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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aggttgtcaggggtataccattgttccgattttttatttcgacccttttctgtgacgaaatttgccatttctcattctgttgcaactcgctgtggggcagCCGTGGATTTTTTCAACCAGGTGAATCTACTCTATGGAACATTGACCGAGTTCTGCACACCTGAGAACTGTCCTACTATGTCCGCAGGACCCAA

Basic information

species Physcomitrella patens
transcript PP1S99_129V6.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S99_129V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: GLYMA09G34550.1 (Glycine max), 3'ss of exon 3
-----------------------------------------------------aggttgtcaggggtataccattgttccgattttt--------tatttcgacccttttctgtgacgaaatttgccatttctcattctgttgcaactcgctgtggggcagCCGTGGATTTTTTCAACCAGGTGAATCTACTCTATGGAACATTGACCGAGTTCTGCACACCTGAGAACTGTCCTACTATGTCCGCAGGACCCAA
                                                     | ||| ||    |  |   ||| |   | ||  |        ||||   |   | | |  |   |||||     |   || | | | || |  ||  |||     |||| || ||||| ||||||||||||||||| || ||||| ||  | || |||||||| || |||||||| ||||  || |||||||||||||||||
gtaaatatttttgtctctaatgcactgtttaagggcagtgtacagtcttgttgaagttttcttttgccttttattctctagtttcctcaactacgtattcacaatttatacaattctgaaatgcagtaag-ctgactttttttcttcttcctgcattacagCTGTTGATTTCTTCAACCAGGTGAATCTGCTTTATGGTACCCTTACAGAGTTCTGTACTCCTGAGAATTGTCGGACGATGTCCGCAGGACCCAA

upper sequence: PP1S99_129V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: GLYMA01G35130.2 (Glycine max), 3'ss of exon 3
aggttgtcaggggtatacca-ttgttccgattttttatttcgacccttttctgtgacgaaatttgcc--atttctcattctgttgcaactcgctgtggggcagCCGTGGATTTTTTCAACCAGGTGAATCTACTCTATGGAACATTGACCGAGTTCTGCACACCTGAGAACTGTCCTACTATGTCCGCAGGACCCAA
   ||| |     |   | | ||    | | | | ||||   |   | | |  |   |||||       | |      | | || |  ||  |||     |||| || ||||| ||||| ||||||||||| || ||||| ||  | || |||||||| || |||||||| ||||  || ||||| |||||||||||
---ttgccttttattctctagtttcctcaactatatattcataatttatacaattctgaaatgcagtaaactgacttctttttttcttcttcctgcattacagCTGTTGATTTCTTCAATCAGGTGAATCTGCTTTATGGTACCCTTACAGAGTTCTGTACTCCTGAGAATTGTCGGACAATGTCTGCAGGACCCAA

upper sequence: PP1S99_129V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: GLYMA01G35130.1 (Glycine max), 3'ss of exon 3
------------------------------------------------------aggttgtcaggggtataccattgttccgattttt--------tatttcgacccttttctgtgacgaaatttgcca--tttctcattctgttgcaactcgctgtggggcagCCGTGGATTTTTTCAACCAGGTGAATCTACTCTATGGAACATTGACCGAGTTCTGCACACCTGAGAACTGTCCTACTATGTCCGCAGGACCCAA
                                                      | ||| ||    |  |   ||| |   | ||  |        ||||   |   | | |  |   |||||     |   |      | | || |  ||  |||     |||| || ||||| ||||| ||||||||||| || ||||| ||  | || |||||||| || |||||||| ||||  || ||||| |||||||||||
gtaactattttttctctgtaatgcactgtttaagggcagtgtatagtctcgttgaagttttcttttgccttttattctctagtttcctcaactatatattcataatttatacaattctgaaatgcagtaaactgacttctttttttcttcttcctgcattacagCTGTTGATTTCTTCAATCAGGTGAATCTGCTTTATGGTACCCTTACAGAGTTCTGTACTCCTGAGAATTGTCGGACAATGTCTGCAGGACCCAA

