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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgcaaatcacttagtgtagctctcaggcttctctaaacgtatgtctcctctctttcagGCCAATTCAAGGCTATCAACGATGAAGGAATGCCTCACCACCAGAGACCCTTCATGAAGGGAACCCTGTACATCCACTTCTCGGTCGACTTCCCCGAGTC

Basic information

species Selaginella moellendorffii
transcript EFJ24912
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ24912 (Selaginella moellendorffii), 3'ss of exon 6
lower sequence: Vv15s0021g02090.t01 (Vitis vinifera), 3'ss of exon 7
------------gtatgcaaatcacttagtg-tagctctcaggc-----------ttctctaaacgtatgtctcctct-----ctttca--------gGCCAATTCAAGGCTATCAACGATGAAGGAATGCCTCACCACCAGAGACCCTTCATGAAGGGAACCCTGTACATCCACTTCTCGGTCGACTTCCCCGAGTC
              | |||| |  | | ||  | |||||  |             | ||| | | ||   ||  | ||     ||||||        |  |||| ||| || ||||| ||||| |||||||| |||||||| ||||||||||||||||| |  || |||||||| ||    || || ||||| |||||
gtaaaaatcactaaaagcaatttcccttgtacttgctcttggatgaaaacattattcctcaatatgttcatcatcccttggtactttcatggatgcagATCAATACAAAGCAATCAATGATGAGGGAATGCCGCACCACCAAAGACCCTTCATGAAGGGTAAGCTTTACATCCATTTTGATGTGGAGTTCCCAGAGTC

upper sequence: EFJ24912 (Selaginella moellendorffii), 3'ss of exon 6
lower sequence: PP1S17_208V6.1 (Physcomitrella patens), 3'ss of exon 5
--------------------------------------------------------------------------------------------------------gtatgcaaatcacttagtgtag-ctctcaggcttctctaaacgtatgtctcctctcttt--cagGCCAATTCAAGGCTATCAACGATGAAGGAATGCCTCACCACCAGAGACCCTTCATGAAGGGAACCCTGTACATCCACTTCTCGGTCGACTTCCCCGAGTC
                                                                                                        || | |   |  | | |||||| |  |   |    |  |    | ||| |  |    ||  |||| ||||| ||||||||||||||||| || ||||||||  ||||||| || ||||||||||| |  || |   | || ||    ||||| ||||| |||||
gtattgattcctgaaaccgggaaaggcttccagggggtttcggtgtacaatttagctacttcaacataatttcattttccaatagtttatttttattttatttggtttactggttccat-gtgtagacctttttgtaggttgacgtttttgtgtatttcgattgacagGTCAATTTAAGGCTATCAACGATGAGGGTATGCCTCATTACCAGAGGCCTTTCATGAAGGGCAGGCTATTTTTGCATTTTAACGTCGAGTTCCCTGAGTC
















