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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAATTGGAAGCCACTGTCGTCGATGGCAATGGCACAGAGACTGGCCACATTATAGCTACGACGATAGGAGGCCGCAATGGCCAGCCAAAGCAGgtatttttattcttctcagcttctcggagtgggagtagtgacagtggtctcttctccag

Basic information

species Selaginella moellendorffii
transcript EFJ04915
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ04915 (Selaginella moellendorffii), 5'ss of exon 2
lower sequence: PP1S52_55V6.1 (Physcomitrella patens), 5'ss of exon 3
GAATTGGAAGCCACTGTCGTCGATGGCAATGGCACAGAGACTGGCCACATTATAGCTACGACGATAGGAGGCCGCAATGGCCAGCCAAAGCAGgtatttttattcttctcagcttctcggagtgggagtagtgacagtggtct-cttctccag-----------------------------------------
||  | ||||| || || || ||||| |||||||| ||||| |||||||| |||||||| || || ||||| ||||||||||| || |||||||||   |  |    ||| |||  || || |     |      ||     | |  | |||                                          
GAGATTGAAGCAACAGTAGTTGATGGAAATGGCACCGAGACAGGCCACATCATAGCTACCACTATTGGAGGACGCAATGGCCAACCGAAGCAGgtaggatagtgaggctctgcta-tcagaatattcattacaggagcaacttgccgcgccaaaaccgcgtctaatgaatacccttaagatatttggccatgac

upper sequence: EFJ04915 (Selaginella moellendorffii), 5'ss of exon 2
lower sequence: PP1S60_100V6.1 (Physcomitrella patens), 5'ss of exon 3
GAATTGGAAGCCACTGTCGTCGATGGCAATGGCACAGAGACTGGCCACATTATAGCTACGACGATAGGAGGCCGCAATGGCCAGCCAAAGCAGgtattt---ttattcttctcagcttctcggagtgggagtagtgacagtggtctcttctccag----------------------------------------
||| | || ||  | || || | ||| |||||||| ||||||||||| || |||||||| || || ||||| || ||||| || || ||||||||||     | |   |||| ||    |  ||||    || ||| | | || ||| | |||                                          
GAAATCGAGGCGTCAGTAGTAGCTGGGAATGGCACGGAGACTGGCCATATCATAGCTACCACAATTGGAGGGCGAAATGGGCAACCTAAGCAGgtatggcaatgacaattctgagtagttgagagtaaatgt-gtggc-gcggcctcgtgtccgcaaaccctcctggcatcgcaggacgctgtagtcttcccgaa
















