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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agaaatttagaacgcaacataaaaattttagttcttaatgaaccacgaatgaattgttcaaggatcaactgtctcatagttcttttaattcatgtcccagACAATTGGAGCGTGAAGGCTATCAGGAGGAAGACTACCGGAACTGGACGTATGCGCCACCTGCGTCATCTTCCCCGTCGATTTTCTAACAATTTCAGAGA

Basic information

species Physcomitrella patens
transcript PP1S475_18V6.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S475_18V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: LOC_Os02g56990.1 (Oryza sativa), 3'ss of exon 2
agaaatttagaacgcaacataaaaattt--tagttcttaatgaa--ccacgaatgaattgttcaaggatcaactgtctcatagttcttttaattcatgtcccagACAATTGGAGCGTGAAGGCTATCAGGAGGAAGACTACCGGAACTGGACGTATGCGCCACCTGCGTCATCTTCCCCGTCGATTTTCTAACAATTTCAGAGA
     |   |    ||      || |||  |||    |  | |   || |  ||   | ||||   ||  |  |   |  |  ||||   ||||     | ||||||| ||||| |||||||| |||||||||||||| || ||||||||  | ||| |  |||| || ||  | |||    | ||    |  || ||||||||
tctcttgctgttttcattgatgaagtttgatagaatctgctcagctcctctgatatgtagttct--gactactttgattct--ttctcgaaatttgaaacacagACAACTGGAGTGTGAAGGCCATCAGGAGGAAGACCACTGGAACTGGGAGGATGAGGTACCTTCGCCACGTGCCCAAGAGGTTCAAGAGTAACTTCAGAGA

upper sequence: PP1S475_18V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GLYMA08G21960.1 (Glycine max), 3'ss of exon 2
agaaatttagaacgcaacataaaaattttagttcttaatgaaccacgaatgaattgttcaaggatcaactgtctcatagttcttttaattcatgtcccagACAATTGGAGCGTGAAGGCTATCAGGAGGAAGACTACCGGAACTGGACGTATGCGCCACCTGCGTCATCTTCCCCGTCGATTTTCTAACAATTTCAGAGA
                   |||   ||||| || |||| | |  | |  |     ||  ||  |    | || |   | || |||  |||   || ||||| || |||||||||||||| || ||||| ||||| |||||||||||| | ||| |  || ||||| |  | || ||  ||||    | |   ||||||||
------------------gtaagttttttacttgttaaagtaatagggtt----cgtgtaaaaact--cggtttttgaattgtttcgatt---gttccagATAACTGGAGCGTGAAGGCCATTAGGAGAAAGACCACCGGAACTGGAAGGATGAGGTACTTGCGTAACGTGCCTCGCAGATTCAAGAGCGGCTTCAGAGA

upper sequence: PP1S475_18V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GLYMA07G00700.1 (Glycine max), 3'ss of exon 2
agaaatttagaacgcaacataaaaattttagttcttaatgaaccacgaatgaattgttcaaggatcaactgtctcatagttcttttaattcatgtcccagACAATTGGAGCGTGAAGGCTATCAGGAGGAAGACTACCGGAACTGGACGTATGCGCCACCTGCGTCATCTTCCCCGTCGATTTTCTAACAATTTCAGAGA
                        | |||  | |||| | ||  |  |  | |||||  ||  ||   | ||||   | || ||| |      || ||||| || |||||||||||||| || ||||| ||||| |||||||||||| | ||| |  || ||||| |  | |||||| |||||   |     ||||||||
---------------------gtgagttttttacttactaaagta-aatgggattgtgtaaaaatt--cggtctttgaattgtttgatg----gttccagATAACTGGAGCGTGAAGGCCATTAGGAGAAAGACCACCGGAACTGGAAGGATGAGGTACTTGCGTAACGTGCCCCGTAGATTTAAGAGTGGCTTCAGAGA