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|169047450|gb|FE455645.1|FE455645
EST:     CGGCAGGCAACTCCTCGTCAAGTCGAGACCGGGCGAGATTATCAAACCAG                         GCCAATTCAAGGCTATCAACGATGAAGGAATGCCTCACCACCAGAGACCCT
genomic: CGGCAGGCAACTCCTCGTCAAGTCGAGACCGGGCGAGATTATCAAACCAGgtatgcaaat ... tctctttcagGCCAATTCAAGGCTATCAACGATGAAGGAATGCCTCACCACCAGAGACCCT
EST: gi|169113322|gb|FE515273.1|FE515273
EST:     CGGCAGGCAACTCCTCGTCAAGTCGAGACCGGGCGAGATTATCAAGCCAG                         GCCAATTCAAGGCTATCAACGATGAAGGGATGCCTCACCACCAGAGACCCT
genomic: CGGCAGGCAACTCCTCGTCAAGTCGAGACCGGGCGAGATTATCAAACCAGgtatgcaaat ... tctctttcagGCCAATTCAAGGCTATCAACGATGAAGGAATGCCTCACCACCAGAGACCCT
EST: gi|169050972|gb|FE458142.1|FE458142
EST:     CGGCAGGCAACTCCTCGTCAAGTCGAGACCGGGCGAGATTATCAAGCCAG                         GCCAATTCAAGGCTATCAACGATGAAGGGATGCCTCACCACCAGAGACCCT
genomic: CGGCAGGCAACTCCTCGTCAAGTCGAGACCGGGCGAGATTATCAAACCAGgtatgcaaat ... tctctttcagGCCAATTCAAGGCTATCAACGATGAAGGAATGCCTCACCACCAGAGACCCT
EST: gi|169104150|gb|FE507139.1|FE507139
EST:     CGGCAGGCAACTCCTCGTCAAGTCGAGACCGGGCGAGATTATCAAACCAG                         GCCAATTCAAGGCTATCAACGATGAAGGAATGCCTCACCACCAGAGACCCT
genomic: CGGCAGGCAACTCCTCGTCAAGTCGAGACCGGGCGAGATTATCAAACCAGgtatgcaaat ... tctctttcagGCCAATTCAAGGCTATCAACGATGAAGGAATGCCTCACCACCAGAGACCCT
EST: gi|169087097|gb|FE496203.1|FE496203
EST:     CGGCAGGCAACTCCTCGTCAAGTCGAGACCGGGCGAGATTATCAAGCCAG                         GCCAATTCAAGGCTATCAACGATGAAGGGATGCCTCACCACCAGAGACCCT
genomic: CGGCAGGCAACTCCTCGTCAAGTCGAGACCGGGCGAGATTATCAAACCAGgtatgcaaat ... tctctttcagGCCAATTCAAGGCTATCAACGATGAAGGAATGCCTCACCACCAGAGACCCT
EST: gi|169104151|gb|FE507140.1|FE507140
EST:     CGGCAGGCAACTCCTCGTCAAGTCGAGACCGGGCGAGATTATCAAACCAG                         GCCAATTCAAGGCTATCAACGATGAAGGAATGCCTCACCACCAGAGACCCT
genomic: CGGCAGGCAACTCCTCGTCAAGTCGAGACCGGGCGAGATTATCAAACCAGgtatgcaaat ... tctctttcagGCCAATTCAAGGCTATCAACGATGAAGGAATGCCTCACCACCAGAGACCCT
EST: gi|169083692|gb|FE494866.1|FE494866
EST:     ACCGGGCGAGATTATCAAGCCAG                         GCCAATTCAAGGCTATCAACGATGAAGGGATGCCTCACCACCAGAGACCCT
genomic: ACCGGGCGAGATTATCAAACCAGgtatgcaaat ... tctctttcagGCCAATTCAAGGCTATCAACGATGAAGGAATGCCTCACCACCAGAGACCCT
EST: gi|169112343|gb|FE512919.1|FE512919
EST:     CGGCAGGCAACTCCTCGTCAAGTCGAGACCGGGCGAGATTATCAAGCCAG                         GCCAATTCAAGGCTATCAACGATGAAGGGATGCCTCACCACCAGAGACCCT
genomic: CGGCAGGCAACTCCTCGTCAAGTCGAGACCGGGCGAGATTATCAAACCAGgtatgcaaat ... tctctttcagGCCAATTCAAGGCTATCAACGATGAAGGAATGCCTCACCACCAGAGACCCT
EST: gi|169062696|gb|FE470782.1|FE470782
EST:     CGGCAGGCAACTCCTCGTCAAGTCGAGACCGGGCGAGATTATCAAACCAG                         GCCAATTCAAGGCTATCAACGATGAAGGAATGCCTCACCACCAGAGACCCT
genomic: CGGCAGGCAACTCCTCGTCAAGTCGAGACCGGGCGAGATTATCAAACCAGgtatgcaaat ... tctctttcagGCCAATTCAAGGCTATCAACGATGAAGGAATGCCTCACCACCAGAGACCCT
EST: gi|169057318|gb|FE464218.1|FE464218
EST:     CGGCAGGCAACTCCTCGTCAAGTCGAGACCGGGCGAGATTATCAAACCAG                         GCCAATTCAAGGCTATCAACGATGAAGGAATGCCTCACCACCAGAGACCCT
genomic: CGGCAGGCAACTCCTCGTCAAGTCGAGACCGGGCGAGATTATCAAACCAGgtatgcaaat ... tctctttcagGCCAATTCAAGGCTATCAACGATGAAGGAATGCCTCACCACCAGAGACCCT

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), 35 (downstream exon)
Score: 14

TCTTTGCTGGATGCTCTCTGCGGTTTCCAGTTCACCATCACTCACCTCGACGGCAGGCAACTCCTCGTCAAGTCGAGACCGGGCGAGATTATCAAACCAGgtatgcaaat ... tctctttcagGCCAATTCAAGGCTATCAACGATGAAGGAATGCCTCACCACCAGAGACCCTTCATGAAGGGAACCCTGTACATCCACTTCTCGGTCGACTTCCCCGAGTC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaatcacttagtgtagctctcaggcttctctaaacgtatgtctcctctctttcagGCCAATTCAAGGCTATCAACGATGAAGGAATGCCTCACCACCAGAGACCCTTCATGAAGGGAACCCTGTACATCCACTTCTCGGTCGACTTCCCCGAGTC
                           ctctaaa  putative branch site (score: 14)
                                    tatgtctcctctcttt  putative PPT