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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtttctttctcattcttcatgggagttcgttctgacattttccttaaactgatgaagGCAGATAGCCTCTGATTGCAAGTTCCTCGAGTCTCAACATATAATGGATTACAGCCTCCTGTTGGGGCTTCACTTTCGAGCGCCACACTTTTATCAACCT

Basic information

species Selaginella moellendorffii
transcript EFJ05102
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ05102 (Selaginella moellendorffii), 3'ss of exon 5
lower sequence: GLYMA08G19860.1 (Glycine max), 3'ss of exon 5
--------------------------gtaagtttctttctcattcttca--tgggagttcg---ttctgacattttccttaaactgat--------gaagGCAGATAGCCTCTGATTGCAAGTTCCTCGAGTCTCAACATATAATGGATTACAGCCTCCTGTTGGGGCTTCACTTTCGAGCGCCACACTTTTATCAACCT
                           | | | ||    | | |    |  ||| |  | |   |||| |   |  ||  ||  ||||        ||||||| ||  ||   |||||||||||| | |||||||| |||||||| ||||||||||| ||||||||  | || || ||||| ||| |   |    |  | 
tgtatcatgacaaattgacaattgcattcaatatcccattaactgcatagttggtaaattgaccttctaatcataaccagaatttgattttctgttgaagGCAAATTTCCCTAGATTGCAAGTTCTTGGAGTCTCAGCATATAATTGATTACAGCCTTCTGTTGGGATTACATTTCCGAGCTCCAGAGAATATGAAGGCC

upper sequence: EFJ05102 (Selaginella moellendorffii), 3'ss of exon 5
lower sequence: GLYMA15G05150.2 (Glycine max), 3'ss of exon 5
--------------------------gtaagtttctttctcattcttca--tgggagttcg---ttctgacattttccttaaactgat--------gaagGCAGATAGCCTCTGATTGCAAGTTCCTCGAGTCTCAACATATAATGGATTACAGCCTCCTGTTGGGGCTTCACTTTCGAGCGCCACACTTTTATCAACCT
                           | |   ||    | | |    |  ||| |  | |   |||| |   |  ||  ||| ||||        ||||||| ||  ||   |||||||||||| | |||||||| |||||||| ||||||||||| ||||||||  | || || ||||| ||| |   |    |  | 
tgtatcatggcaaattgacaattgcattcaacatcccattaactgcatagttggtaaattgaccttctaatcataaccagaaattgattttctggtgaagGCAAATTTCCCTAGATTGCAAGTTCTTGGAGTCTCAGCATATAATTGATTACAGCCTTCTGTTGGGATTACATTTCCGAGCTCCAGAGAATATGAAGGCC
