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|169026283|gb|FE432646.1|FE432646
EST:     GCCACATTATAGCTACGACGATAGGAGGCCGCAATGGCCAGCCAAAGCAG                         ACGATTAGCTATGTCGCGGAACGTGTTGTAGGAACCGGATCGTTTGGCATC
genomic: GCCACATTATAGCTACGACGATAGGAGGCCGCAATGGCCAGCCAAAGCAGgtatttttat ... tcttctccagACGATTAGCTATGTCGCGGAACGTGTTGTAGGAACCGGATCGTTTGGCATC
EST: gi|169036066|gb|FE446772.1|FE446772
EST:     GCCACATTATAGCTACGACGATAGGAGGCCGCAATGGCCAGCCAAAGCAG                         ACGATTAGCTATGTCGCGGAACGTGTTGTATGAACCGGATCGTTTGGCATC
genomic: GCCACATTATAGCTACGACGATAGGAGGCCGCAATGGCCAGCCAAAGCAGgtatttttat ... tcttctccagACGATTAGCTATGTCGCGGAACGTGTTGTAGGAACCGGATCGTTTGGCATC
EST: gi|169111672|gb|FE511910.1|FE511910
EST:     GCCACATTATAGCTACGACGATTGGAGGCCGCAATGGCCAGCCAAAGCAG                         ACGATTAGCTATGTCGCGGAACGTGTTGTAGGAACTGGATCGTTTGGCATC
genomic: GCCACATTATAGCTACGACGATAGGAGGCCGCAATGGCCAGCCAAAGCAGgtatttttat ... tcttctccagACGATTAGCTATGTCGCGGAACGTGTTGTAGGAACCGGATCGTTTGGCATC
EST: gi|169051268|gb|FE457618.1|FE457618
EST:     GCCACATTATAGCTACGACGATTGGAGGCCGCAATGGCCAGCCAAAGCAG                         ACGATTAGCTATGTCGCGGAACGTGTTGTAGGAACTGGATCGTTTGGCATC
genomic: GCCACATTATAGCTACGACGATAGGAGGCCGCAATGGCCAGCCAAAGCAGgtatttttat ... tcttctccagACGATTAGCTATGTCGCGGAACGTGTTGTAGGAACCGGATCGTTTGGCATC
EST: gi|169020214|gb|FE430317.1|FE430317
EST:     GCCACATTATAGCTACGACGATAGGAGGCCGCAATGGCCAGCCAAAGCAG                         ACGATTAGCTATGTCGCGGAACGTGTTGTAGGAACCGGATCGTTTGGCATC
genomic: GCCACATTATAGCTACGACGATAGGAGGCCGCAATGGCCAGCCAAAGCAGgtatttttat ... tcttctccagACGATTAGCTATGTCGCGGAACGTGTTGTAGGAACCGGATCGTTTGGCATC
EST: gi|169046998|gb|FE454570.1|FE454570
EST:     GCCACATTATAGCTACGACGATTGGAGGCCGCAATGGCCAGCCAAAGCAG                         ACGATTAGCTATGTCGCGGAACGTGTTGTAGGAACTGGATCGTTTGGCATC
genomic: GCCACATTATAGCTACGACGATAGGAGGCCGCAATGGCCAGCCAAAGCAGgtatttttat ... tcttctccagACGATTAGCTATGTCGCGGAACGTGTTGTAGGAACCGGATCGTTTGGCATC
EST: gi|169054529|gb|FE462613.1|FE462613
EST:     GCCACATTATAGCTACGACGATTGGAGGCCGCAATGGCCAGCCAAAGCAG                         ACGATTAGCTATGTCGCGGAACGTGTTGTAGGAACTGGATCGTTTGGCATC
genomic: GCCACATTATAGCTACGACGATAGGAGGCCGCAATGGCCAGCCAAAGCAGgtatttttat ... tcttctccagACGATTAGCTATGTCGCGGAACGTGTTGTAGGAACCGGATCGTTTGGCATC
EST: gi|169057379|gb|FE466814.1|FE466814
EST:     GCCACATTATAGCTACGACGATAGGAGGCCGCAATGGCCAGCCAAAGCAG                         ACGATTAGCTATGTCGCGGAACGTGTTGTAGGAACCGGATCGTTTGGCATC
genomic: GCCACATTATAGCTACGACGATAGGAGGCCGCAATGGCCAGCCAAAGCAGgtatttttat ... tcttctccagACGATTAGCTATGTCGCGGAACGTGTTGTAGGAACCGGATCGTTTGGCATC
EST: gi|169051816|gb|FE458998.1|FE458998
EST:     GCCACATTATAGCTACGACGATAGGAGGCCGCAATGGCCAGCCAAAGCAG                         ACGATTAGCTATGTCGCGGAACGTGTTGTAGGAACCGGATCGTTTGGCATC
genomic: GCCACATTATAGCTACGACGATAGGAGGCCGCAATGGCCAGCCAAAGCAGgtatttttat ... tcttctccagACGATTAGCTATGTCGCGGAACGTGTTGTAGGAACCGGATCGTTTGGCATC

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: 33 (upstream exon), 35 (downstream exon)
Score: 28

GAATTGGAAGCCACTGTCGTCGATGGCAATGGCACAGAGACTGGCCACATTATAGCTACGACGATAGGAGGCCGCAATGGCCAGCCAAAGCAGgtatttttat ... tcttctccagACGATTAGCTATGTCGCGGAACGTGTTGTAGGAACCGGATCGTTTGGCATCGTCTTCCAG




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