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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gcaaggcattttattcttttcttgcattgcttgcaatacagatctaaaagcttcgtccagGCTCTTGACACATTCAACACAGCGGTTGTGTCACCAATCTACTATGTAATGTTCACGACGTTCACGATTGTTGCTAGCGTGATTATGTTCAAG

Basic information

species Selaginella moellendorffii
transcript EFJ22449
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ22449 (Selaginella moellendorffii), 3'ss of exon 6
lower sequence: GLYMA02G44980.2 (Glycine max), 3'ss of exon 5
-----------------------------------gcaaggcattttattcttttcttgcattgcttgcaat--aca-gatctaaaagc--ttcgtccagGCTCTTGACACATTCAACACAGCGGTTGTGTCACCAATCTACTATGTAATGTTCACGACGTTCACGATTGTTGCTAGCGTGATTATGTTCAAG
                                     | |  |||||       |     ||| ||    |   ||| |||   |  |   ||  | |||||||||||||| |||||||||||  |||| || || || |||||||| |||||||| ||  | || ||  | || || || || ||||| |||
agattttctgtgtattatatacaaagttcttatatatatgaaattttggatcaattactaattactcttcactgacatgattgtattgtaattatttcagGCTCTTGACACCTTCAACACAGCAATTGTATCTCCTATATACTATGTCATGTTCACAACACTTACAATACTAGCCAGTGTAATAATGTTTAAG

upper sequence: EFJ22449 (Selaginella moellendorffii), 3'ss of exon 6
lower sequence: GLYMA14G03790.1 (Glycine max), 3'ss of exon 6
-----------------------------------gcaaggcattt-tat-tcttttcttgcattgcttg--caatacagatctaaaagcttcgtc-cagGCTCTTGACACATTCAACACAGCGGTTGTGTCACCAATCTACTATGTAATGTTCACGACGTTCACGATTGTTGCTAGCGTGATTATGTTCAAG
                                    ||| |   || ||| |    | ||| ||   ||   |   || ||  | |  ||    |  |||||||||||||| |||||||||||  |||| || || || |||||||| |||||||| ||  | || ||  | || || || || ||||| |||
ttctagagaattcagattttctctgtgcattatatacaaagttcttatatatgaaattttggatcaattattcttcactgacatgattgcaatatttcagGCTCTTGACACCTTCAACACAGCAATTGTATCTCCTATATACTATGTCATGTTCACAACACTTACAATACTAGCCAGTGTAATAATGTTTAAG

upper sequence: EFJ22449 (Selaginella moellendorffii), 3'ss of exon 6
lower sequence: AT2G21120.1 (Arabidopsis thaliana), 3'ss of exon 6
---------------------------gcaaggcattttattcttttcttgcattgcttgc-aatac---agatc---------taaaagcttcgtccagGCTCTTGACACATTCAACACAGCGGTTGTGTCACCAATCTACTATGTAATGTTCACGACGTTCACGATTGTTGCTAGCGTGATTATGTTCAAG
                             | |   | |    ||    | |||||| |  | ||  |   ||||          ||  |  ||  | |||||| | |||||||||||| ||||  |||| || ||| | ||||||||||||||||| ||  |||| ||||||||||| |  || |||||||||
ttgaaggtctcttttttcccagcaaacatatgaactctagaactcacttggcattgttgactaaggcctaagattgttacttgttatgatttttttgcagGCTTTGGACACATTCAACGCAGCCATTGTTTCTCCAGTATACTATGTAATGTTCACAACCCTCACAATTGTTGCTAGTGCAATAATGTTCAAG

