGTGGTCACCAGCGATGACCGTGAGCTCTGTCTGTATCAGTATCCTGTCTATGTTGTCTAGTTCGCCAGCAAAGgtgacactta--gtcatcatacta--cttgatctattcaaacctcggtgctctcactccatagccagactctaactagctagaatgtattgtttgcag----

upper sequence: PP1S211_21V6.1 (Physcomitrella patens), 5'ss of exon 5
lower sequence: GRMZM2G018447_T01 (Zea mays), 5'ss of exon 5
ATATTCTTTATGACTCTTGGTCACCAGCAATGACCGTGAGTTCTATCTGCATCAGCATCCTGTCCATGTTGTCTAGTTCAACTGTGAAGgtactttttaaagtttccacactagcctccacgtattgaattttcagtatatcgcatgtaaaaatggggactgttcttttagtgtcctgctttctaactt
||||| | |||||||| ||||| ||||| ||||||||||| ||| |||| ||||| |||||||| ||||||||||||||  | |  ||||||   ||||   || | | ||||  ||| |  |||| ||   |||||     |  |  | ||   |   ||       ||         ||  |     
ATATTTTGTATGACTCGTGGTCTCCAGCGATGACCGTGAGCTCTGTCTGTATCAGTATCCTGTCTATGTTGTCTAGTTCGCCAGCAAAGgtagcgtttagtcttacta-acta--ctcgatctattaaaacctcagtgccctgactccataatcagactctaactagctaacaatgcatttgttgcag-

upper sequence: PP1S211_21V6.1 (Physcomitrella patens), 5'ss of exon 5
lower sequence: GRMZM2G018447_T02 (Zea mays), 5'ss of exon 5
ATATTCTTTATGACTCTTGGTCACCAGCAATGACCGTGAGTTCTATCTGCATCAGCATCCTGTCCATGTTGTCTAGTTCAACTGTGAAGgtactttttaaagtttccacactagcctccacgtattgaattttcagtatatcgcatgtaaaaatggggactgttcttttagtgtcctgctttctaactt---------
||||| | |||||||| ||||| ||||| ||||||||||| ||| |||| ||||| |||||||| ||||||||||||||  | |  ||||||   ||||   || | | ||||  ||| |  |||| ||   |||||     |  |  | ||   |   ||       ||         ||  |              
ATATTTTGTATGACTCGTGGTCTCCAGCGATGACCGTGAGCTCTGTCTGTATCAGTATCCTGTCTATGTTGTCTAGTTCGCCAGCAAAGgtagcgtttagtcttacta-acta--ctcgatctattaaaacctcagtgccctgactccataatcagactctaactagctaacaatgcatttgttgcagcaacgtccag

upper sequence: PP1S211_21V6.1 (Physcomitrella patens), 5'ss of exon 5
lower sequence: GRMZM2G148130_T03 (Zea mays), 5'ss of exon 5
ATATTCTTTATGACTCTTGGTCACCAGCAATGACCGTGAGTTCTATCTGCATCAGCATCCTGTCCATGTTGTCTAGTTCAACTGTGAAGgtactttttaaagtttccacactagcctccacgtattgaattttcagtatatcgcatgtaaaa-atggggactgttcttttagtgtcctgctttctaactt
||||  | |||||||| ||||| ||||||||||| || ||||||||||| ||||||||  | || ||| |||| || ||| | |  |||||    | |    | | || |      | ||     ||  | ||  |  |   |  || || | ||           ||  ||                  
ATATATTGTATGACTCGTGGTCCCCAGCAATGACTGTCAGTTCTATCTGTATCAGCATATTATCTATGCTGTCCAGCTCACCAGCAAAGgttacatatttcctctacatatccttgttcaatcggtgggtctt--gctttctgactgcaatacatacatgtaccgattgcag------------------

upper sequence: PP1S211_21V6.1 (Physcomitrella patens), 5'ss of exon 5
lower sequence: GRMZM2G116840_T03 (Zea mays), 5'ss of exon 6
ATATTCTTTATGACTCTTGGTCACCAGCAATGACCGTGAGTTCTATCTGCATCAGCATCCTGTCCATGTTGTCTAGTTCAACTGTGAAGgtactttttaaagtttccacactagcctccacgtattgaattttcagtatatcgcatgtaaaaatggggactgttcttttagtgtcctgctttctaactt
|||| || |||||||| ||||| ||||| ||||| || ||||||||||| ||||||||  | || ||| |||| || ||  | |  |||||  |   ||   | || |||  | | |       |||||||    |  | | || | | |          |   |  ||   |                
ATATACTGTATGACTCGTGGTCCCCAGCGATGACTGTCAGTTCTATCTGTATCAGCATATTATCTATGCTGTCCAGCTCGCCAGAAAAGgt--tacatattttctctacatcacctt------gttgaattggtgg-gtcttgcttttgactgcaatacattaccgattgcag----------------