upper sequence: PP1S475_18V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: AT3G16080.1 (Arabidopsis thaliana), 3'ss of exon 2
------agaaatttagaacgcaacataaaaattttagttcttaatgaaccacgaatgaattgttcaaggatc--aactgtctcatagttcttttaattcatgtcccagACAATTGGAGCGTGAAGGCTATCAGGAGGAAGACTACCGGAACTGGACGTATGCGCCACCTGCGTCATCTTCCCCGTCGATTTTCTAACAATTTCAGAGA
        |  | |      |||   |    ||  | ||  | | | |  |   |||  |  ||   |  ||  | ||   |  | ||   |||  || |     ||||||| ||||| |||||||| ||||||||||||||||| || || ||| | ||| |  | || ||| || |||| ||||| ||    |     ||||||||
gttctttaatgtctttgcttcaattgattggttggaatt--tgagggattatctatgt-tcatttctgtctctgagctcaattcttgtctctttggttaa-----cagACAACTGGAGTGTGAAGGCCATCAGGAGGAAGACTACTGGTACCGGAAGGATGAGGTATCTCCGTAATGTTCCTCGTCGGTTCAAGACTGGATTCAGAGA

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|18333142|gb|BJ165156.1|BJ165156
EST:     GAAGAGCCGCTGCTCGGCTTGTGCCTACCCTGCCGCGAGAGTTCGCAGCT                         ACAATTGGAGCGTGAAGGCTATCAGGAGGAAGACTACCGGAACTGGACGTA
genomic: GAAGAGCCGCTGCTCGGCTTGTGCCTACCCTGCCGCGAGAGTTCGCAGCTgtaagtggct ... catgtcccagACAATTGGAGCGTGAAGGCTATCAGGAGGAAGACTACCGGAACTGGACGTA
EST: gi|162230854|gb|FC406693.1|FC406693
EST:     GAAGAGCCGCTGCTCGGCTTGTGCCTACCCTGCCGCGAGAGTTCGCAGCT                         ACAATTGGAGCGTGAAGGCTATCAGGAGGAAGACTACCGGAACTGGACGTA
genomic: GAAGAGCCGCTGCTCGGCTTGTGCCTACCCTGCCGCGAGAGTTCGCAGCTgtaagtggct ... catgtcccagACAATTGGAGCGTGAAGGCTATCAGGAGGAAGACTACCGGAACTGGACGTA
EST: gi|67571436|gb|BJ944260.1|BJ944260
EST:     GAAGAGCCGCTGCTCGGCTTGTGCCTACCCTGCCGCGAGAGTTCGCAGCT                         ACAATTGGAGCGTGAAGGCTATCAGGAGGAAGACTACCGGAACTGGACGTA
genomic: GAAGAGCCGCTGCTCGGCTTGTGCCTACCCTGCCGCGAGAGTTCGCAGCTgtaagtggct ... catgtcccagACAATTGGAGCGTGAAGGCTATCAGGAGGAAGACTACCGGAACTGGACGTA
EST: gi|162231822|gb|FC408584.1|FC408584
EST:     GAAGAGCCGCTGCTCGGCTTGTGCCTACCCTGCCGCGAGAGTTCGCAGCT                         ACAATTGGAGCGTGAAGGCTATCAGGAGGAAGACTACCGGAACTGGACGTA
genomic: GAAGAGCCGCTGCTCGGCTTGTGCCTACCCTGCCGCGAGAGTTCGCAGCTgtaagtggct ... catgtcccagACAATTGGAGCGTGAAGGCTATCAGGAGGAAGACTACCGGAACTGGACGTA
EST: gi|162231823|gb|FC408585.1|FC408585
