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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTAAAACAAGTATCATCACGCGATTCATGTATGACAAATTTGACAACACGTACCAGgttagcttctttccctcctagtcttcttgcataaaaattgtgtgctgctgacatttctggtttgccgtacatcaataactccatactctggatggtttcattctttttgttttttctagtaagaacctgtcctggcaggttcaaggttggtgctattgatgagttttcccttgataactttggcag

Basic information

species Physcomitrella patens
transcript PP1S39_147V6.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S39_147V6.2 (Physcomitrella patens), 5'ss of exon 2
lower sequence: GLYMA01G41090.1 (Glycine max), 5'ss of exon 1
GTAAAACAAGTATCATCACGCGATTCATGTATGACAAATTTGACAACACGTACCAGgttagcttctttccctcctagtcttcttgcataaaaattgtgtgctgctgacatttctggtttgccgtacatcaataactccatactctggatggtttcattctttttgttttttctagtaagaacctgtcctggcaggttcaaggttggtg-ctattgatgagttttcccttgataactttggcag
       |||||  | |  | | ||| ||  |||  | | ||     |      |   |||| || |  |   ||     || || || | || | ||  |  |  || | || ||| ||        || || |||       |     |||||| | | |||  |||    ||  | |     |   | ||  | |     || |  | |||                             
TCTTGCAAAGTACAAGCTGGTG-TTCTTGGGTGATCAGTCTGTGGGAA------AAACTAGCATCATCACTCGCT-----TCATGTATGACAAATTTG-ACAAC--ACTTATCAGgtctgatcagatccactatctcagccactttttaagtttcaatgtgtttcctttgatcagggaaataaaatgacgacaaatgctgcactgctaaccatta----------------------------

upper sequence: PP1S39_147V6.2 (Physcomitrella patens), 5'ss of exon 2
lower sequence: AT4G39890.1 (Arabidopsis thaliana), 5'ss of exon 1
GTAAAACAAGTATCATCACGCGATTCATGTATGACAAA-TTTGACAACACGTACCAGgttagcttctttccctcctagtcttcttgcataaaaattgtgtgctgc-tgacatttctggtttgccgtacatcaataactccatactctggatggtttcattctttttgttttttctagtaagaacctgtcctggcaggttcaaggttggtgctattgatgagttttcccttgataactttggcag
                             | || |||| ||| |      || |   |    |   | |  |    |  |      ||| |   | || |  ||  |||||  |  |     ||    | ||   | |   ||| | |  |  ||||| |  |||||||| |||   |||   | | ||   ||     |||| ||  |    ||  |   ||||   ||| |   | ||    
-----------------------------TTTGGCAAAGTTTAAACTGGTGTTCTTAGGAGACCAATCTGTCGGAAAAACCAGCATCATCAC--TCGTTTCATGTATGACAAATTCGAC--ACCACGTACCAGgtatt---tacacagattcctttcacttgttttgtttattcatttaaattcttctct--gcgacaacaagtttcttttgttt--tcgtttttttattgtttgatctg----

upper sequence: PP1S39_147V6.2 (Physcomitrella patens), 5'ss of exon 2
lower sequence: AT2G44610.1 (Arabidopsis thaliana), 5'ss of exon 1
GTAAAACAAGTATCATCACGCGATTCATGTATGACAAATTTGACAACACGTACCAGgttagcttctttccctcctagtcttcttgcataa-aaattgtgtgctgctgacatttctggtttgccgtacatcaataactccatactctggatggtttcattctttttgttttttctagtaagaacctgtcctggcaggttcaaggttggtgctattgatgagttttcccttgataactttggcag
       |||||| | |  | | ||| ||   ||  |||  | |  ||      |    ||  || || |    |     || || |  | |||||        || ||        ||| |  |     |||      ||  ||| || | |      | |||  || | | | |   ||   |   | || |  | | |||   ||   ||||                            
ACTCGCTAAGTATAAGCTGGTGTTTC-TGGGAGATCAATCCGTCGGCA------AAACCAGTATCATTACTCGAT-----TCATGTACGACAAATTCGACAACACTTACCAGgtaaatttccattgttcaaatctaggtattatctcgacgatgcacgacgtttgcttctattttgagggattatagtcgggaaaatcccagg---gtttgattg----------------------------

upper sequence: PP1S39_147V6.2 (Physcomitrella patens), 5'ss of exon 2
lower sequence: Vv15s0021g00640.t01 (Vitis vinifera), 5'ss of exon 1
GTAAAACAAGTATCATCACGCGATTCATGTATGACAAATTTGACAACACGTACCAGgttagc-ttctttccctcctagtcttcttgcataaaaattgtgtgctgctgacatttctggtttgcc-gtacatcaataactccatactctggatggtttcattctttttgttttttctagtaagaacctgtcctggcaggttcaaggttggtgctattgatgagttttcccttgataactttggcag
      ||||||  | | ||   ||| ||   ||| |||  | |   | |       | | |  ||  | | |    | |   ||  | || |  | |  | |     | ||   | | |||  ||  ||| ||   ||   | | | | ||||||   | ||  | ||  || | ||  |||  |||     |  | ||                                            
TCTCGCCAAGTACAAGCTCGTC-TTCTTGGGAGACCAATCCGTCGGAAAGACTAGCATCATCACTCGATTCATGTACGACAAATTCGACAACACCTATCAGgtcaaatctttatggatctgcttgtttatcgatt-ttcagcaattttgttggtttgtgttttggttttagttttggtgcgaatttgtttgatcccgatcct------------------------------------------

