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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGATGCGGAAGGATACGCTGACAGAGAACGAAGCGAAGTTTTACATTGCGGAAGCGGTTCTAGCTATTGAATCCATTCACAAGCACAAATACATTCACAGgtgttacttcaacttctattgtcttttgattgtgcttttactgacacgattccgtcggcag

Basic information

species Selaginella moellendorffii
transcript EFJ08009
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ08009 (Selaginella moellendorffii), 5'ss of exon 4
lower sequence: LOC_Os12g19290.1 (Oryza sativa), 5'ss of exon 4
TGATGCGGAAGGATACGCTGACAGAGAACGAAGCGAAGTTTTACATTGCGGAAGCGGTTCTAGCTATTGAATCCATTCACAAGCACAAATACATTCACAGgtgttacttcaac-------ttctattgtcttttgattgtgcttttactgacacgattccgtcg-gcag------
| ||||| |||||||| || |||||  | ||| | |  |||||  |||||||  |  ||||||| ||||||||||| ||||||||||| || ||||| ||||  | | |  |         |    || | || | | |    ||| |     |   |  |     ||       
TAATGCGCAAGGATACACTTACAGATGATGAATCTAGATTTTATGTTGCGGAGACAATTCTAGCAATTGAATCCATACACAAGCACAATTATATTCATAGgtaattcattgataataaaaattgcatggcattcggtagcaaatttgccactccatctttgctatacattttcag

upper sequence: EFJ08009 (Selaginella moellendorffii), 5'ss of exon 4
lower sequence: AT4G14350.3 (Arabidopsis thaliana), 5'ss of exon 5
TGATGCGGAAGGATACGCTGACAGAGAACGAAGCGAAGTTTTACATTGCGGAAGCGGTTCTAGCTATTGAATCCATTCACAAGCACAAATACATTCACAGgt-gttacttcaacttctattgtct---------tttgattgtgcttttact---gacacgattccgtcggcag----------
| ||| |||| || || || || ||  |||| || | |||||| |||| |||| | || || |||||||| |||||||| |||||||| |||||||||||||   |    ||   | |||  | |         |   |||||  ||||  |    ||    ||   ||  ||           
TTATGAGGAAAGACACCCTCACTGAAGACGAGGCCAGGTTTTATATTGGGGAAACTGTCCTGGCTATTGAGTCCATTCATAAGCACAACTACATTCACAGgtcagtgaagcagaatatatgatttagttctagctcccattgttattttgttctaaacgtctttttttctccaatgtgatacag
















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|169047815|gb|FE454671.1|FE454671
EST:     GAAGCGGTTCTAGCTATTGAATCCATTCACAAGCACAAATACATTCACAG                         GGATATCAAGCCTGACAATCTACTCCTCGATAAGAATGGCCATCTCAAGCT
genomic: GAAGCGGTTCTAGCTATTGAATCCATTCACAAGCACAAATACATTCACAGgtgttacttc ... ccgtcggcagGGATATCAAGCCTGACAATCTACTCCTCGATAAGAATGGCCATCTCAAGCT
EST: gi|169061623|gb|FE469410.1|FE469410
EST:     GAAGCGGTTCTAGCTATTGAGTCCATTCACAAGCACAAATACATTCACAG                         GGATATCAAGCCTGACAATCTACTCCTCGATAAGAATGGCCATCTCAAGCT
genomic: GAAGCGGTTCTAGCTATTGAATCCATTCACAAGCACAAATACATTCACAGgtgttacttc ... ccgtcggcagGGATATCAAGCCTGACAATCTACTCCTCGATAAGAATGGCCATCTCAAGCT

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: 11

TGATGCGGAAGGATACGCTGACAGAGAACGAAGCGAAGTTTTACATTGCGGAAGCGGTTCTAGCTATTGAATCCATTCACAAGCACAAATACATTCACAGgtgttacttc ... ccgtcggcagGGATATCAAGCCTGACAATCTACTCCTCGATAAGAATGGCCATCTCAAGCTTTCTGACTTTGGTCTCTGCAAGCCGCTGGATTGCAGCAACTTTCCCATG




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