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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tcgtattgtcaatgatttctggtagtaaaaaacaggactaagtcatcttctctgcgatttttgttgttttcttttcttcttcttttttattttacctcagGCTAAGACTACCAAGAAGATTGTACTGAGGTTACAGTGCCAGGCTTGCAAGCACGTGACACAACATCCTATCAAG

Basic information

species Physcomitrella patens
transcript PP1S22_326V6.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S22_326V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: GLYMA08G19320.1 (Glycine max), 3'ss of exon 2
tcgtattgtcaatgatttctggtagtaaaaaacaggactaagt-catcttctctgcgatttttgttgttttctttt-cttcttcttttttattttacctcagGCTAAGACTACCAAGAAGATTGTACTGAGGTTACAGTGCCAGGCTTGCAAGCACGTGACACAACATCCTATCAAG
                     |||             |||||| |||      |  || |||| ||  |  |     | | ||  |||||| || |  | |||||||||| |||||||||||||| |||||||| || ||||||| ||||||||| ||  | |||||  |||| |||
---------------------gtaacctctcgttaacctaagtgcataggaattaggagtttttttcctgacaaaaacatttttatttttaattga--ttagGCTAAGACCACCAAGAAGATTGTTCTGAGGTTGCAATGCCAGGGTTGCAAGCATGTCTCCCAACACGCTATTAAG

upper sequence: PP1S22_326V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: GLYMA15G05670.1 (Glycine max), 3'ss of exon 2
--tcgtattgtcaatgatttctggtagtaaaaaacaggactaagtcatcttctctgcgatttttgttgttttcttttcttcttcttttttattttacctcagGCTAAGACTACCAAGAAGATTGTACTGAGGTTACAGTGCCAGGCTTGCAAGCACGTGACACAACATCCTATCAAG
  |||| | || ||  ||||| | ||  |    | |||| | ||  ||||| | |    |||||| ||       |   |      |||||||| |  | ||||||| || |||||||||||||| |||||||| || ||||||| ||||||||| ||  | |||||  |||| |||
gttcgt-tggttaaatatttc-gttataagtgcataggaattagg-atctttttt----tttttgctgacaaaaatatat------ttttatttaaaat-agGCTAAAACCACCAAGAAGATTGTTCTGAGGTTGCAATGCCAGGGTTGCAAGCATGTCTCCCAACACGCTATTAAG

upper sequence: PP1S22_326V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: GLYMA15G05670.2 (Glycine max), 3'ss of exon 2
--tcgtattgtcaatgatttctggtagtaaaaaacaggactaagtcatcttctctgcgatttttgttgttttcttttcttcttcttttttattttacctcagGCTAAGACTACCAAGAAGATTGTACTGAGGTTACAGTGCCAGGCTTGCAAGCACGTGACACAACATCCTATCAAG----
  |||| | || ||  ||||| | ||  |    | |||| | ||  ||||| | |    |||||| ||       |   |      |||||||| |  | ||||||| || |||||||||||||| |||||||| || ||||||| ||||||||| ||  | |||||  |||| |||    
gttcgt-tggttaaatatttc-gttataagtgcataggaattagg-atctttttt----tttttgctgacaaaaatatat------ttttatttaaaat-agGCTAAAACCACCAAGAAGATTGTTCTGAGGTTGCAATGCCAGGGTTGCAAGCATGTCTCCCAACACGCTATTAAGGTTA

upper sequence: PP1S22_326V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: Vv13s0064g00880.t01 (Vitis vinifera), 3'ss of exon 2
------tcgtattgtcaatgatttctggtagtaaaaaacaggactaagtcatcttctctgcgatttttgttgttttcttttcttcttcttttttattttacctcagGCTAAGACTACCAAGAAGATTGTACTGAGGTTACAGTGCCAGGCTTGCAAGCACGTGACACAACATCCTATCAAG
        ||||  | |    | |  | |  | |||   |  |  ||| ||  |         | ||  | | ||     |    |||  || |   ||| |  |||||||||| |||||||||||||| |||||| | |||||||||| |||||| |||||  | || || || ||||||
ggttaactgtatccttagaattgttggcttctcaaattaactatcaagccaattgaggctaattcttcatagattgaccat----ttcccttgtgccttaac--agGCTAAGACCACCAAGAAGATTGTTCTGAGGCTCCAGTGCCAGGGTTGCAAACACGTATCCCAGCACCCAATCAAG