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|169082030|gb|FE487487.1|FE487487
EST:     TTGGACTACGTCTTCCATCTGGAACCAAGTTGGCGCGACGCTTTGATAAA                         GCAGATAGCCTCTGATTGCAAGTTCCTCGAGTCTCAACATATAATGGATTA
genomic: TTGGACTACGTCTTCCATCTGGAACCAAGTTGGCGCGACGCTTTGATAAAgtaagtttct ... actgatgaagGCAGATAGCCTCTGATTGCAAGTTCCTCGAGTCTCAACATATAATGGATTA
EST: gi|169047215|gb|FE456464.1|FE456464
EST:     TTGGACTACGTCTTCCATCTGGAACCAAGTTGGCGCGACGCTTTGATAAA                         GCAGATAGCCTCTGATTGCAAGTTCCTCGAGTCTCAACATATAATGGATTA
genomic: TTGGACTACGTCTTCCATCTGGAACCAAGTTGGCGCGACGCTTTGATAAAgtaagtttct ... actgatgaagGCAGATAGCCTCTGATTGCAAGTTCCTCGAGTCTCAACATATAATGGATTA
EST: gi|169100307|gb|FE501104.1|FE501104
EST:     TTGGACTACGTCTTCCATCTGGAACCAAGTTGGCGCGACGCTTTGATAAA                         GCAGATAGCCTCTGATTGCAAGTTCCTCGAGTCTCAACATATAATGGATTA
genomic: TTGGACTACGTCTTCCATCTGGAACCAAGTTGGCGCGACGCTTTGATAAAgtaagtttct ... actgatgaagGCAGATAGCCTCTGATTGCAAGTTCCTCGAGTCTCAACATATAATGGATTA
EST: gi|169109610|gb|FE510044.1|FE510044
EST:     TTGGACTACGTCTTCCATCTGGAACCAAGTTGGCGCGACGCTTTGATAAA                         GCAGATAGCCTCTGATTGCAAGTTCCTCGAGTCTCAACATATAATGGATTA
genomic: TTGGACTACGTCTTCCATCTGGAACCAAGTTGGCGCGACGCTTTGATAAAgtaagtttct ... actgatgaagGCAGATAGCCTCTGATTGCAAGTTCCTCGAGTCTCAACATATAATGGATTA
EST: gi|169055652|gb|FE465296.1|FE465296
EST:     TTGGACTACGTCTTCCATCTGGAACCAAGTTGGCGCGACGCTTTGATAAA                         GCAGATAGCCTCTGATTGCAAGTTCCTCGAGTCTCAACATATAATGGATTA
genomic: TTGGACTACGTCTTCCATCTGGAACCAAGTTGGCGCGACGCTTTGATAAAgtaagtttct ... actgatgaagGCAGATAGCCTCTGATTGCAAGTTCCTCGAGTCTCAACATATAATGGATTA
EST: gi|169055653|gb|FE465297.1|FE465297
EST:     TTGGACTACGTCTTCCATCTGGAACCAAGTTGGCGCGACGCTTTGATAAA                         GCAGATAGCCTCTGATTGCAAGTTCCTCGAGTCTCAACATATAATGGATTA
genomic: TTGGACTACGTCTTCCATCTGGAACCAAGTTGGCGCGACGCTTTGATAAAgtaagtttct ... actgatgaagGCAGATAGCCTCTGATTGCAAGTTCCTCGAGTCTCAACATATAATGGATTA
EST: gi|169093546|gb|FE492330.1|FE492330
EST:     TTGGACTACGTCTTCCATCTGGAACCAAGTTGGCGCGACGCTTTGATAAA                         GCAGATAGCCTCTGATTGCAAGTTCCTCGAGTCTCAACATATAATGGATTA
genomic: TTGGACTACGTCTTCCATCTGGAACCAAGTTGGCGCGACGCTTTGATAAAgtaagtttct ... actgatgaagGCAGATAGCCTCTGATTGCAAGTTCCTCGAGTCTCAACATATAATGGATTA
EST: gi|169093547|gb|FE492331.1|FE492331
EST:     TTGGACTACGTCTTCCATCTGGAACCAAGTTGGCGCGACGCTTTGATAAA                         GCAGATAGCCTCTGATTGCAAGTTCCTCGAGTCTCAACATATAATGGATTA
genomic: TTGGACTACGTCTTCCATCTGGAACCAAGTTGGCGCGACGCTTTGATAAAgtaagtttct ... actgatgaagGCAGATAGCCTCTGATTGCAAGTTCCTCGAGTCTCAACATATAATGGATTA
EST: gi|169065916|gb|FE475364.1|FE475364
EST:     TTGGACTACGTCTTCCATCTGGAACCAAGTTGGCGCGACGCTTTGATAAA                         GCAGATAGCCTCTGATTGCAAGTTCCTCGAGTCTCAACATATAATGGATTA
genomic: TTGGACTACGTCTTCCATCTGGAACCAAGTTGGCGCGACGCTTTGATAAAgtaagtttct ... actgatgaagGCAGATAGCCTCTGATTGCAAGTTCCTCGAGTCTCAACATATAATGGATTA

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), 29 (downstream exon)
Score: 13

GCACTGGCGAGGCCGACATCGATGAGAACACCACGTTGAAAGACTTGGATTTGGACTACGTCTTCCATCTGGAACCAAGTTGGCGCGACGCTTTGATAAAgtaagtttct ... actgatgaagGCAGATAGCCTCTGATTGCAAGTTCCTCGAGTCTCAACATATAATGGATTACAGCCTCCTGTTGGGGCTTCACTTTCGAGCGCCACACTTTTATCAACCT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttctttctcattcttcatgggagttcgttctgacattttccttaaactgatgaagGCAGATAGCCTCTGATTGCAAGTTCCTCGAGTCTCAACATATAATGGATTACAGCCTCCTGTTGGGGCTTCACTTTCGAGCGCCACACTTTTATCAACCT
                                acatttt  TA-rich tract