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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacgcattcttgaacttggagctagcatgtataactttgtgtcatacagTTTGAAGAAACTTTTAATTTCACTCAAGACGATCTCCTGAGTGACGACATCATGATCCTTGATACCCGGTGTGAACTGAGTGTTTGGATTGGTCAAAACG

Basic information

species Selaginella moellendorffii
transcript EFJ19773
intron # 15
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ19773 (Selaginella moellendorffii), 3'ss of exon 15
lower sequence: PP1S20_92V6.1 (Physcomitrella patens), 3'ss of exon 16
--------------------------------------------------gtacgcattcttgaacttggagctagcatgtataactttgtgtcatacagTTTGAAGAAACTTTTAATTTCACTCAAGACGATCTCCTGAGTGACGACATCATGATCCTTGATACCCGGTGTGAACTGAGTGTTTGGATTGGTCAAAACG
                                                   |  |   |       |    ||||| |     || |  |  |  ||||| |    |||      |||||||| ||||| ||||| ||||||||||| ||||||||||| ||    |    ||   |    |  ||| |||| ||  | |
ctgtttttatgtccctctcattgcaaagcgtctagtgctgcgatgattttatcagagcttactgcgtgtctgctagtaaactgaattgggaattgtacagGTGACTGAAGTGCACAATTTCACACAAGATGATCTTCTGAGTGACGATATCATGATCCTGGACTGTCACAATGTCATCTACGAGTGGGTTGGCCAGCATG

upper sequence: EFJ19773 (Selaginella moellendorffii), 3'ss of exon 15
lower sequence: PP1S100_30V6.1 (Physcomitrella patens), 3'ss of exon 18
---------------------------------------gtacgcattct-tgaacttggagctagcatgt---ataactttgtg-------tcatacagTTTGAAGAAACTTTTAATTTCACTCAAGACGATCTCCTGAGTGACGACATCATGATCCTTGATACCCGGTGTGAACTGAGTGTTTGGATTGGTCAAAACG
                                         |   ||| | | |  |   |   ||  | |   | || | || |          ||||| |    |||      |||||||||||||| ||||| |||||||| || ||||||||| | |||   |    ||   ||   |  ||| |||| ||  | |
cgtccagatatttttcataattgtaaagcgaccattcctacaattattttatcagatcacactgagtgtatgataaaattctgaggtgggaactgtacagGTGACTGAAGTGCACAATTTCACTCAAGATGATCTTCTGAGTGATGATATCATGATCATGGATTGTCACAATGTCTTGTACGAGTGGGTTGGCCAGCATG
















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|169080133|gb|FE487941.1|FE487941
EST:     ATAAGGATCCACGCTTGTTTGAGTACACAAGAAAGCCAGGCAATCTATTG                         TTTGAAGAAACTTTTAATTTCACTCAAGACGATCTCCTGAGTGACGACATC
genomic: ATAAGGATCCACGCTTGTTTGAGTACACAAGAAAGCCAGGCAATCTATTGgtacgcattc ... tgtcatacagTTTGAAGAAACTTTTAATTTCACTCAAGACGATCTCCTGAGTGACGACATC




















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), 33 (downstream exon)
Score: 24

TCTTGGAGGAAAGAAGGTATATCCCAGCCAGAGAGAACTTGTTGACTCCGATAAGGATCCACGCTTGTTTGAGTACACAAGAAAGCCAGGCAATCTATTGgtacgcattc ... tgtcatacagTTTGAAGAAACTTTTAATTTCACTCAAGACGATCTCCTGAGTGACGACATCATGATCCTTGATACCCGGTGTGAACTGAGTGTTTGGATTGGTCAAAACG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtacgcattcttgaacttggagctagcatgtataactttgtgtcatacagTTTGAAGAAACTTTTAATTTCACTCAAGACGATCTCCTGAGTGACGACATCATGATCCTTGATACCCGGTGTGAACTGAGTGTTTGGATTGGTCAAAACG
                                  gtataac  putative branch site (score: 24)
                                        tataacttt  TA-rich tract