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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGATACTGCTGGCCAGGAGCGCTTCCGGAGTTTGATTCCCAGCTACATACGGGATTCGTCCGTGGCAGTCGTCGTGTACGATGTAGCGAgtaagttcttgcttctttgcgtttctcgatcatactgagggagtaaaacttcggttccag

Basic information

species Selaginella moellendorffii
transcript EFJ22994
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ22994 (Selaginella moellendorffii), 5'ss of exon 3
lower sequence: PP1S39_147V6.1 (Physcomitrella patens), 5'ss of exon 5
GGATACTGCTGGCCAGGAGCGCTTCCGGAGTTTGATTCCCAGCTACATACGGGATTCGTCCGTGGCAGTCGTCGTGTACGATGTAGCGAgtaagttcttgcttctttgcgtttctcgatcatactgagggagtaaaacttcggttccag-----------------------------------------
||| |||||||| |||||| | ||  |||||||||||||||||||||| |||||||||||||||||||| || || || |||||  | |||||||  ||| ||  ||   || | | |    |||| |    || | |||  |||   |                                         
GGACACTGCTGGACAGGAGAGGTTTAGGAGTTTGATTCCCAGCTACATCCGGGATTCGTCCGTGGCAGTGGTTGTCTATGATGTTTCCAgtaagtatttgtttgattttcttacccaagagcactgtgtctttaca-cttgagttgttgcgtaagatttgttagaaggatggcctctactggtgtatcaa

upper sequence: EFJ22994 (Selaginella moellendorffii), 5'ss of exon 3
lower sequence: PP1S346_29V6.1 (Physcomitrella patens), 5'ss of exon 4
GGATACTGCTGGCCAGGAGCGCTTCCGGAGTTTGATTCCCAGCTACATACGGGATTCGTCCGTGGCAGTCGTCGTGTACGATGTAGCGAgtaagttcttgcttcttt---------gcgtttctcgatcatactgagggagtaaaacttcggttccag-------------------------------
|||||| ||||| |||||| | ||| ||||||| ||||| || ||||| |||||||||||||||||||| || |||||||||||  | ||||||| | |  || |              ||| |   ||| || |  | |        || ||   ||                               
GGATACCGCTGGACAGGAGAGGTTCAGGAGTTTAATTCCTAGTTACATTCGGGATTCGTCCGTGGCAGTGGTTGTGTACGATGTTTCAAgtaagtacatttttgtgacaaaagaggaattttgttcctcacacagttgtacggttggctcagtattagtacattaattgtttcactgatgtaacacggg

upper sequence: EFJ22994 (Selaginella moellendorffii), 5'ss of exon 3
lower sequence: PP1S2_143V6.1 (Physcomitrella patens), 5'ss of exon 5
GGATACTGCTGGCCAGGAGCGCTTCCGGAGTTTGATTCCCAGCTACATACGGGATTCGTCCGTGGCAGTCGTCGTGTACGATGTAGCGAgtaagttcttgct---tctttgcgtttctcgatcat-actgagggagtaaaacttcggttccag-------------------------------
||| || ||||| || ||||| ||| ||||||||||||| |||||||| ||||| |||||||||||||| || ||||| |||||  ||||| |||  ||| |   ||||| |  |    || ||| |      |   ||||  | |  || ||                               
GGACACAGCTGGACAAGAGCGGTTCAGGAGTTTGATTCCTAGCTACATTCGGGACTCGTCCGTGGCAGTGGTTGTGTATGATgtttcgagtgagtatttgttgaatcttttcaatgaaagagcattaacacctgcacaaaaagttg--tcaaggtttgcatctgtaaaaatttttccatcattg