EST:     GAAGAGCCGCTGCTCGGCTTGTGCCTACCCTGCCGCGAGAGTTCGCAGCT                         ACAATTGGAGCGTGAAGGCTATCAGGAGGAAGACTACCGGAACTGGACGTA
genomic: GAAGAGCCGCTGCTCGGCTTGTGCCTACCCTGCCGCGAGAGTTCGCAGCTgtaagtggct ... catgtcccagACAATTGGAGCGTGAAGGCTATCAGGAGGAAGACTACCGGAACTGGACGTA
EST: gi|67694768|gb|BJ955001.1|BJ955001
EST:     GAAGAGCCGCTGCTCGGCTTGTGCCTACCCTGCCGCGAGAGTTCGCAGCT                         ACAATTGGAGCGTGAAGGCTATCAGGAGGAAGACTACCGGAACTGGACGTA
genomic: GAAGAGCCGCTGCTCGGCTTGTGCCTACCCTGCCGCGAGAGTTCGCAGCTgtaagtggct ... catgtcccagACAATTGGAGCGTGAAGGCTATCAGGAGGAAGACTACCGGAACTGGACGTA
EST: gi|37837255|gb|BJ595263.1|BJ595263
EST:     GAAGAGCCGCTGCTCGGCTTGTGCCTACCCTGCCGCGAGAGTTCGCAGCT                         ACAATTGGAGCGTGAAGGCTATCAGGAGGAAGACTACCGGAACTGGACGTA
genomic: GAAGAGCCGCTGCTCGGCTTGTGCCTACCCTGCCGCGAGAGTTCGCAGCTgtaagtggct ... catgtcccagACAATTGGAGCGTGAAGGCTATCAGGAGGAAGACTACCGGAACTGGACGTA
EST: gi|18338750|gb|BJ170774.1|BJ170774
EST:     GAAGAGCCGCTGCTCGGCTTGTGCCTACCCTGCCGCGAGAGTTCGCAGCT                         ACAATTGGAGCGTGAAGGCTATCAGGAGGAAGACTACCGGAACTGGACGTA
genomic: GAAGAGCCGCTGCTCGGCTTGTGCCTACCCTGCCGCGAGAGTTCGCAGCTgtaagtggct ... catgtcccagACAATTGGAGCGTGAAGGCTATCAGGAGGAAGACTACCGGAACTGGACGTA
EST: gi|18325185|gb|BJ157181.1|BJ157181
EST:     GAAGAGCCGCTGCTCGGCTTGTGCCTACCCTGCCGCGAGAGTTCGCAGCT                         ACAATTGGAGCGTGAAGGCTATCAGGAGGAAGACTACCGGAACTGGACGTA
genomic: GAAGAGCCGCTGCTCGGCTTGTGCCTACCCTGCCGCGAGAGTTCGCAGCTgtaagtggct ... catgtcccagACAATTGGAGCGTGAAGGCTATCAGGAGGAAGACTACCGGAACTGGACGTA
EST: gi|67718429|gb|BJ968688.1|BJ968688
EST:     GAAGAGCCGCTGCTCGGCTTGTGCCTACCCTGCCGCGAGAGTTCGCAGCT                         ACAATTGGAGCGTGAAGGCTATCAGGAGGAAGACTACCGGAACTGGACGTA
genomic: GAAGAGCCGCTGCTCGGCTTGTGCCTACCCTGCCGCGAGAGTTCGCAGCTgtaagtggct ... catgtcccagACAATTGGAGCGTGAAGGCTATCAGGAGGAAGACTACCGGAACTGGACGTA
EST: gi|67701834|gb|BJ962067.1|BJ962067
EST:     GAAGAGCCGCTGCTCGGCTTGTGCCTACCCTGCCGCGAGAGTTCGCAGCT                         ACAATTGGAGCGTGAAGGCTATCAGGAGGAAGACTACCGGAACTGGACGTA
genomic: GAAGAGCCGCTGCTCGGCTTGTGCCTACCCTGCCGCGAGAGTTCGCAGCTgtaagtggct ... catgtcccagACAATTGGAGCGTGAAGGCTATCAGGAGGAAGACTACCGGAACTGGACGTA
EST: gi|18326076|gb|BJ158075.1|BJ158075