upper sequence: PP1S39_147V6.2 (Physcomitrella patens), 5'ss of exon 2
lower sequence: EDP09951 (Chlamydomonas reinhardtii), 5'ss of exon 2
-------------------------GTAAAACAAGTATCATCACGCGATTCATGTATGACAAATTTGACAACACGTACCAGgttagcttctttccctcctagtcttcttgcataaaaattgtgtgctgctgacatttctggtttgccgtacatcaataactccatactctggatggtttcattctttttgttttttctagtaagaacctgtcctggcaggttcaaggttggtgctattgatgagttttcccttgataactttggcag
                         | || ||    |||||||| ||||||||||||||||| || || ||||||||||||||  || |  |   | | |    ||| |  | ||  |    |     |   | |||  ||| | |||| ||                                                                                                                   
GTCTTCCTGGGAGACCAGTCTGTGGGCAAGACCTCCATCATCACCCGATTCATGTATGACAAGTTCGATAACACGTACCAGgt--gcgtactctgcgcat----ttcctttacaacgacaacgcctgacatgcttttgcggtct-ccgtgcag------------------------------------------------------------------------------------------------------------------

upper sequence: PP1S39_147V6.2 (Physcomitrella patens), 5'ss of exon 2
lower sequence: EFJ30542 (Selaginella moellendorffii), 5'ss of exon 1
GTAAAACAAGTATCATCACGCGATTCATGTATGACAAATTTGACAACACGTACCAGgttagcttctttccctcctagtcttcttgcataaaaattgtgtgctgctgacatttctggtttgccgtacatcaataactccatactctggatggtttcattctttttgttttttctagtaagaacctgtcctggcaggttcaaggttggtgctattgatgagttttcccttgataactttggcag
                                       |||  ||   |||| || |   |||  |   |    |||||    |     ||   | |        ||     |  | |    ||  |     |   |||||   | |||   | |    |||  | | |   | |  |   |      |  |  ||||||                                         
-------------------------------------GCTTGCAAA---GTACAAGCTCGTCTTTCTCGGCGATCAGTCT----GTGGGGAAGACGAGCATCATC-ACGCGATTCATGTATGATAAGTTTGACAACACATACCAGgtatgagattacgagtttcttctctctcactttgg--caaattggaaattttcaag-----------------------------------------

upper sequence: PP1S39_147V6.2 (Physcomitrella patens), 5'ss of exon 2
lower sequence: EFJ22994 (Selaginella moellendorffii), 5'ss of exon 1
GTAAAACAAGTATCATCACGCGATTCATGTATGACAAATTTGACAACACGTACCAGgttagcttctttccctcctagtcttcttgcataaaaattgtgtgctgctgacatttctggtttgccgtacatcaataactccatactctggatggtttcattctttttgttttttctagtaagaacctgtcctggcaggttcaaggttggtgctattgatgagttttcccttgataactttggcag
                                       |||  ||   |||| || |   |||  |   |    |||||    |     ||   | |        ||     |  | |    ||  |     |   |||||   | |||   | |    |||  | | |     |   ||  ||    |     ||||||                                         
-------------------------------------GCTTGCGAA---GTACAAGCTCGTCTTTCTCGGCGATCAGTCT----GTGGGGAAGACGAGCATCATC-ACGCGATTCATGTATGATAAGTTTGACAACACATACCAGgtatgagattacgagtttcttctctcactttggcaaattg----gaatttttcaag-----------------------------------------

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|208346149|gb|DC917102.1|DC917102
EST:     CAAGTATCATCACGCGATTCANGTATGACAAA-TTGACAACACGTACCAG                         GCAACTATTGGTATTGATTTTCTCTCCAAGACCATGTATCNTGAGGATCGC
genomic: CAAGTATCATCACGCGATTCATGTATGACAAATTTGACAACACGTACCAGgttagcttct ... actttggcagGCAACTATTGGTATTGATTTTCTCTCCAAGACCATGTATCTTGAGGATCGC
EST: gi|208390126|gb|DC941947.1|DC941947
EST:     CAAGTATCATCACGCGATTCATGTATGACAAATTTGACAACACGTACCAG                         GCAACTATTGGTATTGATTTTCTCTCCAAGACCATGTATCTTGAGGATCGC
genomic: CAAGTATCATCACGCGATTCATGTATGACAAATTTGACAACACGTACCAGgttagcttct ... actttggcagGCAACTATTGGTATTGATTTTCTCTCCAAGACCATGTATCTTGAGGATCGC

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: 12 (upstream exon), 24 (downstream exon)
Score: 2

GTAAAACAAGTATCATCACGCGATTCATGTATGACAAATTTGACAACACGTACCAGgttagcttct ... actttggcagGCAACTATTGGTATTGATTTTCTCTCCAAGACCATGTATCTTGAGGATCGCACTGTTAGACTACAGCTCTG




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