upper sequence: PP1S211_21V6.1 (Physcomitrella patens), 5'ss of exon 5
lower sequence: AT5G42990.1 (Arabidopsis thaliana), 5'ss of exon 5
ATATTCTTTATGACTCTTGGTCACCAGCAATGACCGTGAGTTCTATCTGCATCAGCATCCTGTCCATGTTGTCTAGTTCAACTGTGAAGgtactt--tttaaagtttccacactagcctccacgtattgaattttcagtatatcgcatgtaaaaatggggactgttcttttagtgtcctgctttctaactt--------
||||||| |||||||| ||||| ||||||||||| ||||||||  |||||||||||||||| || ||| | || |||||  | |  |||||   |   ||  |  |  ||||||          | |   |  ||||   | |   |       |     ||   ||||    |||| |  | || |            
ATATTCTGTATGACTCATGGTCTCCAGCAATGACAGTGAGTTCAGTCTGCATCAGCATCCTCTCAATGCTATCAAGTTCCCCCGAAAAGgtttctacatttgatctctcacactttgtattgt-tgtcacaaattcaaactttttgaccctgccac----acaactcttactatgtcttattgtcgatgacaatatcag

upper sequence: PP1S211_21V6.1 (Physcomitrella patens), 5'ss of exon 5
lower sequence: AT1G45050.1 (Arabidopsis thaliana), 5'ss of exon 5
ATATTCTTTATGACTCTTGGTCACCAGCAATGACCGTGAGTTCTATCTGCATCAGCATCCTGTCCATGTTGTCTAGTTCAACTGTGAAGgtacttt-------ttaaagtttccacactagcct-ccacgtattgaattttcagtatatcgcatgtaaaaatgggga---ctgttcttttagtgtcctgctttctaactt
||||||| |||||||| ||||||||||||||||| |||| |||  ||||||||||||| || || ||| | || |||||| | |  ||||| ||||       ||   ||||||  | |  |     ||  |  | | | | | | |||    | | ||| |  | |   |  |   |||  | | | || || |  |  
ATATTCTATATGACTCATGGTCACCAGCAATGACAGTGAATTCAGTCTGCATCAGCATTCTTTCGATGCTATCAAGTTCACCCGCAAAGgttctttcttcttcttcgtgtttccctattgacaagttacccaaagtactgtgaat-tatgaggtctgaaactaagaatatcaatgtgttttttattccgccttattgcag

upper sequence: PP1S211_21V6.1 (Physcomitrella patens), 5'ss of exon 5
lower sequence: AT1G75440.1 (Arabidopsis thaliana), 5'ss of exon 5
ATATTCTTTATGACTCTTGGTCACCAGCAATGACCGTGAGTTCTATCTGCATCAGCATCCTGTCCATGTTGTCTAGTTCAACTGTGAAGgtactttttaaagtttccacactagcctccacgtattgaattttcagtatatcgcatgtaaaaatggggactgttcttttagtgtcctgctttctaactt
||||| | ||||| || ||||| ||||| ||||| ||||||||||||||||| |||||||| |||||| | || || || ||||  |||||||||   | || |   |||||  ||   |  |||  ||  ||   | | |    ||   ||   |   ||     |    || | || ||| |  |  
ATATTTTGTATGATTCGTGGTCTCCAGCCATGACGGTGAGTTCTATCTGCATTAGCATCCTCTCCATGCTCTCAAGCTCGACTGAAAAGgtactt---acagctcttacactcaccatta-atatataaactttgatctctttgttgctgaagctgaaccttcgtctcgcttggcttgttttgttgcag

