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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTGGGAGGAACGACCGTTAAGATCGGTGGCATGGCGAAAGGATCTGGGATGATCCATCCAAACATGGCGACGATGCTTAGTgtaatccttatttgattatcaagaatgaatcttgagtttattcgcag

Basic information

species Selaginella moellendorffii
transcript EFJ32643
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ32643 (Selaginella moellendorffii), 5'ss of exon 9
lower sequence: LOC_Os03g17120.2 (Oryza sativa), 5'ss of exon 9
GTGGGAGGAACGACCGTTAAGATCGGTGGCATGGCGAAAGGATCTGGGATGATCCATCCAAACATGGCGACGATGCTTAGTgtaatccttatttgattatca----------agaatgaatcttgagtttattcgcag-------------------------------------------
 | ||||||  | |  | || || || || ||||| ||||| ||||||||||| |||||||| ||||| || |||||| ||||||    | | | | | |||          ||    | || |   || || |                                               
ATTGGAGGAGTGCCTATCAAAATAGGAGGAATGGCCAAAGGTTCTGGGATGATTCATCCAAATATGGCAACAATGCTTGGTgtaagttctgtatcaatctcattttccacacagtcctactcctctattgatccctttctcaaggcatgtatgagcttcattataaccctttttcttacag

upper sequence: EFJ32643 (Selaginella moellendorffii), 5'ss of exon 9
lower sequence: Vv08s0040g03320.t01 (Vitis vinifera), 5'ss of exon 10
GTGGGAGGAACGACCGTTAAGATCGGTGGCATGGCGAAAGGATCTGGGATGATCCATCCAAACATGGCGACGATGCTTAGTgtaatccttatttgattatcaagaatgaatcttgagtt---tattcgcag--------------------------------
|| ||||| || |   |||   | || || ||||| || || |||||||||||||||||||| ||||| || |||||| ||||    ||   ||   ||       ||       |  |   |||||  |                                 
GTTGGAGGGACAAATATTAGAGTTGGGGGAATGGCAAAGGGTTCTGGGATGATCCATCCAAATATGGCTACCATGCTTGGTgtgcgtctctgttttctacatgtcctgttctgcaaagtaaatattcttattccactttcttgataggactactttgttccag

upper sequence: EFJ32643 (Selaginella moellendorffii), 5'ss of exon 9
lower sequence: PP1S90_220V6.2 (Physcomitrella patens), 5'ss of exon 11
GTGGGAGGAACGACCGTTAAGATCGGTGGCATGGCGAAAGGATCTGGGATGATCCATCCAAACATGGCGACGATGCTTAGTgta-atccttatttgattatcaagaatgaatcttgagtttattcgcag----------------------------------------------------------------------------
 | || ||||| || || |   | |||||||| |||||||||||||| ||||| ||||||||||||||||| |||||  | ||| ||||      || |       |||||| |  |   | ||  |||                                                                            
ATAGGGGGAACAACAGTGAGACTAGGTGGCATAGCGAAAGGATCTGGCATGATTCATCCAAACATGGCGACCATGCTCGGAgtacatccgacaacgacttaactctatgaatgtatacagtgttatcagcctgtttccaatacttctcatttactactctcgttttaatgttcactactatcactaatgctgtggctgtgagcag

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|169066726|gb|FE475456.1|FE475456
EST:     TGGCGAAAGGATCTGGGATGATCCATCCAAACATGGCGACGATGCTTAGT                         GTTGTAACATGCGATGCTCACGTTTCATCGGATGTGTGGCAAGATCTGGTC
genomic: TGGCGAAAGGATCTGGGATGATCCATCCAAACATGGCGACGATGCTTAGTgtaatcctta ... ttattcgcagGTTGTAACATGCGATGCTCACGTTGCATCGGATGTGTGGCAAGATCTGGTC
EST: gi|169066699|gb|FE475455.1|FE475455
EST:     -GCGAAAAGGATCTGGGATGATCCATCCAAACATGGCGACGATGCTTAGT                         GTTGTAACATGCGATGCTCACGTTTCATCGGATGTGTGGCAAGATCTGGTC
genomic: GGCG-AAAGGATCTGGGATGATCCATCCAAACATGGCGACGATGCTTAGTgtaatcctta ... ttattcgcagGTTGTAACATGCGATGCTCACGTTGCATCGGATGTGTGGCAAGATCTGGTC
EST: gi|169024736|gb|FE435766.1|FE435766
EST:     TGGCGAAAGGATCTGGGATGATCCATCCAAACATGGCGACGATGCTTAGT                         GTTGTAACATGCGATGCTCACGTTTCATCGGATGTGTGGCAAGATCTGGTC
genomic: TGGCGAAAGGATCTGGGATGATCCATCCAAACATGGCGACGATGCTTAGTgtaatcctta ... ttattcgcagGTTGTAACATGCGATGCTCACGTTGCATCGGATGTGTGGCAAGATCTGGTC
EST: gi|169074320|gb|FE482474.1|FE482474
EST:     TGGCGAAAGGATCTGGGATGATCCATCCAAACATGGCGACGATGCTTAGT                         GTTGTAACATGCGATGCTCACGTTTCATCGGATGTGTGGCAAGATCTGGTC
genomic: TGGCGAAAGGATCTGGGATGATCCATCCAAACATGGCGACGATGCTTAGTgtaatcctta ... ttattcgcagGTTGTAACATGCGATGCTCACGTTGCATCGGATGTGTGGCAAGATCTGGTC

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: 22 (upstream exon), 26 (downstream exon)
Score: 6

GTGGGAGGAACGACCGTTAAGATCGGTGGCATGGCGAAAGGATCTGGGATGATCCATCCAAACATGGCGACGATGCTTAGTgtaatcctta ... ttattcgcagGTTGTAACATGCGATGCTCACGTTGCATCGGATGTGTGGCAAGATCTGGTCAAAACTGCTGTTGGCCGGAGCTTCAACCAGATCACG




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