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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatggctattcaatttaaaaacatcccttacgctttggtttcgtttcagGTCTTAGTGAAAGACTTGGTGAGAAAGTACCCAGAATGGAGTCATGACTGCATTGCGGTTGTTGGAAATGTGAGTAGCAAAAGTATTCAGGAACCGAAAG

Basic information

species Selaginella moellendorffii
transcript EFJ07665
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ07665 (Selaginella moellendorffii), 3'ss of exon 5
lower sequence: Vv04s0008g03880.t01 (Vitis vinifera), 3'ss of exon 6
----------------------------------------------------------------------------------------------------------------gtatggct--attcaatttaaaaacatcccttacgctttggtttcgtttca----gGTCTTAGTGAAAGACTTGGTGAGAAAGTACCCAGAATGGAGTCATGACTGCATTGCGGTTGTTGGAAATGTGAGTAGCAAAAGTATTCAGGAACCGAAAG
                                                                                                                 ||||  |  | |    ||||  | ||   |     | |||  |  | |||    |||  | || |||||  || | || || || ||| ||||||||||||| |||||||| |||||||| ||| | || ||||||| | ||||||| || || |
gtgaatttttacagctgtgcctagatgcttggatttttattgtgattgaatttgaacattgaaccaaactccaaaaaaatttatgctcttcatgcatagaagtaacatgagcatatgatttaactgttattaatcagattgatacaagtctggagttctctcatgtagGTGCTTGTAAAAGATCTGCTAAGGAAATATCCACAATGGAGTCATGATTGCATTGCAGTTGTTGGGAATATCAGCAGCAAAAATGTTCAGGAGCCCAAGG
















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|169100527|gb|FE502715.1|FE502715
EST:     TGCTTCAGTTTTTAGAGATGGAGCGGGATTATGTTACTGCGGAAACACTG                         GTCTTAGTGAAAGACTTGGTGAGAAAGTACCCAGAATGGAGTCATGACTGC
genomic: TGCTTCAGTTTTTAGAGATGGAACGGGATTATGTTACTGCGGAAACACTGgtatggctat ... ttcgtttcagGTCTTAGTGAAAGACTTGGTGAGAAAGTACCCAGAATGGAGTCATGACTGC
EST: gi|169041436|gb|FE449501.1|FE449501
EST:     TGCTTCAGTTTTTAGAGATGGAGCGGGATTATGTTACTGCGGAAACACTG                         GTCTTAGTGAAAGACTTGGTGAGAAAGTACC
genomic: TGCTTCAGTTTTTAGAGATGGAACGGGATTATGTTACTGCGGAAACACTGgtatggctat ... ttcgtttcagGTCTTAGTGAAAGACTTGGTGAGAAAGTACC

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: 29 (upstream exon), 32 (downstream exon)
Score: 7

GGGAAAAATCGCGTTAAACCTTTGCGACGTCAATGCGATCGTTGATCGGCTGCTTCAGTTTTTAGAGATGGAACGGGATTATGTTACTGCGGAAACACTGgtatggctat ... ttcgtttcagGTCTTAGTGAAAGACTTGGTGAGAAAGTACCCAGAATGGAGTCATGACTGCATTGCGGTTGTTGGAAATGTGAGTAGCAAAAGTATTCAGGAACCGAAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtatggctattcaatttaaaaacatcccttacgctttggtttcgtttcagGTCTTAGTGAAAGACTTGGTGAGAAAGTACCCAGAATGGAGTCATGACTGCATTGCGGTTGTTGGAAATGTGAGTAGCAAAAGTATTCAGGAACCGAAAG
                              cccttac  putative branch site (score: 7)
                                            tttcgtttc  putative PPT
            tattcaatttaaaaac  TA-rich tract