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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagcgactctctttcgatatcttcgtgtctcttacgtcgtgaaccgacttgcttgagcagAATTTCGTTGGATTGTCTGTATCCGATGGCTACATCGCGTGTGGCTCAGAGACAAACGCC

Basic information

species Selaginella moellendorffii
transcript EFJ14473
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ14473 (Selaginella moellendorffii), 3'ss of exon 7
lower sequence: GLYMA12G25240.1 (Glycine max), 3'ss of exon 7
-------------------------------gtagcgactctctttc--gatatcttcgtgtctcttacgtcgtga------accgacttgcttgagcagAATTTCGTTGGATTGTCTGTATCCGATGGCTACATCGCGTGTGGCTCAGAGACAAACGCC---------------------
                                  || | | |  |    | ||| |   | |||    |    |||      |||  | |  |   |||||||||||| || ||||||||||| ||||| ||||| ||   ||| |||||||||||||                       
tatgcaaaatttgggccatttgtaattaattactgcaaattttatatatggtatttaaatttctgcggcaatatgatgatgcaccttccttttgttgcagAATTTCGTGGGGTTGTCTGTATCTGATGGTTACATTGCTACTGGTTCAGAGACAAACGAGGCATTTCATTTTTCCTCTCTC
















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|169071372|gb|FE479648.1|FE479648
EST:     ACTCTAGCAACGCGTGCGGCTTGACTTACACGGGGCATACAAACGAGAAG                         AATTTCGTTGGATTGTCTGTATCCGATGGCTACATCGCGTGTGGCTCAGAG
genomic: ACTCTAGCAACGCGTGCGGCTTGACTTACACGGGGCATACAAACGAGAAGgtagcgactc ... gcttgagcagAATTTCGTTGGATTGTCTGTATCCGATGGCTACATCGCGTGTGGCTCAGAG
EST: gi|169064397|gb|FE472064.1|FE472064
EST:     ACTCTAGCAACGCGTGCAGCTTGACTTACACGGGGCATACAAACGAGAAG                         AATTTCGTTGGACTGTCTGTATCCGATGGCTACATCGCGTGTGGCTCAGAG
genomic: ACTCTAGCAACGCGTGCGGCTTGACTTACACGGGGCATACAAACGAGAAGgtagcgactc ... gcttgagcagAATTTCGTTGGATTGTCTGTATCCGATGGCTACATCGCGTGTGGCTCAGAG
EST: gi|169070974|gb|FE477365.1|FE477365
EST:     ACTCTAGCAACGCGTGCGGCTTGACTTACACGGGGCATACAAACGAGAAG                         AATTTCGTTGGATTGTCTGTATCCGATGGCTACATCGCGTGTGGCTCAGAG
genomic: ACTCTAGCAACGCGTGCGGCTTGACTTACACGGGGCATACAAACGAGAAGgtagcgactc ... gcttgagcagAATTTCGTTGGATTGTCTGTATCCGATGGCTACATCGCGTGTGGCTCAGAG
EST: gi|169102857|gb|FE508641.1|FE508641
EST:     ACTCTAGCAACGCGTGCGGCTTGACTTACACGGGGCATACAAACGAGAAG                         AATTTCGTTGGATTGTCTGTATCCGATGGCTACATCGCGTGTGGCTCAGAG
genomic: ACTCTAGCAACGCGTGCGGCTTGACTTACACGGGGCATACAAACGAGAAGgtagcgactc ... gcttgagcagAATTTCGTTGGATTGTCTGTATCCGATGGCTACATCGCGTGTGGCTCAGAG
EST: gi|169059482|gb|FE468508.1|FE468508
EST:     ACTCTAGCAACGCGTGCGGCTTGACTTACACGGGGCATACAAACGAGAAG                         AATTTCGTTGGATTGTCTGTATCCGATGGCTACATCGCGTGTGGCTCAGAG
genomic: ACTCTAGCAACGCGTGCGGCTTGACTTACACGGGGCATACAAACGAGAAGgtagcgactc ... gcttgagcagAATTTCGTTGGATTGTCTGTATCCGATGGCTACATCGCGTGTGGCTCAGAG

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: 31 (upstream exon), 35 (downstream exon)
Score: 7

GGATAACACACTCAAGCTGTGGGACCTGAGCAAAGTGATGAGAAATGGAAACTCTAGCAACGCGTGCGGCTTGACTTACACGGGGCATACAAACGAGAAGgtagcgactc ... gcttgagcagAATTTCGTTGGATTGTCTGTATCCGATGGCTACATCGCGTGTGGCTCAGAGACAAACGCC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

actctctttcgatatcttcgtgtctcttacgtcgtgaaccgacttgcttgagcagAATTTCGTTGGATTGTCTGTATCCGATGGCTACATCGCGTGTGGCTCAGAGACAAACGCC
                       ctcttac  putative branch site (score: 7)
                                          cttgctt  putative PPT
           atatctt  TA-rich tract