upper sequence: PP1S211_21V6.1 (Physcomitrella patens), 5'ss of exon 5
lower sequence: Vv04s0023g02620.t01 (Vitis vinifera), 5'ss of exon 5
ATATTCTTTATGACTCTTGGTCACCAGCAATGACCGTGAGTTCTATCTGCATCAGCATCCTGTCCATGTTGTCTAGTTCAACTGTGAAGgtactttttaaagtttccacactagcctccacgtattgaattttcagtatatcgcatgtaaaaatggggactgttcttttagtgtcctgctttctaactt------
||||| | ||||| |||||||| ||||| ||||| || |||||||||||||||||||| || |||||| | || || |||||||||||||| ||| |  |  ||||   ||||||     | |||    || || ||   || ||  | ||  |||      || |  ||   | |   | |||           
ATATTTTGTATGATTCTTGGTCCCCAGCCATGACAGTTAGTTCTATCTGCATCAGCATTCTCTCCATGCTATCAAGCTCAACTGTGAAGgttcttgtccatctttct-tactagcactttcatatcc--ttctcggt---tcacaattcaacttggttttccttgtgctatgattcaattctctggggcaaagct

upper sequence: PP1S211_21V6.1 (Physcomitrella patens), 5'ss of exon 5
lower sequence: Vv18s0001g13180.t01 (Vitis vinifera), 5'ss of exon 5
ATATTCTTTATGACTCTTGGTCACCAGCAATGACCGTGAGTTCTATCTGCATCAGCATCCTGTCCATGTTGTCTAGTTCAACTGTGAAGgt--------actttttaaagtttccacactagcctccacgtattgaattttcagtatatcgcatgtaaaaatggggactgttctt---ttagtgtcctgctttctaactt-------------
||||||| ||||| || ||||| ||||| ||||| || ||||| ||||| |||||||| || |||||||| || || ||||||||||||||        | || | |||||||  |   |      | | |  |   || | | | |  |   | |     |   | || || |    | || |   | ||    |  ||             
ATATTCTATATGATTCATGGTCCCCAGCCATGACAGTTAGTTCAATCTGTATCAGCATACTCTCCATGTTATCGAGCTCAACTGTGAAGgtttggttcaaattgtcaaagttttaagttttttaaacccctcctttcttcttaattttgcttttatctttttccagcctattttagtgtgagagcattactcatgagttttttcattgtgcag

upper sequence: PP1S211_21V6.1 (Physcomitrella patens), 5'ss of exon 5
lower sequence: EFJ27071 (Selaginella moellendorffii), 5'ss of exon 5
ATATTCTTTATGACTCTTGGTCACCAGCAATGACCGTGAGTTCTATCTGCATCAGCATCCTGTCCATGTTGTCTAGTTCAACTGTGAAGgtactttttaaagtttccacactagcctccacgtattgaattttcagtatatcgcatgtaaaaatggggactgttcttttagtgtcctgctttctaactt
||||||| ||||| || ||||| ||||| |||||||| || || ||||||||||||||||| || ||| | || || || || || |||||   || ||     |     |   ||  | || ||   || |    |            |                                       
ATATTCTCTATGATTCGTGGTCGCCAGCCATGACCGTCAGCTCCATCTGCATCAGCATCCTCTCGATGCTCTCGAGCTCCACAGTCAAGgt---ttctagtaacttgtttccttccctcgcgcatctcatctcacatccgctttgatccag--------------------------------------

upper sequence: PP1S211_21V6.1 (Physcomitrella patens), 5'ss of exon 5
lower sequence: EFJ21480 (Selaginella moellendorffii), 5'ss of exon 5
ATATTCTTTATGACTCTTGGTCACCAGCAATGACCGTGAGTTCTATCTGCATCAGCATCCTGTCCATGTTGTCTAGTTCAACTGTGAAGgtactttttaaagtttccacactagcctccacgtattgaattttcagtatatcgcatgtaaaaatggggactgttcttttagtgtcctgctttctaactt
||||||| ||||| || ||||| ||||| |||||||| || || ||||||||||||||||| || ||| | || || || || || |||||  || |   || ||     ||  |   | || ||   || |    |            |                                       
ATATTCTCTATGATTCGTGGTCGCCAGCCATGACCGTCAGCTCCATCTGCATCAGCATCCTCTCGATGCTCTCGAGCTCCACAGTCAAGgt--ttctagtagcttgtttcctt-ctcgcgcgcatctcatctcacatccgctttgatccag--------------------------------------