upper sequence: PP1S22_326V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: Vv01s0011g02090.t01 (Vitis vinifera), 3'ss of exon 2
---------------------------------------tcgt--attgtcaatgatttctggtagtaaaaaa-----caggactaagtcatcttctctgcgatttttgttg-------ttttcttttcttc--ttcttttttattttacctcagGCTAAGACTACCAAGAAGATTGTACTGAGGTTACAGTGCCAGGCTTGCAAGCACGTGACACAACATCCTATCAAG
                                       |  |  |||||      |||||  || | | | |      |||| |     |   | |    ||   || |         |   | |  | |   | | | ||| | | |   ||||| ||||| |||||||||||||| |||||| | || ||||||| |||||| || ||  | ||||| || ||||||
gtaaagaccctttctctggcattctcctcttccttgcaattatcaattgtttcatgtttcttataatgagagagcttgtaggatttttcaaatctgtagtagaagcttataagggcaaatccccatagcattgatccatctttttctcaaaccagGCCAAGACAACCAAGAAGATTGTGCTGAGGCTTCAATGCCAGGGTTGCAAACATGTATCGCAACACCCAATCAAG

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|18368682|gb|BJ200767.1|BJ200767
EST:     GGAAACAATCAGGATACGGAGGTCAGACCAAGCCTGTCTTCCACAAGAAG                         GCTAAGACTACCAAGAAGATTGTACTGAGGTTACAGTGCCAGGCTTGCAAG
genomic: GGAAACAATCAGGATACGGAGGTCAGACCAAGCCTGTCTTCCACAAGAAGgtatgttgcg ... tttacctcagGCTAAGACTACCAAGAAGATTGTACTGAGGTTACAGTGCCAGGCTTGCAAG
EST: gi|162262338|gb|FC437665.1|FC437665
EST:     GGAAACAATCAGGATACGGAGGTCAGACCAAGCCTGTCTTCCACAAGAAG                         GCTAAGACTACCAAGAAGATTGTACTGAGGTTACAGTGCCAGGCTTGCAAG
genomic: GGAAACAATCAGGATACGGAGGTCAGACCAAGCCTGTCTTCCACAAGAAGgtatgttgcg ... tttacctcagGCTAAGACTACCAAGAAGATTGTACTGAGGTTACAGTGCCAGGCTTGCAAG
EST: gi|162228552|gb|FC404150.1|FC404150
EST:     GGAAACAATCAGGATACGGAGGTCAGACCAAGCCTGTCTTCCACAAGAAG                         GCTAAGACTACCAAGAAGATTGTACTGAGGTTACAGTGCCAGGCTTGCAAG
genomic: GGAAACAATCAGGATACGGAGGTCAGACCAAGCCTGTCTTCCACAAGAAGgtatgttgcg ... tttacctcagGCTAAGACTACCAAGAAGATTGTACTGAGGTTACAGTGCCAGGCTTGCAAG
EST: gi|18335674|gb|BJ167694.1|BJ167694
EST:     GGAAACAATCAGGATACGGAGGTCAGACCAAGCCTGTCTTCCACAAGAAG                         GCTAAGACTACCAAGAAGATTGTACTGAGGTTACAGTGCCAGGCTTGCAAG
genomic: GGAAACAATCAGGATACGGAGGTCAGACCAAGCCTGTCTTCCACAAGAAGgtatgttgcg ... tttacctcagGCTAAGACTACCAAGAAGATTGTACTGAGGTTACAGTGCCAGGCTTGCAAG
EST: gi|18360736|gb|BJ192799.1|BJ192799
EST:     GGAAACAATCAGGATACGGAGGTCAGACCAAGCCTGTCTTCCACAAGAAG                         GCTAAGACTACCAAGAAGATTGTACTGAGGTTACAGTGCCAGGCTTGCAAG
