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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATGCTGCCCTCTCCAGTCGGCCACTTGCTGCGACGATCACTACCACTGCTGCCCGTCCGACTTCCCGATCTGCAACTTAAAGGCCAACACTTGCCTCAGGgtaagttagctcgtttgtttttttgtttgcatacccgttgtggctgatcgttcgttcgttgtgatcttccgcag

Basic information

species Selaginella moellendorffii
transcript EFJ36576
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ36576 (Selaginella moellendorffii), 5'ss of exon 4
lower sequence: PP1S285_10V6.1 (Physcomitrella patens), 5'ss of exon 4
ATGCTGCCCTCTCCAGTCGGCCACTTGCTGCGACGATCACTACCACTGCTGCCCGTCCGACTTCCCGATCTGCAACTTAAAGGCCAACACTTGCCTCAGGgtaagttagctcgtttgtttttttgtttgcatacccgttgtggctgatcgttcgttcgttgtgatcttccgcag--------------------------
 || |||||  |  | || ||||| |||||||| ||||||||||| |||||||| || ||||||||| | |||||| |    |||      || |||| ||||| ||    | || | ||| |||||    |    |  |    || | |    ||     |  |    |  |                           
CTGTTGCCCGATGGAATCCGCCACCTGCTGCGAGGATCACTACCATTGCTGCCCCTCGGACTTCCCGGTTTGCAACCTGCGAGCCGGACAGTGTCTCAAGgtaacttgctcctttcgatttcttgttatgttttttgccgcctgtgtttgccgattaaccttacttcagcataactgcataaagagtattaatgtaaatt

upper sequence: EFJ36576 (Selaginella moellendorffii), 5'ss of exon 4
lower sequence: PP1S49_32V6.1 (Physcomitrella patens), 5'ss of exon 4
ATGCTGCCCTCTCCAGTCGGCCACTTGCTGCGACGATCACTACCACTGCTGCCCGTCCGACTTCCCGATCTGCAACTTAAAGGCCAACACTTGCCTCAGGgtaagttagctcgtttgtttttttgtttgcatacccgttgtggct-gatcgttcgttcgttgtgatc----ttccgcag----------------------
 ||||||||| |  | || |||||||||||||| || ||||||||||||||||| || || |||||  |||| |||||    ||       ||  ||| || ||  || ||| |   |||||      |  |       |    | ||  |     | | ||  | |    ||||   |                      
TTGCTGCCCTATGGAATCTGCCACTTGCTGCGAGGACCACTACCACTGCTGCCCCTCGGATTTCCCCGTCTGTAACTTGCGCGCTGGACAATGTGTCAAGgcaatata-ctcttcactttttgcacacgattggaatgggcaattagaaagcctagttggtgaaaccccggttcctacgctttgcttgggggctttcttgg

upper sequence: EFJ36576 (Selaginella moellendorffii), 5'ss of exon 4
lower sequence: PP1S19_362V6.2 (Physcomitrella patens), 5'ss of exon 5
ATGCTGCCCTCTCCAGTCGGCCACTTGCTGCGACGATCACTACCACTGCTGCCCGTCCGACTTCCCGATCTGCAACTTAAAGGCCAACACTTGCCTCAGGgtaagt--tagctcgtttgtttttttg-----tttgcatacccgttgtggctgatcgttcgttcgttgtgatcttccgcag-------------------
 |||||| || |  | || || || |||||||||||||||||||||||||| |||  ||| |  ||  | || |||||    ||      |||||| | |||  |   | | ||     || |  |      | |||  |   |     ||   || |   |  |     |  ||| |||                    
TTGCTGCTCTTTGGACTCCGCAACCTGCTGCGACGATCACTACCACTGCTGTCCGCACGATTATCCTGTTTGTAACTTGGCTGCTGGGCTTTGCCTTAAGgtgtgccctcgttctacaattgtactaaaacttatgcgaaataggcactgcaattcttgattctgcatccagattctgcatccagatttatttctgaatg

upper sequence: EFJ36576 (Selaginella moellendorffii), 5'ss of exon 4
lower sequence: PP1S292_39V6.2 (Physcomitrella patens), 5'ss of exon 4
ATGCTGCCCTCTCCAGTCGGCCACTTGCTGCGACGATCACTACCACTGCTGCCCGTCCGACTTCCCGATCTGCAACTTAAAGGCCAACACTTGCCTCAGGgtaagttagctcgtttgtttttttgtttgcatacccgttgtggc-tgatcgttcgttcgttgtgatcttccgcag------------------------------------------------------------------------------------------------
||| ||| |  |  | || || || |||||||| ||||||||||||||||||||   ||| | ||| ||||||||| |  | ||      |||||||| |||       | |  ||  |   |     |||    | ||||  | | |  | |  | |  | || ||      |                                                                                                 
ATGTTGCGCCTTGGACTCAGCGACCTGCTGCGATGATCACTACCACTGCTGCCCTCACGAGTACCCAATCTGCAACCTGGATGCAGGACTTTGCCTCAAGgtgcagcgccactctt-ctcactcaaaagcaacgtccttgtatcatcacagcttctgctatctgctcgcagctaatgtttcaattctgagaataccaccatcagtgcccagttttgaggtatgcagatgtctaaaagctaattgtgtgagtcgaatgttgtgctactgcag

