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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtgtttcttcgtgtttgtctctacttgtgatcgagtgatctctcgcagCATCCCAGTCGGTGAAGAAAATTCTGGAAATCAATCCATATCTCCTGGGAACCATGGCTGGGGGTGCGGCCGATTGTCAGTTCTGGCAGAGAAATCTCGG

Basic information

species Selaginella moellendorffii
transcript EFJ25863
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ25863 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: GLYMA04G37030.3 (Glycine max), 3'ss of exon 3
------------------------------------------------------------------------------------------------------------gtaagtgttt-cttcgtgtttg-tctctacttgtgatcgagtgatctctcgcagCATCCCAGTCGGTGAAGAAAATTCTGGAAATCAATCCATATCTCCTGGGAACCATGGCTGGGGGTGCGGCCGATTGTCAGTTCTGGCAGAGAAATCTCGG
                                                                                                             ||  | ||| | | ||||||| |||  | || |||  |   | | |||| |||| || ||||| |||||||||||| | ||||||||||| ||| | || || || |||||||| ||||| || ||||| ||||| ||||| || ||||||||
gtgagtatttgttagattttaatttcatttttcactgttctttgttcctttggctgaggcagagttttttgtttttgtgctaattgctgcaaattaaaatgatgggttttatctatttgcattgtgtttgatcttgaattctgactgttggctgtctc-cagCGTCGCAGTCTGTGAAGAAAATTATCGAAATCAATCCGTATATGCTTGGGACAATGGCTGGTGGTGCTGCTGATTGCCAGTTTTGGCACAGGAATCTCGG

upper sequence: EFJ25863 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: GLYMA06G17960.1 (Glycine max), 3'ss of exon 3
-------------------------------------------------------------------------------gtaagtgtttcttcgtgtttgtctctacttgtga---tcgagtgatctct---cgcagCATCCCAGTCGGTGAAGAAAATTCTGGAAATCAATCCATATCTCCTGGGAACCATGGCTGGGGGTGCGGCCGATTGTCAGTTCTGGCAGAGAAATCTCGG
                                                                                    | | | || ||| |||||| |  |  |||   | ||||| |  ||     ||||||| ||||| |||||||| ||| | ||||| ||||| ||| | || || || |||||||| ||||| || ||||||||||| ||||| || ||||| ||
gtgagtgtttgttaattttaactttaatttcactattctttgttcctttggtgaatgctgagtttttatgttacttgttacttttatctatttgtggttgtctttgttcttgaattttgagtgttggctgtctccagCATCGCAGTCTGTGAAGAAGATTATTGAAATTAATCCGTATATGCTTGGGACAATGGCTGGAGGTGCTGCTGATTGTCAGTTTTGGCACAGGAATCTTGG

upper sequence: EFJ25863 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: PP1S2_300V6.1 (Physcomitrella patens), 3'ss of exon 2
----------------------------------------------gtaagtgtttc-ttcgtgtttgtctct-acttgtgatcgagtgatctctcgcagCATCCCAGTCGGTGAAGAAAATTCTGGAAATCAATCCATATCTCCTGGGAACCATGGCTGGGGGTGCGGCCGATTGTCAGTTCTGGCAGAGAAATCTCGG
                                              | ||| ||||  || ||   | |  || ||  |||      |  ||  || |||| || || ||||||||||||||| |||||||||| || ||  |  |||| || |||||||| ||||| || ||||||||||| |||||  ||||||| ||
agtgaggtttcccaaggttgcactatttaaatgtatggagcatgaagaaagggtttagttggtacatcttgctgacaagtgcattgtttttccatcacagCCTCGCAATCGGTGAAGAAAATTTTGGAAATCAACCCTTACTTGTTGGGCACAATGGCTGGAGGTGCTGCAGATTGTCAGTTTTGGCAACGAAATCTAGG