genomic: GGAAACAATCAGGATACGGAGGTCAGACCAAGCCTGTCTTCCACAAGAAGgtatgttgcg ... tttacctcagGCTAAGACTACCAAGAAGATTGTACTGAGGTTACAGTGCCAGGCTTGCAAG
EST: gi|162225415|gb|FC401193.1|FC401193
EST:     GGAAACAATCAGGATACGGAGGTCAGACCAAGCCTGTCTTCCACAAGAAG                         GCTAAGACTACCAAGAAGATTGTACTGAGGTTACAGTGCCAGGCTTGCAAG
genomic: GGAAACAATCAGGATACGGAGGTCAGACCAAGCCTGTCTTCCACAAGAAGgtatgttgcg ... tttacctcagGCTAAGACTACCAAGAAGATTGTACTGAGGTTACAGTGCCAGGCTTGCAAG
EST: gi|162221524|gb|FC397541.1|FC397541
EST:     GGAAACAATCAGGATACGGAGGTCAGACCAAGCCTGTCTTCCACAAGAAG                         GCTAAGACTACCAAGAAGATTGTACTGAGGTTACAGTGCCAGGCTTGCAAG
genomic: GGAAACAATCAGGATACGGAGGTCAGACCAAGCCTGTCTTCCACAAGAAGgtatgttgcg ... tttacctcagGCTAAGACTACCAAGAAGATTGTACTGAGGTTACAGTGCCAGGCTTGCAAG
EST: gi|67575316|gb|BJ948140.1|BJ948140
EST:     GGAAACAATCAGGATACGGAGGTCAGACCAAGCCTGTCTTCCACAAGAAG                         GCTAAGACTACCAAGAAGATTGTACTGAGGTTACAGTGCCAGGCTTGCAAG
genomic: GGAAACAATCAGGATACGGAGGTCAGACCAAGCCTGTCTTCCACAAGAAGgtatgttgcg ... tttacctcagGCTAAGACTACCAAGAAGATTGTACTGAGGTTACAGTGCCAGGCTTGCAAG
EST: gi|67698779|gb|BJ959012.1|BJ959012
EST:     GGAAACAATCAGGATACGGAGGTCAGACCAAGCCTGTCTTCCACAAGAAG                         GCTAAGACTACCAAGAAGATTGTACTGAGGTTACAGTGCCAGGCTTGCAAG
genomic: GGAAACAATCAGGATACGGAGGTCAGACCAAGCCTGTCTTCCACAAGAAGgtatgttgcg ... tttacctcagGCTAAGACTACCAAGAAGATTGTACTGAGGTTACAGTGCCAGGCTTGCAAG
EST: gi|18327408|gb|BJ159410.1|BJ159410
EST:     GGAAACAATCAGGATACGGAGGTCAGACCAAGCCTGTCTTCCACAAGAAG                         GCTAAGACTACCAAGAAGATTGTACTGAGGTTACAGTGCCAGGCTTGCAAG
genomic: GGAAACAATCAGGATACGGAGGTCAGACCAAGCCTGTCTTCCACAAGAAGgtatgttgcg ... tttacctcagGCTAAGACTACCAAGAAGATTGTACTGAGGTTACAGTGCCAGGCTTGCAAG

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), 31 (downstream exon)
Score: 39

GTAAGAGGAGATATGACAGGAAACAATCAGGATACGGAGGTCAGACCAAGCCTGTCTTCCACAAGAAGgtatgttgcg ... tttacctcagGCTAAGACTACCAAGAAGATTGTACTGAGGTTACAGTGCCAGGCTTGCAAGCACGTGACACAACATCCTATCAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcttctctgcgatttttgttgttttcttttcttcttcttttttattttacctcagGCTAAGACTACCAAGAAGATTGTACTGAGGTTACAGTGCCAGGCTTGCAAGCACGTGACACAACATCCTATCAAG
            tttttgttgttttctt  CT-rich tract
                     ttttcttttcttcttc  TA-rich tract