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|169099938|gb|FE503426.1|FE503426
EST:     GAATGGTTCTTGTCACCTGTGTGGTCACTCAGATGAACTACCTCAACAAG                         GCTCTTGACACATTCAACACAGCGGTTGTGTCACCAATCTACTATGTAATG
genomic: GAATGGTTCTTGTCACCTGTGTGGTCACTCAGATGAACTACCTCAACAAGgcaaggcatt ... cttcgtccagGCTCTTGACACATTCAACACAGCGGTTGTGTCACCAATCTACTATGTAATG
EST: gi|169026886|gb|FE434237.1|FE434237
EST:     GAATGGTTCTTGTCACCTGTGTGGTCACTCAGATGAACTACCTCAACAAG                         GCTCTTGACACATTCAACACAGCGGTTGTGTCACCAATCTACTATGTAATG
genomic: GAATGGTTCTTGTCACCTGTGTGGTCACTCAGATGAACTACCTCAACAAGgcaaggcatt ... cttcgtccagGCTCTTGACACATTCAACACAGCGGTTGTGTCACCAATCTACTATGTAATG
EST: gi|169082616|gb|FE489087.1|FE489087
EST:     GAATGGTTCTTGTCACCTGTGTGGTCACTCAGATGAATTACCTCAACAAG                         GCTCTTGACACATTCAACACAGCGGTTGTGTCACCAATCTACTATGTAATG
genomic: GAATGGTTCTTGTCACCTGTGTGGTCACTCAGATGAACTACCTCAACAAGgcaaggcatt ... cttcgtccagGCTCTTGACACATTCAACACAGCGGTTGTGTCACCAATCTACTATGTAATG
EST: gi|169100905|gb|FE502235.1|FE502235
EST:     GAATGGTTCTTGTCACCTGTGTGGTCACTCAGATGAACTACCTCAACAAG                         GCTCTTGACACATTCAACACAGCGGTTGTGTCACCAATCTACTATGTAATG
genomic: GAATGGTTCTTGTCACCTGTGTGGTCACTCAGATGAACTACCTCAACAAGgcaaggcatt ... cttcgtccagGCTCTTGACACATTCAACACAGCGGTTGTGTCACCAATCTACTATGTAATG
EST: gi|169082615|gb|FE489086.1|FE489086
EST:     GAATGGTTCTTGTCACCTGTGTGGTCACTCAGATGAATTACCTCAACAAG                         GCTCTTGACACATTCAACACAGCGGTTGTGTCACCAATCTACTATGTAATG
genomic: GAATGGTTCTTGTCACCTGTGTGGTCACTCAGATGAACTACCTCAACAAGgcaaggcatt ... cttcgtccagGCTCTTGACACATTCAACACAGCGGTTGTGTCACCAATCTACTATGTAATG
EST: gi|169098839|gb|FE502236.1|FE502236
EST:     GAATGGTTCTTGTCACCTGTGTGGTCACTCAGATGAACTACCTCAACAAG                         GCTCTTGACACATTCAACACAGCGGTTGTGTCACCAATCTACTATGTAATG
genomic: GAATGGTTCTTGTCACCTGTGTGGTCACTCAGATGAACTACCTCAACAAGgcaaggcatt ... cttcgtccagGCTCTTGACACATTCAACACAGCGGTTGTGTCACCAATCTACTATGTAATG
EST: gi|169095049|gb|FE498023.1|FE498023
EST:     GAATGGTTCTTGTCACCTGTGTGGTCACTCAGATGAACTACCTCAACAAG                         GCTCTTGACACATTCAACACAGCGGTTGTGTCACCAATCTACTATGTAATG
genomic: GAATGGTTCTTGTCACCTGTGTGGTCACTCAGATGAACTACCTCAACAAGgcaaggcatt ... cttcgtccagGCTCTTGACACATTCAACACAGCGGTTGTGTCACCAATCTACTATGTAATG
EST: gi|169043583|gb|FE450805.1|FE450805
EST:     GAATGGTTCTTGTCACCTGTGTGGTCACTCAGATGAACTACCTCAACAAG                         GCTCTTGACACATTCAACACAGCGGTTGTGTCACCAATCTACTA
genomic: GAATGGTTCTTGTCACCTGTGTGGTCACTCAGATGAACTACCTCAACAAGgcaaggcatt ... cttcgtccagGCTCTTGACACATTCAACACAGCGGTTGTGTCACCAATCTACTA

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), 31 (downstream exon)
Score: 5

TACATTCCAGGGCTCTAATCAGCTTATTTACTCGCAAACGTGGGTGTTTGGAATGGTTCTTGTCACCTGTGTGGTCACTCAGATGAACTACCTCAACAAGgcaaggcatt ... cttcgtccagGCTCTTGACACATTCAACACAGCGGTTGTGTCACCAATCTACTATGTAATGTTCACGACGTTCACGATTGTTGCTAGCGTGATTATGTTCAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcattttattcttttcttgcattgcttgcaatacagatctaaaagcttcgtccagGCTCTTGACACATTCAACACAGCGGTTGTGTCACCAATCTACTATGTAATGTTCACGACGTTCACGATTGTTGCTAGCGTGATTATGTTCAAG
                                    atctaaa  putative branch site (score: 5)
                                             cttcgtcc  putative PPT
     ttattctttt  TA-rich tract