upper sequence: PP1S99_129V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: AT5G45550.1 (Arabidopsis thaliana), 3'ss of exon 3
-------------------------------------------------------------------------------------aggttgtcaggggtataccattgttccgattt-tttatttcgacccttttctgt-gacgaaatttgcca-tttctcattctgttgcaactcgctgtggggcagCCGTGGATTTTTTCAACCAGGTGAATCTACTCTATGGAACATTGACCGAGTTCTGCACACCTGAGAACTGTCCTACTATGTCCGCAGGACCCAA
                                                                                        || ||     | |  |  ||||   | |  | ||| |  |  |   |   | ||    |||||| | ||  | ||  | ||||   ||  | |    |||| |||||||| || || ||||||||| | || ||||| ||  | |||||||||||||||||||| ||||||||||| ||| | || || || ||
gtgagtaccactctgcttgcagtctcatggtcacttttttgtgtacttagtcttggggatgtaatgcaggcgttgaataattactgatttctctttctttttacgatgttgaaactcatatatgtacatacacatagattgagaggatttgctaattgttgatatttttgcttttcctttt----cagCTGTGGATTTCTTTAATCAGGTGAATTTGCTATATGGCACCCTTACCGAGTTCTGCACACCTGATAACTGTCCTACAATGACTGCTGGCCCAAA

upper sequence: PP1S99_129V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: Vv04s0043g00130.t01 (Vitis vinifera), 3'ss of exon 3
-----aggttgtcaggggtataccattgttccgattttttatttcgacccttttctgtgacgaaatttgccatttctcattctgttgcaactcgctgtggggcagCCGTGGATTTTTTCAACCAGGTGAATCTACTCTATGGAACATTGACCGAGTTCTGCACACCTGAGAACTGTCCTACTATGTCCGCAGGACCCAA
     | ||    |    | |         || |   |    |  |  | |  | || ||| || | |      ||      ||||| |  |          |||| || ||||| ||||||||||||||||| |||||||| ||  | || |||||||| ||||| |||||||||||||| ||| | || || |||||
tttctatgtatctaattctctgaggccacaccaaaagtaggatcagggc-tactgtgggacaaattctaa----tccagggttgttggatgttttcaactttcagCTGTTGATTTCTTCAACCAGGTGAATCTGCTCTATGGTACGCTCACTGAGTTCTGTACACCAGAGAACTGTCCTACAATGACTGCTGGCCCCAA

upper sequence: PP1S99_129V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: EFJ17641 (Selaginella moellendorffii), 3'ss of exon 3
aggttgtcaggggtataccattgttccgattttttatttcgaccctttt-ctgtgacgaaatttgcc---atttctcattctg------ttgcaactcgctgtggggcagCCGTGGATTTTTTCAACCAGGTGAATCTACTCTATGGAACATTGACCGAGTTCTGCACACCTGAGAACTGTCCTACTATGTCCGCAGGACCCAA
  ||  ||  |  | | || | | | || |||||| ||| |    | ||  |||        ||||    ||| |   || ||       | ||| ||  ||    ||||| ||||| |||||||| ||||||||||| ||||| || || ||||| ||||| ||||| || ||||| ||||| || ||||| || ||||| ||
--gtaatctcgt-tcttccctcgctgcgttttttttttttgttgttgttgttgttgttgttcttgctcgtattccaggttttgagctaacttcaagtctttgctatgcagCGGTGGACTTTTTCAATCAGGTGAATCTTCTCTACGGGACGTTGACGGAGTTTTGCACGCCAGAGAATTGTCCAACCATGTCTGCTGGACCGAA