EST:     GAAGAGCCGCTGCTCGGCTTGTGCCTACCCTGCCGCGAGAGTTCGCAGCT                         ACAATTGGAGCGTGAAGGCTATCAGGAGGAAGACTACCGGAACTGGACGTA
genomic: GAAGAGCCGCTGCTCGGCTTGTGCCTACCCTGCCGCGAGAGTTCGCAGCTgtaagtggct ... catgtcccagACAATTGGAGCGTGAAGGCTATCAGGAGGAAGACTACCGGAACTGGACGTA
EST: gi|18357894|gb|BJ189953.1|BJ189953
EST:     GAAGAGCCGCTGCTCGGCTTGTGCCTACCCTGCCGCGAGAGTTCGCAGCT                         ACAATTGGAGCGTGAAGGCTATCAGGAGGAAGACTACCGGAACTGGACGTA
genomic: GAAGAGCCGCTGCTCGGCTTGTGCCTACCCTGCCGCGAGAGTTCGCAGCTgtaagtggct ... catgtcccagACAATTGGAGCGTGAAGGCTATCAGGAGGAAGACTACCGGAACTGGACGTA
EST: gi|67720324|gb|BJ970583.1|BJ970583
EST:     GAAGAGCCGCTGCTCGGCTTGTGCCTACCCTGCCGCGAGAGTTCGCAGCT                         ACAATTGGAGCGTGAAGGCTATCAGGAGGAAGACTACCGGAACTGGACGTA
genomic: GAAGAGCCGCTGCTCGGCTTGTGCCTACCCTGCCGCGAGAGTTCGCAGCTgtaagtggct ... catgtcccagACAATTGGAGCGTGAAGGCTATCAGGAGGAAGACTACCGGAACTGGACGTA
EST: gi|162224987|gb|FC401403.1|FC401403
EST:     GAAGAGCCGCTGCTCGGCTTGTGCCTACCCTGCCGCGAGAGTTCGCAGCT                         ACAATTGGAGCGTGAAGGCTATCAGGAGGAAGACTACCGGAACTGGACGTA
genomic: GAAGAGCCGCTGCTCGGCTTGTGCCTACCCTGCCGCGAGAGTTCGCAGCTgtaagtggct ... catgtcccagACAATTGGAGCGTGAAGGCTATCAGGAGGAAGACTACCGGAACTGGACGTA
EST: gi|18333873|gb|BJ165889.1|BJ165889
EST:     GAAGAGCCGCTGCTCGGCTTGTGCCTACCCTGCCGCGAGAGTTCGCAGCT                         ACAATTGGAGCGTGAAGGCTATCAGGAGGAAGACTACCGGAACTGGACGTA
genomic: GAAGAGCCGCTGCTCGGCTTGTGCCTACCCTGCCGCGAGAGTTCGCAGCTgtaagtggct ... catgtcccagACAATTGGAGCGTGAAGGCTATCAGGAGGAAGACTACCGGAACTGGACGTA

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), 35 (downstream exon)
Score: 50

AAGTCACACACGCTGTGCAGGCGCTGTGGCCGCAGAAGCTTTCACATCCAGAAGAGCCGCTGCTCGGCTTGTGCCTACCCTGCCGCGAGAGTTCGCAGCTgtaagtggct ... catgtcccagACAATTGGAGCGTGAAGGCTATCAGGAGGAAGACTACCGGAACTGGACGTATGCGCCACCTGCGTCATCTTCCCCGTCGATTTTCTAACAATTTCAGAGA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cgaatgaattgttcaaggatcaactgtctcatagttcttttaattcatgtcccagACAATTGGAGCGTGAAGGCTATCAGGAGGAAGACTACCGGAACTGGACGTATGCGCCACCTGCGTCATCTTCCCCGTCGATTTTCTAACAATTTCAGAGA
                                     ttttaat  putative branch site (score: 50)
                              atagttcttttaatt  TA-rich tract