upper sequence: EFJ22994 (Selaginella moellendorffii), 5'ss of exon 3
lower sequence: PP1S456_9V6.1 (Physcomitrella patens), 5'ss of exon 4
GGATACTGCTGGCCAGGAGCGCTTCCGGAGTTTGATTCCCAGCTACATACGGGATTCGTCCGTGGCAGTCGTCGTGTACGATGTAGCGAgtaagttcttgctt----ctttgcgtttctcgatcatactgagggagtaaaacttcggttccag------------------------------------
||| || ||||| || ||| | ||| ||||||| |||||||||||||| || || ||||| |||||||| || || ||||||||  |||||||||   |   |    | |||             |  | |   ||     ||  |||  | |                                    
GGACACAGCTGGACAAGAGAGGTTCAGGAGTTTAATTCCCAGCTACATTCGAGACTCGTCTGTGGCAGTAGTTGTTTACGATGTTTCGAgtaagtatatatataaggcattgtaaggagtttcgttcttcacctagctgtgctgtggtcactgtattcgcgtgttaatagttgcattgacataacaaga

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|169040413|gb|FE450298.1|FE450298
EST:     CCGTGGCAGTCGTCGTGTACGATGTAGCGA                         ATCGCCAGTCGTTTCTAAACACGGCCAGATGGGTGGAAGAAGTCCGCACGG
genomic: CCGTGGCAGTCGTCGTGTACGATGTAGCGAgtaagttctt ... tcggttccagATCGCCAGTCGTTTCTAAACACGGCCAGATGGGTGGAAGAAGTCCGCACGG
EST: gi|169042135|gb|FE454178.1|FE454178
EST:     CAGCTACATACGGGATTCGTCCGTGGCAGTCGTCGTGTACGATGTAGCGA                         ATCGCCAGTCGTTTCTAAACACGGCCAGATGGGTGGAAGAAGTCCGCACGG
genomic: CAGCTACATACGGGATTCGTCCGTGGCAGTCGTCGTGTACGATGTAGCGAgtaagttctt ... tcggttccagATCGCCAGTCGTTTCTAAACACGGCCAGATGGGTGGAAGAAGTCCGCACGG
EST: gi|169040414|gb|FE450299.1|FE450299
EST:     CAGCTACATACGGGATTCGTCCGTGGCAGTCGTCGTGTACGATGTAGCGA                         ATCGCCAGTCGTTTCTAAACACGGCCAGATGGGTGGAAGAAGTCCGCACGG
genomic: CAGCTACATACGGGATTCGTCCGTGGCAGTCGTCGTGTACGATGTAGCGAgtaagttctt ... tcggttccagATCGCCAGTCGTTTCTAAACACGGCCAGATGGGTGGAAGAAGTCCGCACGG
EST: gi|169033383|gb|FE441762.1|FE441762
EST:     CAGCTACATACGGGATTCGTCCGTGGCAGTCGTCGTGTACGATGTAGCGA                         ATCGCCAGTCGTTTCTAAACACGGCCAGATGGGTGGAAGAAGTCCGCACGG
genomic: CAGCTACATACGGGATTCGTCCGTGGCAGTCGTCGTGTACGATGTAGCGAgtaagttctt ... tcggttccagATCGCCAGTCGTTTCTAAACACGGCCAGATGGGTGGAAGAAGTCCGCACGG
EST: gi|169039199|gb|FE447795.1|FE447795
EST:     CAGCTACATACGGGATTCGTCCGTGGCAGTCGTCGTGTACGATGTAGCGA                         ATCGCCAGTCGTTTCTAAACACGGCCAGATGGGTGGAAGAAGTCCGCACGG
genomic: CAGCTACATACGGGATTCGTCCGTGGCAGTCGTCGTGTACGATGTAGCGAgtaagttctt ... tcggttccagATCGCCAGTCGTTTCTAAACACGGCCAGATGGGTGGAAGAAGTCCGCACGG
EST: gi|169047766|gb|FE454622.1|FE454622
EST:     CAGCTACATACGGGATTCGTCCGTGGCAGTCGTCGTGTACGATGTAGCGA                         ATCGCCAGTCGTTTCTAAACACGGCCAGATGGGTGGAAGAAGTCCGCACGG