upper sequence: PP1S99_129V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: EFJ29107 (Selaginella moellendorffii), 3'ss of exon 3
aggttgtcaggggtataccattgttccgattttttatttcgacccttttctgtgacgaaatttgccatttctca--ttctg------ttgcaactcgctgtggggcagCCGTGGATTTTTTCAACCAGGTGAATCTACTCTATGGAACATTGACCGAGTTCTGCACACCTGAGAACTGTCCTACTATGTCCGCAGGACCCAA
  ||  ||  |  | | || | | | || |||||| |||      || |   ||  |   ||   | | |  ||  || ||       | ||| ||  ||    ||||| ||||| |||||||| ||||||||||| ||||| || || ||||| ||||| ||||| || ||||| ||||| || ||||| || ||||| ||
--gtaatctcgt-tcttccctcgctgcgttttttttttttttttgttgttgttgttgttcttgctcgtattccaggttttgagctaacttcaagtctttgctatgcagCGGTGGACTTTTTCAATCAGGTGAATCTTCTCTACGGGACGTTGACGGAGTTTTGCACGCCAGAGAATTGTCCAACCATGTCTGCTGGACCGAA

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|162246776|gb|FC423874.1|FC423874
EST:     CGTGCGCCTACCTCCTGGCGAAGATCTCTACGAGTGGTTGGCTGTTAATA                         CCGTGGATTTTTTCAACCAGGTGAATCTACTCTATGGAACATTGACCGAGT
genomic: CGTGCGCCTACCTCCTGGCGAAGATCTCTACGAGTGGTTGGCTGTTAATAgtaagtttta ... tgtggggcagCCGTGGATTTTTTCAACCAGGTGAATCTACTCTATGGAACATTGACCGAGT
EST: gi|67575885|gb|BJ948709.1|BJ948709
EST:     CGTGCGCCTACCTCCTGGCGAAGATCTCTACGAGTGGTTGGCTGTTAATA                         CCGTGGATTTTTTCAACCAGGTGAATCTACTCTATGGAACATTGACCGAGT
genomic: CGTGCGCCTACCTCCTGGCGAAGATCTCTACGAGTGGTTGGCTGTTAATAgtaagtttta ... tgtggggcagCCGTGGATTTTTTCAACCAGGTGAATCTACTCTATGGAACATTGACCGAGT
EST: gi|162170894|gb|FC346585.1|FC346585
EST:     CGTGCGCCTACCTCCTGGCGAAGATCTCTACGAGTGGTTGGCTGTTAATA                         CCGTGGATTTTTTCAACCAGGTGAATCTACTCTATGGAACATTGACCGAGT
genomic: CGTGCGCCTACCTCCTGGCGAAGATCTCTACGAGTGGTTGGCTGTTAATAgtaagtttta ... tgtggggcagCCGTGGATTTTTTCAACCAGGTGAATCTACTCTATGGAACATTGACCGAGT
EST: gi|162266887|gb|FC443001.1|FC443001
EST:     CGTGCGCCTACCTCCTGGCGAAGATCTCTACGAGTGGTTGGCTGTTAATA                         CCGTGGATTTTTTCAACCAGGTGAATCTACTCTATGGAACATTGACCGAGT
genomic: CGTGCGCCTACCTCCTGGCGAAGATCTCTACGAGTGGTTGGCTGTTAATAgtaagtttta ... tgtggggcagCCGTGGATTTTTTCAACCAGGTGAATCTACTCTATGGAACATTGACCGAGT
EST: gi|67726815|gb|BJ977074.1|BJ977074
EST:     TACGAGTGGTTGGCTGTTAATA                         CCGTGGANNNNNNNCAACCAGGTGAATCTACTCTATGGAACATTGACCGAG
genomic: TACGAGTGGTTGGCTGTTAATAgtaagtttta ... tgtggggcagCCGTGGA-TTTTTTCAACCAGGTGAATCTACTCTATGGAACATTGACCGAG
EST: gi|67570910|gb|BJ943734.1|BJ943734
