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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCTGTGGTGCACCAGGCAGGAGACAAGTGTCCTGAACATTGACATGAAGGCAAACATTTGCTGTGTCAAATACAATCCCGGATCTAGCAATTTTGTCGCGgtatttctttcaactagcaaagattcttgttgtgtttgacagtgcctttgtttactttttctag

Basic information

species Selaginella moellendorffii
transcript EFJ28584
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ28584 (Selaginella moellendorffii), 5'ss of exon 10
lower sequence: GLYMA14G05430.1 (Glycine max), 5'ss of exon 10
GCTGTGGTGCACCAGGCAGGAGACAAGTGTCCTGAACATTGACATGAAGGCAAACATTTGCTGTGTCAAATACAATCCCGGATCTAGCAATTTTGTCGCGgta--tttctttcaactagcaaagattcttgttgtgtttgacagtgcctttgt-ttactttttctag--------------------------------------
  | ||||| || |  |||||  | ||||| || || || |||||||| |||||||| |||||||||||||| ||||| |||||| |||||| | | || |||  |  ||||||   ||  || | |     |   |||||   |  |  ||| |||  || | | |                                      
AATTTGGTGTACAAATCAGGAAGCTAGTGTTCTAAATATAGACATGAAAGCAAACATATGCTGTGTCAAATATAATCCTGGATCTGGCAATTATATTGCAgtaagtacctttcattcagtcaaaact-----tagatttgatcctatccatgtattatcttgtgtcgatcattcagcttagcttccaacttgtgacattgcttgg

upper sequence: EFJ28584 (Selaginella moellendorffii), 5'ss of exon 10
lower sequence: GLYMA02G43540.1 (Glycine max), 5'ss of exon 10
GCTGTGGTGCACCAGGCAGGAGACAAGTGTCCTGAACATTGACATGAAGGCAAACATTTGCTGTGTCAAATACAATCCCGGATCTAGCAATTTTGTCGCGgta--tttctttcaactagcaaagattcttgttgtgtttgacagtgcctttgtttactttttctag------------------------------------
  | |||||||| |  |||||  | ||||| || || || |||||||| |||||||| || ||||||||||| ||||| |||||| |||||| | | || |||  |  ||||||   ||  || | | | |  | |  |  | | |  || ||| ||| |   ||                                     
AATTTGGTGCACTAATCAGGAAGCTAGTGTTCTAAATATAGACATGAAAGCAAACATATGTTGTGTCAAATATAATCCTGGATCTGGCAATTATATTGCAgtaagtacctttcattcagttaaaact-tagaagagaatatctg-gatttagttcactctagatatgatcctatccatgttttatcttgtgtctatcattca

upper sequence: EFJ28584 (Selaginella moellendorffii), 5'ss of exon 10
lower sequence: Vv12s0059g01420.t01 (Vitis vinifera), 5'ss of exon 10
GCTGTGGTGCACCAGGCAGGAGACAAGTGTCCTGAACATTGACATGAAGGCAAACATTTGCTGTGTCAAATACAATCCCGGATCTAGCAATTTTGTCGCGgtatttctttcaactagcaaagattcttgt-tgtgtttgacagtgcctttgttt---actttttctag---------------------------------
  | |||||||| |  |||||| | || || || |||||||||||||| ||||| || || |||||||| || ||||| |||||||||| || | | |||||||  ||   |      | | |||||| | |   | |  | ||     |||||   |  | |||  |                                 
AGTTTGGTGCACAAACCAGGAGGCTAGCGTTCTTAACATTGACATGAAAGCAAATATATGTTGTGTCAAGTATAATCCTGGATCTAGCATTTATATTGCGgtatg-ctcctattccatacatattcttttattaatgtagctgtaaacctgttttgcatatattcctgtctaaacctgacaactttgtgaggccacagttt

upper sequence: EFJ28584 (Selaginella moellendorffii), 5'ss of exon 10
lower sequence: PP1S135_17V6.1 (Physcomitrella patens), 5'ss of exon 10
GCTGTGGTGCACCAGGCAGGAGACAAGTGTCCTGAACATTGACATGAAGGCAAACATTTGCTGTGTCAAATACAATCCCGGATCTAGCAATTTTGTCGCGgta----tttctttcaactagcaaagattcttgtt-gtgtttgacagtgcctttgtttact--ttttctag----------------------------------------------------------------------------
| | |||||||| ||||| ||| |||| ||  | || || |||||||||||||| ||||||||||| || || ||||| ||||| ||||  | ||| || |||      || |||  | |  || || || |||  || |      || || |  |||| |  |  ||||                                                                             
GATATGGTGCACGAGGCAAGAGTCAAGCGTGATAAATATAGACATGAAGGCAAATATTTGCTGTGTGAAGTATAATCCTGGATCAAGCAGCTATGTTGCAgtaagatcctcattcctccaa-aatgactcatgtcagtatccatttgtaccctcatttaatagtggtctactggatctttgattttccaacatgtataccttgggtttgtgctattaccttagattgtggatttcatctggttgcag

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|169083268|gb|FE491884.1|FE491884
EST:     CAAACATTTGCTGTGTCAAATACAATCCCGGATCTAGCAATTTTGTCGCG                         GTGGGCTCGGCCGATCATCATATCCACTATTACGATCTCCGGAACTCCAAG
genomic: CAAACATTTGCTGTGTCAAATACAATCCCGGATCTAGCAATTTTGTCGCGgtatttcttt ... ctttttctagGTGGGCTCGGCCGATCATCATATCCACTATTACGATCTCCGGAACTCCAAG
EST: gi|169077264|gb|FE485150.1|FE485150
EST:     CAAACATTTGCTGTGTCAAATACAATCCCGGATCTAGCAATTTTGTCGCG                         GTGGGCTCGGCCGATCATCATATCCACTATTACGATCTCCGGAACTCCAAG
genomic: CAAACATTTGCTGTGTCAAATACAATCCCGGATCTAGCAATTTTGTCGCGgtatttcttt ... ctttttctagGTGGGCTCGGCCGATCATCATATCCACTATTACGATCTCCGGAACTCCAAG

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: 33 (upstream exon), 35 (downstream exon)
Score: 51

GCTGTGGTGCACCAGGCAGGAGACAAGTGTCCTGAACATTGACATGAAGGCAAACATTTGCTGTGTCAAATACAATCCCGGATCTAGCAATTTTGTCGCGgtatttcttt ... ctttttctagGTGGGCTCGGCCGATCATCATATCCACTATTACGATCTCCGGAACTCCAAGTCGCCTCTACATGTCTTTAGTGGTCACCGAAAAGCCGTCTCGTATGTAA




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