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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGGTGAGCCTCTGAGAGCAATGGTGATGGGTGCTCCACTCGAAGATGCACGCCATCTGACACAGCGATACGATCGCCTTCGGCAGGAAGCCGAAGTACAGgttagtttggcctcactttcttgctttgtgtttacatgggggaatgacag

Basic information

species Selaginella moellendorffii
transcript EFJ37265
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ37265 (Selaginella moellendorffii), 5'ss of exon 5
lower sequence: PP1S34_169V6.1 (Physcomitrella patens), 5'ss of exon 6
TGGTGAGCCTCTGAGAGCAATGGTGATGGGTGCTCCACTCGAAGATGCACGCCATCTGACACAGCGATACGATCGCCTTCGGCAGGAAGCCGAAGTACAGgttagtttggcctcactttcttgctttgtgtttacatgggggaatgacag--------------------------------------------------
 |  || ||| ||||||||||||| ||||| || ||  | |||||||| || |||||| |||| |||||||||||| | || || || || |||   |||||  |     | |        | |||| |  ||  |   |  | |  ||                                                   
GGCAGAACCTTTGAGAGCAATGGTAATGGGCGCACCTTTGGAAGATGCTCGTCATCTGGCACAACGATACGATCGCTTACGTCAAGAGGCTGAAAATCAGgtatgccaatcatgtaaaatattctttatcatttgaattgcaactatcacctcattaattttttagacatatcctttcaaggaaacaaacctcacctcag
















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|169023852|gb|FE436403.1|FE436403
EST:     GCCATCTGACACAGCGATACGATCGCCTTCGGCAGGAAGCCGAAGTACAG                         GGGGAAGATGTTCGGAAGAGGCAGGCAAGGTCCCGAGAAGGCGGTGGAAAT
genomic: GCCATCTGACACAGCGATACGATCGCCTTCGGCAGGAAGCCGAAGTACAGgttagtttgg ... ggaatgacagGGGGAAGATGTTCGGAAGAGGCAGGCAAGGTCCCGAGAAGGCGGTGGAAAT
EST: gi|169078306|gb|FE490339.1|FE490339
EST:     GCCATCTGACACAGCGATACGATCGCCTTCGGCAGGAAGCCGAAGTACAG                         GGGGAAGATGTTCGGAAGAGGCAGGCAAGGTCCCGAGAAGGCGGTGGAAAT
genomic: GCCATCTGACACAGCGATACGATCGCCTTCGGCAGGAAGCCGAAGTACAGgttagtttgg ... ggaatgacagGGGGAAGATGTTCGGAAGAGGCAGGCAAGGTCCCGAGAAGGCGGTGGAAAT
EST: gi|169040026|gb|FE447025.1|FE447025
EST:     GCCATCTGACACAGCGATACGATCGCCTTCGGCAGGAAGCCGAAGTACAG                         GGGGAAGATGTTCGGAAGAGGCAGGCAAGGTCCCGAGAAGGCGGTGGAAAT
genomic: GCCATCTGACACAGCGATACGATCGCCTTCGGCAGGAAGCCGAAGTACAGgttagtttgg ... ggaatgacagGGGGAAGATGTTCGGAAGAGGCAGGCAAGGTCCCGAGAAGGCGGTGGAAAT
EST: gi|169023851|gb|FE436402.1|FE436402
EST:     GCCATCTGACACAGCGATACGATCGCCTTCGGCAGGAAGCCGAAGTACAG                         GGGGAAGATGTTCGGAAGAGGCAGGCAAGGTCCCGAGAAGGCGGTGGAAAT
genomic: GCCATCTGACACAGCGATACGATCGCCTTCGGCAGGAAGCCGAAGTACAGgttagtttgg ... ggaatgacagGGGGAAGATGTTCGGAAGAGGCAGGCAAGGTCCCGAGAAGGCGGTGGAAAT
EST: gi|169088940|gb|FE492892.1|FE492892
EST:     GACACAGCGATACGATCGCCTTCGGCAGGAAGCCGAAGTACAG                         GGGGAAGATGTTCGGAAGAGGCAGGCAAGGTCCCGAGAAGGCGGTGGAAAT
genomic: GACACAGCGATACGATCGCCTTCGGCAGGAAGCCGAAGTACAGgttagtttgg ... ggaatgacagGGGGAAGATGTTCGGAAGAGGCAGGCAAGGTCCCGAGAAGGCGGTGGAAAT
EST: gi|169103099|gb|FE505581.1|FE505581
EST:     GCCATCTGACACAGCGATACGATCGCCTTCGGCAGGAAGCCGAAGTACAG                         GGGGAAGATGTTCGGAAGAGGCAGGCAAGGTCCCGAGAAGGCGGTGGAAAT
genomic: GCCATCTGACACAGCGATACGATCGCCTTCGGCAGGAAGCCGAAGTACAGgttagtttgg ... ggaatgacagGGGGAAGATGTTCGGAAGAGGCAGGCAAGGTCCCGAGAAGGCGGTGGAAAT
EST: gi|169103098|gb|FE505580.1|FE505580
EST:     GCCATCTGACACAGCGATACGATCGCCTTCGGCAGGAAGCCGAAGTACAG                         GGGGAAGATGTTCGGAAGAGGCAGGCAAGGTCCCGAGAAGGCGGTGGAAAT
genomic: GCCATCTGACACAGCGATACGATCGCCTTCGGCAGGAAGCCGAAGTACAGgttagtttgg ... ggaatgacagGGGGAAGATGTTCGGAAGAGGCAGGCAAGGTCCCGAGAAGGCGGTGGAAAT
EST: gi|169025066|gb|FE434679.1|FE434679
EST:     GCAGGAAGCCGAAGTACAG                         GGGGAAGATGTTCGGAAGAGGCAGGCAAGGTCCCGAGAAGGCGGTGGAAAT
genomic: GCAGGAAGCCGAAGTACAGgttagtttgg ... ggaatgacagGGGGAAGATGTTCGGAAGAGGCAGGCAAGGTCCCGAGAAGGCGGTGGAAAT

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), 35 (downstream exon)
Score: 41

TGGTGAGCCTCTGAGAGCAATGGTGATGGGTGCTCCACTCGAAGATGCACGCCATCTGACACAGCGATACGATCGCCTTCGGCAGGAAGCCGAAGTACAGgttagtttgg ... ggaatgacagGGGGAAGATGTTCGGAAGAGGCAGGCAAGGTCCCGAGAAGGCGGTGGAAATGCCGAGAACGCCGTGAAGCTACAAATGGCAGAAGCAAGAATGCAAGAGC




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