genomic: CAGCTACATACGGGATTCGTCCGTGGCAGTCGTCGTGTACGATGTAGCGAgtaagttctt ... tcggttccagATCGCCAGTCGTTTCTAAACACGGCCAGATGGGTGGAAGAAGTCCGCACGG
EST: gi|169033384|gb|FE441763.1|FE441763
EST:     CAGCTACATACGGGATTCGTCCGTGGCAGTCGTCGTGTACGATGTAGCGA                         ATCGCCAGTCGTTTCTAAACACGGCCAGATGGGTGGAAGAAGTCCGCACGG
genomic: CAGCTACATACGGGATTCGTCCGTGGCAGTCGTCGTGTACGATGTAGCGAgtaagttctt ... tcggttccagATCGCCAGTCGTTTCTAAACACGGCCAGATGGGTGGAAGAAGTCCGCACGG
EST: gi|169101421|gb|FE502538.1|FE502538
EST:     CAGCTACATACGGGATTCGTCCGTGGCAGTCGTCGTGTACGATGTAGCGA                         ATCGCCAGTCGTTTCTAAACACGGCCAGATGGGTGGAAGAAGTCCGCACGG
genomic: CAGCTACATACGGGATTCGTCCGTGGCAGTCGTCGTGTACGATGTAGCGAgtaagttctt ... tcggttccagATCGCCAGTCGTTTCTAAACACGGCCAGATGGGTGGAAGAAGTCCGCACGG
EST: gi|169039198|gb|FE447794.1|FE447794
EST:     CAGCTACATACGGGATTCGTCCGTGGCAGTCGTCGTGTACGATGTAGCGA                         ATCGCCAGTCGTTTCTAAACACGGCCAGATGGGTGGAAGAAGTCCGCACGG
genomic: CAGCTACATACGGGATTCGTCCGTGGCAGTCGTCGTGTACGATGTAGCGAgtaagttctt ... tcggttccagATCGCCAGTCGTTTCTAAACACGGCCAGATGGGTGGAAGAAGTCCGCACGG
EST: gi|169101420|gb|FE502537.1|FE502537
EST:     CAGCTACATACGGGATTCGTCCGTGGCAGTCGTCGTGTACGATGTAGCGA                         ATCGCCAGTCGTTTCTAAACACGGCCAGATGGGTGGAAGAAGTCCGCACGG
genomic: CAGCTACATACGGGATTCGTCCGTGGCAGTCGTCGTGTACGATGTAGCGAgtaagttctt ... tcggttccagATCGCCAGTCGTTTCTAAACACGGCCAGATGGGTGGAAGAAGTCCGCACGG
EST: gi|169036631|gb|FE446555.1|FE446555
EST:     CAGCTACATACGGGATTCGTCCGTGGCAGTCGTCGTGTACGATGTAGCGA                         ATCGCCAGTCGTTTCTAAACACGGCCAGATGGGTGGAAGAAGTCCGCACGG
genomic: CAGCTACATACGGGATTCGTCCGTGGCAGTCGTCGTGTACGATGTAGCGAgtaagttctt ... tcggttccagATCGCCAGTCGTTTCTAAACACGGCCAGATGGGTGGAAGAAGTCCGCACGG
EST: gi|169104604|gb|FE508204.1|FE508204
EST:     CAGCTACATACGGGATTCGTCCGTGGCAGTCGTCGTGTACGATGTAGCGA                         ATCGCCAGTCGTTTCTAAACACGGCCAGATGGGTGGAAGAAGTCCGCACGG
genomic: CAGCTACATACGGGATTCGTCCGTGGCAGTCGTCGTGTACGATGTAGCGAgtaagttctt ... tcggttccagATCGCCAGTCGTTTCTAAACACGGCCAGATGGGTGGAAGAAGTCCGCACGG

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), 34 (downstream exon)
Score: 49

GGATACTGCTGGCCAGGAGCGCTTCCGGAGTTTGATTCCCAGCTACATACGGGATTCGTCCGTGGCAGTCGTCGTGTACGATGTAGCGAgtaagttctt ... tcggttccagATCGCCAGTCGTTTCTAAACACGGCCAGATGGGTGGAAGAAGTCCGCACGGAGCGGGGTAGCGATGTCATCATCGTTCTCGTCGGGAACAAGACGGATTT




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