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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagtatacatgtttttagttttctcgttcgaacttttatcattgcagAGCCGGAGCCGATGATAAGCCTCTGCGGATGGTGAAGACTGTTCTTCACGAACTAGTAAAGCTTCGTGGAACAGCCATTAAGGGTCACCTTTCCATGGTG

Basic information

species Selaginella moellendorffii
transcript EFJ11209
intron # 44
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ11209 (Selaginella moellendorffii), 3'ss of exon 44
lower sequence: LOC_Os01g60040.2 (Oryza sativa), 3'ss of exon 46
-------------------------------------gtagtatacatgtttttagttttctcgttcga----acttttatcat----tgcagAGCCGGAGCCGATGATAAGCCTCTGCGGATGGTGAAGACTGTTCTTCACGAACTAGTAAAGCTTCGTGGAACAGCCATTAAGGGTCACCTTTCCATGGTG
                                       | | ||  | ||||  | |||    | | |    |   ||  |||    ||||| || ||||||||||| ||||| ||  | ||||| || |||||  | || ||||| |||||||||||||| ||||| || || ||||||||||| ||||| 
gttactgctgttctcctggagcttaatagttagcttttaaatttatttcttttggggttttagatacaagtagatgctttgcatgtcctgcagGGCAGGAGCCGATGACAAGCCACTTAGAATGGTCAAAACTGTGTTGCATGAACTTGTAAAGCTTCGTGGTACAGCAATCAAAGGTCACCTTTCAATGGTT

upper sequence: EFJ11209 (Selaginella moellendorffii), 3'ss of exon 44
lower sequence: Vv00s0652g00030.t01 (Vitis vinifera), 3'ss of exon 18
---------------------------------------------------------------------------------gtagtatacatgtttttagttttctcgttcgaact---tttatcattgca-gAGCCGGAGCCGATGATAAGCCTCTGCGGATGGTGAAGACTGTTCTTCACGAACTAGTAAAGCTTCGTGGAACAGCCATTAAGGGTCACCTTTCCATGGTG
                                                                                 || |  || ||||| ||  |||    |||  ||     |  |  |    | |||| ||||| ||||| || ||  | || ||||| || |||||||| || ||||| || |||||||| ||||| || || |||||||||||||| ||||| 
gtatcccttgtgtaatcaagttccgaaaaatttcaggatttttctttgttttttaggcaatgcagttgatttttatcattagttgctta-atgttcttcttttggctgttacaatgaaatgaactaccataagAGCTGGAGCTGATGACAAACCATTACGCATGGTTAAAACTGTTCTACATGAACTTGTTAAGCTTCGCGGAACTGCAATAAAGGGTCACCTTTCTATGGTT
















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|169093813|gb|FE494755.1|FE494755
EST:     AGTATTCATGAGTATCTTCAAGAGCTAGGGATGGAGGAAATACGGAGACG                         AGCCGGAGCCGATGATAAGCCTCTGCGGATGGTGAAGACTGTTCTTCACGA
genomic: AGTATTCATGAGTATCTTCAAGAGCTAGGGATGGAGGAAATACGGAGACGgtagtataca ... atcattgcagAGCCGGAGCCGATGATAAGCCTCTGCGGATGGTGAAGACTGTTCTTCACGA
EST: gi|169100104|gb|FE501863.1|FE501863
EST:     AGTATTCATGAGTATCTTCAAGAGCTAGGGATGGAGGAAATACGGAGACG                         AGCCGGAGCCGATGATAAGCCTCTGCGGATGGTGAAGACTGTTCTTCACGA
genomic: AGTATTCATGAGTATCTTCAAGAGCTAGGGATGGAGGAAATACGGAGACGgtagtataca ... atcattgcagAGCCGGAGCCGATGATAAGCCTCTGCGGATGGTGAAGACTGTTCTTCACGA
EST: gi|169022630|gb|FE428357.1|FE428357
EST:     AGTATTCATGAGTATCTTCAAGAGCTAGGGATGGAGGAAATACGGAGACG                         AGCCGGAGCCGATGATAAGCCTCTGCGGATGGTGAAGACTGTTCTTCACGA
genomic: AGTATTCATGAGTATCTTCAAGAGCTAGGGATGGAGGAAATACGGAGACGgtagtataca ... atcattgcagAGCCGGAGCCGATGATAAGCCTCTGCGGATGGTGAAGACTGTTCTTCACGA
EST: gi|169077690|gb|FE484952.1|FE484952
EST:     AGTATTCATGAGTATCTTCAAGAGCTAGGGATGGAGGAAATACGGAGACG                         AGCCGGAGCCGATGATAAGCCTCTGCGGATGGTGAAGACTGTTCTTCACGA
genomic: AGTATTCATGAGTATCTTCAAGAGCTAGGGATGGAGGAAATACGGAGACGgtagtataca ... atcattgcagAGCCGGAGCCGATGATAAGCCTCTGCGGATGGTGAAGACTGTTCTTCACGA
EST: gi|169081005|gb|FE486122.1|FE486122
EST:     AGTATTCATGAGTATCTTCAAGAGCTAGGGATGGAGGAAATACGGAGACG                         AGCCGGAGCCGATGATAAGCCTCTGCGGATGGTGAAGACTGTTCTTCACGA
genomic: AGTATTCATGAGTATCTTCAAGAGCTAGGGATGGAGGAAATACGGAGACGgtagtataca ... atcattgcagAGCCGGAGCCGATGATAAGCCTCTGCGGATGGTGAAGACTGTTCTTCACGA
EST: gi|169062797|gb|FE472846.1|FE472846
EST:     AGTATTCATGAGTATCTTCAAGAGCTAGGGATGGAGGAAATACGGAGACG                         AGCCGGAGCCGATGATAAGCCTCTGCGGATGGTGAAGACTGTTCTTCACGA
genomic: AGTATTCATGAGTATCTTCAAGAGCTAGGGATGGAGGAAATACGGAGACGgtagtataca ... atcattgcagAGCCGGAGCCGATGATAAGCCTCTGCGGATGGTGAAGACTGTTCTTCACGA

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), 35 (downstream exon)
Score: 75

GTCCTTGGCTCAACTATTTTTGAGGTGGACCTTGATCGCCTACTGCAAAGTATTCATGAGTATCTTCAAGAGCTAGGGATGGAGGAAATACGGAGACGgtagtataca ... atcattgcagAGCCGGAGCCGATGATAAGCCTCTGCGGATGGTGAAGACTGTTCTTCACGAACTAGTAAAGCTTCGTGGAACAGCCATTAAGGGTCACCTTTCCATGGTG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtagtatacatgtttttagttttctcgttcgaacttttatcattgcagAGCCGGAGCCGATGATAAGCCTCTGCGGATGGTGAAGACTGTTCTTCACGAACTAGTAAAGCTTCGTGGAACAGCCATTAAGGGTCACCTTTCCATGGTG
                                              cttttatc  CT-rich tract
           tatacatgttttta  TA-rich tract