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|208391186|gb|DC938160.1|DC938160
EST:     GTTCTATCTGCATCAGCATCCTGTCCATGTTGTCTAGTTCAACTGTGAAG                         GCCAGACCACCTGATGACGACCGTTATGTGAGGAAATGCCGAAATGGCAGA
genomic: GTTCTATCTGCATCAGCATCCTGTCCATGTTGTCTAGTTCAACTGTGAAGgtacttttta ... gcttgaacagGCCAGACCACCTGATGACGATCGTTATGTGAGGAAATGCCGAAATGGCAGA
EST: gi|162160478|gb|FC336868.1|FC336868
EST:     GTTCTATCTGCATCAGCATCCTGTCCATGTTGTCTAGTTCAACTGTGAAG                         GCCAGACCACCTGATGACGATCGTTATGTGAGGAAATGCCGAAATGGCAGA
genomic: GTTCTATCTGCATCAGCATCCTGTCCATGTTGTCTAGTTCAACTGTGAAGgtacttttta ... gcttgaacagGCCAGACCACCTGATGACGATCGTTATGTGAGGAAATGCCGAAATGGCAGA
EST: gi|208393338|gb|DC942464.1|DC942464
EST:     GTTCTATCTGCATCAGCATCCTGTCCATGTTGTCTAGTTCAACTGTGAAG                         GCCAGACCACCTGATGACGATCGTTATGTGAGGAAATGCCGAAATGGCAGA
genomic: GTTCTATCTGCATCAGCATCCTGTCCATGTTGTCTAGTTCAACTGTGAAGgtacttttta ... gcttgaacagGCCAGACCACCTGATGACGATCGTTATGTGAGGAAATGCCGAAATGGCAGA
EST: gi|208365856|gb|DC955459.1|DC955459
EST:     GTTCTATCTGCATCAGCATCCTGTCCATGTTGTCTAGTTCAACTGTGAAG                         GCCAGACCACCTGATGACGATCGTTATGTGAGGAAATGCCGAAATGGCAGA
genomic: GTTCTATCTGCATCAGCATCCTGTCCATGTTGTCTAGTTCAACTGTGAAGgtacttttta ... gcttgaacagGCCAGACCACCTGATGACGATCGTTATGTGAGGAAATGCCGAAATGGCAGA
EST: gi|67579063|gb|BJ951214.1|BJ951214
EST:     GTTCTATCTGCATCAGCATCCTGTCCATGTTGTCTAGTTCAACTGTGAAG                         GCCAGACCACCTGATGACGATCGTTATGTGAGGAAATGCCGAAATGGCAGA
genomic: GTTCTATCTGCATCAGCATCCTGTCCATGTTGTCTAGTTCAACTGTGAAGgtacttttta ... gcttgaacagGCCAGACCACCTGATGACGATCGTTATGTGAGGAAATGCCGAAATGGCAGA
EST: gi|162221639|gb|FC397864.1|FC397864
EST:     GTTCTATCTGCATCAGCATCCTGTCCATGTTGTCTAGTTCAACTGTGAAG                         GCCAGACCACCTGATGACGATCGTTATGTGAGGAAATGCCGAAATGGCAGA
genomic: GTTCTATCTGCATCAGCATCCTGTCCATGTTGTCTAGTTCAACTGTGAAGgtacttttta ... gcttgaacagGCCAGACCACCTGATGACGATCGTTATGTGAGGAAATGCCGAAATGGCAGA
EST: gi|208366092|gb|DC951209.1|DC951209
EST:     GTTCTATCTGCATCAGCATCCTGTCCATGTTGTCTAGTTCAACTGTGAAG                         GCCAGACCACCTGATGACGACCGTTATGTGAGGAAATGCCGAAATGGCAGA
genomic: GTTCTATCTGCATCAGCATCCTGTCCATGTTGTCTAGTTCAACTGTGAAGgtacttttta ... gcttgaacagGCCAGACCACCTGATGACGATCGTTATGTGAGGAAATGCCGAAATGGCAGA
EST: gi|162160477|gb|FC336867.1|FC336867
EST:     GTTCTATCTGCATCAGCATCCTGTCCATGTTGTCTAGTTCAACTGTGAAG                         GCCAGACCACCTGATGACGATCGTTATGTGAGGAAATGCCGAAATGGCAGA
genomic: GTTCTATCTGCATCAGCATCCTGTCCATGTTGTCTAGTTCAACTGTGAAGgtacttttta ... gcttgaacagGCCAGACCACCTGATGACGATCGTTATGTGAGGAAATGCCGAAATGGCAGA

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: 22 (upstream exon), 35 (downstream exon)
Score: 14

ATATTCTTTATGACTCTTGGTCACCAGCAATGACCGTGAGTTCTATCTGCATCAGCATCCTGTCCATGTTGTCTAGTTCAACTGTGAAGgtacttttta ... gcttgaacagGCCAGACCACCTGATGACGATCGTTATGTGAGGAAATGCCGAAATGGCAGATCTCCCAAGGAAACACGGTGGTGGTTTCATGACGATAAAGTATGAGTTA




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