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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacgtatgctacacatttttctcttttctagatctgtgccctcagGTTTGGGATCGCGAGAAGATTGTGATCATCCCCGATCACTACATCTTTACTGCGGACGAGCGCGCTAATCGAAATGTGGATATTTTGCGGGACTTTTCAA

Basic information

species Selaginella moellendorffii
transcript EFJ16666
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ32611 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: PP1S227_66V6.1 (Physcomitrella patens), 3'ss of exon 3
---------------------------------------gtacgtatgctacacatttttctcttttctagatctg-----tgccct----------cagGTTTGGGATCGCGAGAAGATTGTGATCATCCCCGATCACTACATCTTTACTGCGGACGAGCGCGCTAATCGAAATGTGGATATTTTGCGGGACTTTTCAA
                                        | |  | | |  |  |||||||   |   | | |||      || ||          ||||| |||||||| || ||||| ||| | ||||||||||| ||||| |||||  | ||||| || || ||| |||||||||||||  | || |||||| |  
gcctgtgacaaacttagtggaatttgttctcgtcagaagttgctgacgttggaagtttttctgagtcagaaacctgacagtcgctctgtatgagttgcagGTATGGGATCGTGAAAAGATCGTGCTTATCCCCGATCATTACATTTTTACCTCAGACGAACGAGCCAATAGAAATGTGGATATCCTACGTGACTTTGCTC
















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|169099807|gb|FE500812.1|FE500812
EST:     GGCCTGGGACCATTGGGATTTTCAAGAAGGAATTCGGTGCTAACGCTAAA                         GTTTGGGATCGCGAGAAGATTGTGATCATCCCCGATCACTACATCTTTACT
genomic: GGCCTGGGACCATTGGGATTTTCAAGAAGGAATTCGGTGCTAACGCTAAAgtacgtatgc ... gtgccctcagGTTTGGGATCGCGAGAAGATTGTGATCATCCCCGATCACTACATCTTTACT
EST: gi|169111212|gb|FE511372.1|FE511372
EST:     GGCCTGGGACCATTGGGATCTTCAAGAAGGAATTCGGTGCTAACGCTAAA                         GTTTGGGATCGCGAGAAGATTGTGATCATCCCCGATCACTACATCTTTACT
genomic: GGCCTGGGACCATTGGGATTTTCAAGAAGGAATTCGGTGCTAACGCTAAAgtacgtatgc ... gtgccctcagGTTTGGGATCGCGAGAAGATTGTGATCATCCCCGATCACTACATCTTTACT
EST: gi|169111148|gb|FE509592.1|FE509592
EST:     GGCCTGGGACCATTGGGATTTTCAAGAAGGAATTCGGTGCTAACGCTAAA                         GTTTGGGATCGCGAGAAGATTGTGATCATCCCCGATCACTACATCTTTACT
genomic: GGCCTGGGACCATTGGGATTTTCAAGAAGGAATTCGGTGCTAACGCTAAAgtacgtatgc ... gtgccctcagGTTTGGGATCGCGAGAAGATTGTGATCATCCCCGATCACTACATCTTTACT
EST: gi|169035259|gb|FE442611.1|FE442611
EST:     GGCCTGGGACCATTGGGATCTTCAAGAAGGAATTCGGTGCTAACGCTAAA                         GTTTGGGATCGCGAGAAGATTGTGATCATCCCCGATCACTACATCTTTACT
genomic: GGCCTGGGACCATTGGGATTTTCAAGAAGGAATTCGGTGCTAACGCTAAAgtacgtatgc ... gtgccctcagGTTTGGGATCGCGAGAAGATTGTGATCATCCCCGATCACTACATCTTTACT

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: 34 (upstream exon), 34 (downstream exon)
Score: 19

GGAGAATGTGTGGGTCAATGCCGATGTTCTCATGACACACGATGTTTGCGGGCCTGGGACCATTGGGATTTTCAAGAAGGAATTCGGTGCTAACGCTAAAgtacgtatgc ... gtgccctcagGTTTGGGATCGCGAGAAGATTGTGATCATCCCCGATCACTACATCTTTACTGCGGACGAGCGCGCTAATCGAAATGTGGATATTTTGCGGGACTTTTCAA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtacgtatgctacacatttttctcttttctagatctgtgccctcagGTTTGGGATCGCGAGAAGATTGTGATCATCCCCGATCACTACATCTTTACTGCGGACGAGCGCGCTAATCGAAATGTGGATATTTTGCGGGACTTTTCAA
                                                      tgccctc  CT-rich tract
                      acattttt  TA-rich tract