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|70669750|gb|DN838327.1|DN838327
EST:     AGGGATTATCGTCGCTGCCGACTCTCGAGCTAGCATGGGACAATATATCT                         CATCCCAGTCGGTGAAGAAAATTCTGGAAATCAATCCATATCTCCTGGGAA
genomic: AGGGATTATCGTCGCTGCCGACTCTCGAGCTAGCATGGGACAATATATCTgtaagtgttt ... tctctcgcagCATCCCAGTCGGTGAAGAAAATTCTGGAAATCAATCCATATCTCCTGGGAA
EST: gi|70670787|gb|DN839364.1|DN839364
EST:     AGGGATTATCGTCGCTGCCGACTCTCGAGCTAGCATGGGACAATATATCT                         CATCCCAGTCGGTGAAGAAAATTCTGGAAATCAATCCATATCTCCTGGGAA
genomic: AGGGATTATCGTCGCTGCCGACTCTCGAGCTAGCATGGGACAATATATCTgtaagtgttt ... tctctcgcagCATCCCAGTCGGTGAAGAAAATTCTGGAAATCAATCCATATCTCCTGGGAA
EST: gi|169066324|gb|FE473000.1|FE473000
EST:     AGGGATTATCGTCGCTGCCGACTCTCGAGCTAGCATGGGACAGTATATCT                         CATCCCAGTCGGTGAAGAAAATTCTGGAAATCAACCCATATCTCCTGGGAA
genomic: AGGGATTATCGTCGCTGCCGACTCTCGAGCTAGCATGGGACAATATATCTgtaagtgttt ... tctctcgcagCATCCCAGTCGGTGAAGAAAATTCTGGAAATCAATCCATATCTCCTGGGAA
EST: gi|169047645|gb|FE454813.1|FE454813
EST:     CGCTGCCGACTCTCGAGCTAGCATGGGACAATATATCT                         CATCCCAGTCGGTGAAGAAAATTCTGGAAATCAATCCATATCTCCTGGGAA
genomic: CGCTGCCGACTCTCGAGCTAGCATGGGACAATATATCTgtaagtgttt ... tctctcgcagCATCCCAGTCGGTGAAGAAAATTCTGGAAATCAATCCATATCTCCTGGGAA
EST: gi|169066323|gb|FE472999.1|FE472999
EST:     TCGCTGCCGACTCTCGAGCTAGCATGGGACAGTATATCT                         CATCCCAGTCGGTGAAGAAAATTCTGGAAATCAACCCATATCTCCTGGGAA
genomic: TCGCTGCCGACTCTCGAGCTAGCATGGGACAATATATCTgtaagtgttt ... tctctcgcagCATCCCAGTCGGTGAAGAAAATTCTGGAAATCAATCCATATCTCCTGGGAA
EST: gi|169062114|gb|FE469173.1|FE469173
EST:     TCGCTGCCGACTCTCGAGCTAGCATGGGACAATATATCT                         CATCCCAGTCGGTGAAGAAAATTCTGGAAATCAATCCATATCTCCTGGGAA
genomic: TCGCTGCCGACTCTCGAGCTAGCATGGGACAATATATCTgtaagtgttt ... tctctcgcagCATCCCAGTCGGTGAAGAAAATTCTGGAAATCAATCCATATCTCCTGGGAA
EST: gi|169053896|gb|FE460987.1|FE460987
EST:     AGGGATTATCGTCGCTGCCGACTCTCGAGCTAGCATGGGACAGTATATCT                         CATCCCAGTCGGTGAAGAAAATTCTGGAAATCAACCCATATCTCCTGGGAA
genomic: AGGGATTATCGTCGCTGCCGACTCTCGAGCTAGCATGGGACAATATATCTgtaagtgttt ... tctctcgcagCATCCCAGTCGGTGAAGAAAATTCTGGAAATCAATCCATATCTCCTGGGAA
EST: gi|70669328|gb|DN837905.1|DN837905
EST:     AGGGATTATCGTCGCTGCCGACTCTCGAGCTAGCATGGGACAATATATCT                         CATCCCAGTCGGTGAAGAAAATTCTGGAAATCAATCCATATCTCCTGGGAA
genomic: AGGGATTATCGTCGCTGCCGACTCTCGAGCTAGCATGGGACAATATATCTgtaagtgttt ... tctctcgcagCATCCCAGTCGGTGAAGAAAATTCTGGAAATCAATCCATATCTCCTGGGAA
EST: gi|169062115|gb|FE469174.1|FE469174
EST:     AGGGATTATCGTCGCTGCCGACTCTCGAGCTAGCATGGGACAATATATCT                         CATCCCAGTCGGTGAAGAAAATTCTGGAAATCAATCCATATCTCCTGGGAA
genomic: AGGGATTATCGTCGCTGCCGACTCTCGAGCTAGCATGGGACAATATATCTgtaagtgttt ... tctctcgcagCATCCCAGTCGGTGAAGAAAATTCTGGAAATCAATCCATATCTCCTGGGAA
EST: gi|169019358|gb|FE427668.1|FE427668
EST:     AGGGATTATCGTCGCTGCCGACTCTCGAGCTAGCATGGGACAATATATCT                         CATCCCAGTCGGTGAAGAAAATTCTGGAAATCAATCCATATCTCCTGGGAA
genomic: AGGGATTATCGTCGCTGCCGACTCTCGAGCTAGCATGGGACAATATATCTgtaagtgttt ... tctctcgcagCATCCCAGTCGGTGAAGAAAATTCTGGAAATCAATCCATATCTCCTGGGAA
EST: gi|169106278|gb|FE507992.1|FE507992
EST:     AGGGATTATCGTCGCTGCCGACTCTCGAGCTAGCATGGGACAGTATATCT                         CATCCCAGTCGGTGAAGAAAATTCTGGAAATCAACCCATATCTCCTGGGAA
genomic: AGGGATTATCGTCGCTGCCGACTCTCGAGCTAGCATGGGACAATATATCTgtaagtgttt ... tctctcgcagCATCCCAGTCGGTGAAGAAAATTCTGGAAATCAATCCATATCTCCTGGGAA
EST: gi|169047646|gb|FE454814.1|FE454814
EST:     AGGGATTATCGTCGCTGCCGACTCTCGAGCTAGCATGGGACAATATATCT                         CATCCCAGTCGGTGAAGAAAATTCTGGAAATCAATCCATATCTCCTGGGAA
genomic: AGGGATTATCGTCGCTGCCGACTCTCGAGCTAGCATGGGACAATATATCTgtaagtgttt ... tctctcgcagCATCCCAGTCGGTGAAGAAAATTCTGGAAATCAATCCATATCTCCTGGGAA

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), 34 (downstream exon)
Score: 16

TTGCTGAAGCCAGCGCACGGAACCACGACGCTGGCGTTTGAGTTCCAGGGAGGGATTATCGTCGCTGCCGACTCTCGAGCTAGCATGGGACAATATATCTgtaagtgttt ... tctctcgcagCATCCCAGTCGGTGAAGAAAATTCTGGAAATCAATCCATATCTCCTGGGAACCATGGCTGGGGGTGCGGCCGATTGTCAGTTCTGGCAGAGAAATCTCGG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtaagtgtttcttcgtgtttgtctctacttgtgatcgagtgatctctcgcagCATCCCAGTCGGTGAAGAAAATTCTGGAAATCAATCCATATCTCCTGGGAACCATGGCTGGGGGTGCGGCCGATTGTCAGTTCTGGCAGAGAAATCTCGG
                                               tctctcgc  CT-rich tract