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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTACTCGATGGAGGGATGGTACAACCGGTCAGCATGTAGAATATGACCAAAGGCCTGATGTGTTCCGgtgaggttcttccccctgtcctgatctgtagttgccattcctgttttggctgttttggcggttgggagtgactgttttgcccctgagctatattttgattctgtgtaatttccgtacatgcag

Basic information

species Physcomitrella patens
transcript PP1S131_16V6.1
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S131_16V6.1 (Physcomitrella patens), 5'ss of exon 8
lower sequence: GLYMA08G21570.1 (Glycine max), 5'ss of exon 8
CTACTCGATGGAGGGATGGTACAACCGGTCAGCATGTAGAATATGACCAAAGGCCTGATGTGTTCCGgtgaggttcttccccctgtcctgatctgtagttgccattcctgttttggctgttttggcggttgggagtgactgttttgcccctgagctatattttgattctgtgtaatttccgtacatgcag
|||||   ||||||||| ||||||| ||   |||||| ||||||||||||||||||||||| ||| |||    ||  |         | ||| | | || |  | |  || |    || |||  || |||         ||| |||    | | || |||    | | | |  |                
CTACTAAGTGGAGGGATAGTACAACAGGCTCGCATGTGGAATATGACCAAAGGCCTGATGTTTTCAGgta---tttataattgaaatcggat-tat-gtagaaaatgttgatacaactatttatgcagtttt------ttgtattgatattaacctgtatggaaaatattttcag---------------

upper sequence: PP1S131_16V6.1 (Physcomitrella patens), 5'ss of exon 8
lower sequence: GLYMA07G01890.1 (Glycine max), 5'ss of exon 8
CTACTCGATGGAGGGATGGTACAACCGGTCAGCATGTAGAATATGACCAAAGGCCTGATGTGTTCCGgtgaggttcttccccctgtcctgatc-tgtagttgccattcctgttttggctgttttggcggttgggagtgactgttttgcccctgagctatattttgattctgtgtaatttccgtacatgcag
|||||   ||||||||| ||||||| ||   |||||| ||||||||||||||||| ||||| ||| ||||   ||  |       |   |||| |||||      ||  | | |    |  |   |   || | | |||   |        ||    ||||||| |                         
CTACTAAGTGGAGGGATAGTACAACGGGCTCGCATGTGGAATATGACCAAAGGCCAGATGTTTTCAGgtg---tttataattgaatttggatcatgtagaaaatgtttatatgtctatttatacagttttttgtattgatattaacttgtatggaaaatattttcag------------------------
















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|162252531|gb|FC427340.1|FC427340
EST:     GGTACAACCGGTCAGCATGTAGAATATGACCAAAGGCCTGATGTGTTCCG                         TGGAACTGTTCGCTATGCAAGTGTGCATGCACATTTGGGAAGGACTGGGAG
genomic: GGTACAACCGGTCAGCATGTAGAATATGACCAAAGGCCTGATGTGTTCCGgtgaggttct ... gtacatgcagTGGAACTGTTCGCTATGCAAGTGTGCATGCACATTTGGGAAGGACTGGGAG
EST: gi|162228110|gb|FC405692.1|FC405692
EST:     GGTACAACCGGTCAGCATGTAGAATATGACCAAAGGCCTGATGTGTTCCG                         TGGAACTGTTCGCTATGCAAGTGTGCATGCACATTTGGGAAGGACTGGGAG
genomic: GGTACAACCGGTCAGCATGTAGAATATGACCAAAGGCCTGATGTGTTCCGgtgaggttct ... gtacatgcagTGGAACTGTTCGCTATGCAAGTGTGCATGCACATTTGGGAAGGACTGGGAG
EST: gi|162257792|gb|FC433990.1|FC433990
EST:     GGTACAACCGGTCAGCATGTAGAATATGACCAAAGGCCTGATGTGTTCCG                         TGGAACTGTTCGCTATGCAAGTGTGCATGCACATTTGGGAAGGACTGGGAG
genomic: GGTACAACCGGTCAGCATGTAGAATATGACCAAAGGCCTGATGTGTTCCGgtgaggttct ... gtacatgcagTGGAACTGTTCGCTATGCAAGTGTGCATGCACATTTGGGAAGGACTGGGAG
EST: gi|162184061|gb|FC358807.1|FC358807
EST:     GGTACAACCGGTCAGCATGTAGAATATGACCAAAGGCCTGATGTGTTCCG                         TGGAACTGTTCGCTATGCAAGTGTGCATGCACATTTGGGAAGGACTGGGAG
genomic: GGTACAACCGGTCAGCATGTAGAATATGACCAAAGGCCTGATGTGTTCCGgtgaggttct ... gtacatgcagTGGAACTGTTCGCTATGCAAGTGTGCATGCACATTTGGGAAGGACTGGGAG
EST: gi|162163687|gb|FC340286.1|FC340286
EST:     GGTACAACCGGTCAGCATGTAGAATATGACCAAAGGCCTGATGTGTTCCG                         TGGAACTGTTCGCTATGCAAGTGTGCATGCACATTTGGGAAGGACTGGGAG
genomic: GGTACAACCGGTCAGCATGTAGAATATGACCAAAGGCCTGATGTGTTCCGgtgaggttct ... gtacatgcagTGGAACTGTTCGCTATGCAAGTGTGCATGCACATTTGGGAAGGACTGGGAG
EST: gi|162257871|gb|FC434069.1|FC434069
EST:     GGTACAACCGGTCAGCATGTAGAATATGACCAAAGGCCTGATGTGTTCCG                         TGGAACTGTTCGCTATGCAAGTGTGCATGCACA
genomic: GGTACAACCGGTCAGCATGTAGAATATGACCAAAGGCCTGATGTGTTCCGgtgaggttct ... gtacatgcagTGGAACTGTTCGCTATGCAAGTGTGCATGCACA

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: 34 (upstream exon), 26 (downstream exon)
Score: 14

CTACTCGATGGAGGGATGGTACAACCGGTCAGCATGTAGAATATGACCAAAGGCCTGATGTGTTCCGgtgaggttct ... gtacatgcagTGGAACTGTTCGCTATGCAAGTGTGCATGCACATTTGGGAAGGACTGGGAGTAGGAGGGACGACTTGGAATCACTGGCTTACACTTTGGTATTCCTTCTG




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