EST:     CGTGCGCCTACCTCCTGGCGAAGATCTCTACGAGTGGTTGGCTGTTAATA                         CCGTGGATTTTTTCAACCAGGTGAATCTACTCTATGGAACATTGACCGAGT
genomic: CGTGCGCCTACCTCCTGGCGAAGATCTCTACGAGTGGTTGGCTGTTAATAgtaagtttta ... tgtggggcagCCGTGGATTTTTTCAACCAGGTGAATCTACTCTATGGAACATTGACCGAGT
EST: gi|162230786|gb|FC406417.1|FC406417
EST:     CGTGCGCCTACCTCCTGGCGAAGATCTCTACGAGTGGTTGGCTGTTAATA                         CCGTGGATTTTTTCAACCAGGTGAATCTACTCTATGGAACATTGACCGAGT
genomic: CGTGCGCCTACCTCCTGGCGAAGATCTCTACGAGTGGTTGGCTGTTAATAgtaagtttta ... tgtggggcagCCGTGGATTTTTTCAACCAGGTGAATCTACTCTATGGAACATTGACCGAGT
EST: gi|162240620|gb|FC419163.1|FC419163
EST:     CGTGCGCCTACCTCCTGGCGAAGATCTCTACGAGTGGTTGGCTGTTAATA                         CCGTGGATTTTTTCAACCAGGTGAATCTACTCTATGGAACATTGACCGAGT
genomic: CGTGCGCCTACCTCCTGGCGAAGATCTCTACGAGTGGTTGGCTGTTAATAgtaagtttta ... tgtggggcagCCGTGGATTTTTTCAACCAGGTGAATCTACTCTATGGAACATTGACCGAGT
EST: gi|162215557|gb|FC391649.1|FC391649
EST:     CGTGCGCCTACCTCCTGGCGAAGATCTCTACGAGTGGTTGGCTGTTAATA                         CCGTGGATTTTTTCAACCAGGTGAATCTACTCTATGGAACATTGACCGAGT
genomic: CGTGCGCCTACCTCCTGGCGAAGATCTCTACGAGTGGTTGGCTGTTAATAgtaagtttta ... tgtggggcagCCGTGGATTTTTTCAACCAGGTGAATCTACTCTATGGAACATTGACCGAGT
EST: gi|7207622|gb|AW561562.1|AW561562
EST:     CGTGCGCCTACCTCCTGGCGAAGATCTCTACGAGTGGTTGGCTGTTAATA                         CCGTGGATTTTTTCAACCAGGTGAATCTACTCTATGGAACATTGACCGAGT
genomic: CGTGCGCCTACCTCCTGGCGAAGATCTCTACGAGTGGTTGGCTGTTAATAgtaagtttta ... tgtggggcagCCGTGGATTTTTTCAACCAGGTGAATCTACTCTATGGAACATTGACCGAGT
EST: gi|18364712|gb|BJ196785.1|BJ196785
EST:     CGTGCGCCTACCTCCTGGCGAAGATCTCTACGAGTGGTTGGCTGTTAATA                         CCGTGGATTTTTTCAACCAGGTGAATCTACTCTATGGAACATTGACCGAGT
genomic: CGTGCGCCTACCTCCTGGCGAAGATCTCTACGAGTGGTTGGCTGTTAATAgtaagtttta ... tgtggggcagCCGTGGATTTTTTCAACCAGGTGAATCTACTCTATGGAACATTGACCGAGT

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: 32 (upstream exon), 29 (downstream exon)
Score: 17

CTGCGCAAGCACATTGATGCGACTCTTGGAAGTGGAAACTTACGAGAGGCCGTGCGCCTACCTCCTGGCGAAGATCTCTACGAGTGGTTGGCTGTTAATAgtaagtttta ... tgtggggcagCCGTGGATTTTTTCAACCAGGTGAATCTACTCTATGGAACATTGACCGAGTTCTGCACACCTGAGAACTGTCCTACTATGTCCGCAGGACCCAA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttctgtgacgaaatttgccatttctcattctgttgcaactcgctgtggggcagCCGTGGATTTTTTCAACCAGGTGAATCTACTCTATGGAACATTGACCGAGTTCTGCACACCTGAGAACTGTCCTACTATGTCCGCAGGACCCAA
            aaattt  TA-rich tract