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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CATAGACAGGAAGAAGAACATTTTCAAACTCTCGCAAGGCGAATACGTCGCTGTAGAGAACTTGGAAAACATCTACGGCCAATGCCCGACCTTCGATTCGgttagttgccatgcgagcatcgagattgccaatattaactgctgccctttcgatccag

Basic information

species Selaginella moellendorffii
transcript EFJ25426
intron # 16
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ25426 (Selaginella moellendorffii), 5'ss of exon 16
lower sequence: LOC_Os01g48910.1 (Oryza sativa), 5'ss of exon 16
CATAGACAGGAAGAAGAACATTTTCAAACTCTCGCAAGGCGAATACGTCGCTGTAGAGAACTTGGAAAACATCTACGGCCAATGCCCGACCTTCGATTCGgt--tagttgccatgcgagcatcgagattgccaatattaactgctgccctttcgatccag-------------------------------------------------------
||| ||  | ||||||||||| ||||| ||||| ||||| ||||| |||||||| ||||| ||||| ||||| | ||| |||   ||     | ||||||||   |  ||  |  | ||| |  |  |   ||| |     |  | || ||   | | |                                                        
CATTGATCGCAAGAAGAACATCTTCAAGCTCTCCCAAGGAGAATATGTCGCTGTGGAGAATTTGGAGAACATATTCGGTCAAGCTCCTGGTGTTGATTCGgtacaatctgataacctagctttcatttgctcaaaacc--ttttttccattataaccgatcttacgtttccatatgttgacatgctgactcgccgttatttgacaatctctccag

upper sequence: EFJ25426 (Selaginella moellendorffii), 5'ss of exon 16
lower sequence: AT1G64400.1 (Arabidopsis thaliana), 5'ss of exon 14
CATAGACAGGAAGAAGAACATTTTCAAACTCTCGCAAGGCGAATACGTCGCTGTAGAGAACTTGGAAAACATCTACGGCCAATGCCCGACCTTCGATTCGg--ttagttgccatgcgagcatcgagattgccaatattaactgctgccctttcgatccag---------------
||| ||| | ||||||||||| || ||||| || ||||| |||||||| || || ||||||||||| ||||| ||| | ||   | |  || | || ||||  |||||||  |    | |    |  |  ||  ||   |   ||   ||   ||||                  
CATCGACCGTAAGAAGAACATCTTTAAACTGTCTCAAGGAGAATACGTTGCCGTTGAGAACTTGGAGAACATATACAGTCATGTCGCCGCCATTGAATCGgtattagttgaaaatataactcttaagtaaccgttacataaaacttagctaatgatctgttaaaacattttgcag

upper sequence: EFJ25426 (Selaginella moellendorffii), 5'ss of exon 16
lower sequence: Vv02s0025g01410.t01 (Vitis vinifera), 5'ss of exon 16
CATAGACAGGAAGAAGAACATTTTCAAACTCTCGCAAGGCGAATACGTCGCTGTAGAGAACTTGGAAAACATCTACGGCCAATGCCCGACCTTCGATTCGgttagttgcc-----atgcgagcatcgagattgccaatattaactgctgccctttcgatccag-------------------------------------
 || ||| | ||||||||||| ||||| || || ||||| |||||||| || || ||||||||||||||||| || || |      |     | || |||||  |   |       ||  | |||     || ||   ||| |   || |  |||    || |                                     
TATCGACCGCAAGAAGAACATATTCAAGCTTTCACAAGGAGAATACGTTGCCGTTGAGAACTTGGAAAACATTTATGGTCTTGTTTCTGATATTGACTCGgtatgcctctcaaatgtgtcatcatacgttttacctgaatttatcactcctttttttcccctgattttggttctctctcagtttcattgtgtatgcctct

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|169105098|gb|FE506655.1|FE506655
EST:     CTGTAGAGAACTTGGAAAACATCTACGGCCAATGCCCGACCTTCGATTCG                         ATATGGATATATGGGAACAGCTTCGAATCTTTCTTGGTCGCCGTTGTTATC
genomic: CTGTAGAGAACTTGGAAAACATCTACGGCCAATGCCCGACCTTCGATTCGgttagttgcc ... ttcgatccagATATGGATATATGGGAACAGCTTCGAATCTTTCTTGGTCGCCGTTGTTATC
EST: gi|169098408|gb|FE497762.1|FE497762
EST:     CTGTAGAGAACTTGGAAAACATCTACGGCCAATGCCCGACCTTCGATTCG                         ATATGGATATATGGGAACAGCTTCGAATCTTTCTTGGTCGCCGTTGTTATC
genomic: CTGTAGAGAACTTGGAAAACATCTACGGCCAATGCCCGACCTTCGATTCGgttagttgcc ... ttcgatccagATATGGATATATGGGAACAGCTTCGAATCTTTCTTGGTCGCCGTTGTTATC

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), 32 (downstream exon)
Score: 93

CATAGACAGGAAGAAGAACATTTTCAAACTCTCGCAAGGCGAATACGTCGCTGTAGAGAACTTGGAAAACATCTACGGCCAATGCCCGACCTTCGATTCGgttagttgcc ... ttcgatccagATATGGATATATGGGAACAGCTTCGAATCTTTCTTGGTCGCCGTTGTTATCCCGAACGAGGCAGCGCTCGATGCTTGGGCCAAGGAAAACGACGTCAAGG




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