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|169058163|gb|FE466593.1|FE466593
EST:     GCCCGTCCGACTTCCCGATCTGCAACTTACAGGCCAACACTTGCCTCAGG                         AGCTCCAAGGATTTGCTTGGGACAAAGATGCTGGAACGCACCCCGGCGCGC
genomic: GCCCGTCCGACTTCCCGATCTGCAACTTAAAGGCCAACACTTGCCTCAGGgtaagttagc ... tcttccgcagAGCTCCAAGGATTTGCTTGGGACAAAGATGCTGGAACGCACCCCGGCGCGC
EST: gi|169020788|gb|FE430189.1|FE430189
EST:     GCCCGTCCGACTTCCCGATCTGCAACTTACAGGCCAACACTTGCCTCAGG                         AGCTCCAAGGATTTGCTTG
genomic: GCCCGTCCGACTTCCCGATCTGCAACTTAAAGGCCAACACTTGCCTCAGGgtaagttagc ... tcttccgcagAGCTCCAAGGATTTGCTTG
EST: gi|169068392|gb|FE478982.1|FE478982
EST:     GCCCGTCCGACTTCCCGATCTGCAACTTACAGGCCAACACTTGCCTCAGG                         AGCTCCAAGGATTTGCTTGGGACAAAGATGCTGGAACGCACCCCGGCGCGC
genomic: GCCCGTCCGACTTCCCGATCTGCAACTTAAAGGCCAACACTTGCCTCAGGgtaagttagc ... tcttccgcagAGCTCCAAGGATTTGCTTGGGACAAAGATGCTGGAACGCACCCCGGCGCGC
EST: gi|169040445|gb|FE448445.1|FE448445
EST:     GCCCGTCCGACTTCCCGATCTGCAACTTACAGGCCAACACTTGCCTCAGG                         AGCTCCAAGGATTTGCTTGGGACAAAGATGCTGGAACGCACCCCGGCGCGC
genomic: GCCCGTCCGACTTCCCGATCTGCAACTTAAAGGCCAACACTTGCCTCAGGgtaagttagc ... tcttccgcagAGCTCCAAGGATTTGCTTGGGACAAAGATGCTGGAACGCACCCCGGCGCGC
EST: gi|169111578|gb|FE511868.1|FE511868
EST:     GCCCGTCCGACTTCCCGATCTGCAACTTAAAGGCCAACACTTGCCTCAGG                         AGCTCCAAGGATTTGCTTGGGACAAAGATGCTGGAACGCACCCCGGCGCGC
genomic: GCCCGTCCGACTTCCCGATCTGCAACTTAAAGGCCAACACTTGCCTCAGGgtaagttagc ... tcttccgcagAGCTCCAAGGATTTGCTTGGGACAAAGATGCTGGAACGCACCCCGGCGCGC
EST: gi|169069754|gb|FE478303.1|FE478303
EST:     GCCCGTCCGACTTCCCGATCTGCAACTTAAAGGCCAACACTTGCCTCAGG                         AGCTCCAAGGATTTGCTTGGGACAAAGATGCTGGAACGCACCCCGGCGCGC
genomic: GCCCGTCCGACTTCCCGATCTGCAACTTAAAGGCCAACACTTGCCTCAGGgtaagttagc ... tcttccgcagAGCTCCAAGGATTTGCTTGGGACAAAGATGCTGGAACGCACCCCGGCGCGC
EST: gi|169060244|gb|FE467606.1|FE467606
EST:     GCCCGTCCGACTTCCCGATCTGCAACTTACAGGCCAACACTTGCCTCAGG                         AGCTCCAAGGATTTGCTTGGGACAAAGATGCTGGAACGCACCCCGGCGCGC
genomic: GCCCGTCCGACTTCCCGATCTGCAACTTAAAGGCCAACACTTGCCTCAGGgtaagttagc ... tcttccgcagAGCTCCAAGGATTTGCTTGGGACAAAGATGCTGGAACGCACCCCGGCGCGC
EST: gi|169020787|gb|FE430188.1|FE430188
EST:     GCCCGTCCGACTTCCCGATCTGCAACTTACAGGCCAACACTTGCCTCAGG                         AGCTCCAAGGATTTGCTTGGGACAAAGATGCTGGAACGCACCCCGGCGCGC
genomic: GCCCGTCCGACTTCCCGATCTGCAACTTAAAGGCCAACACTTGCCTCAGGgtaagttagc ... tcttccgcagAGCTCCAAGGATTTGCTTGGGACAAAGATGCTGGAACGCACCCCGGCGCGC

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: 22 (upstream exon), 34 (downstream exon)
Score: 66

ATGCTGCCCTCTCCAGTCGGCCACTTGCTGCGACGATCACTACCACTGCTGCCCGTCCGACTTCCCGATCTGCAACTTAAAGGCCAACACTTGCCTCAGGgtaagttagc ... tcttccgcagAGCTCCAAGGATTTGCTTGGGACAAAGATGCTGGAACGCACCCCGGCGCGCTACACTGGAGGAGTGGACCGCAAATCCATGGCTTCGGCGTGAGACGGGA




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