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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCATCCGGCGAGCTCATGTGGTGCATCCGATCACTGCTGTTCAGCTGGAGTGGTCACTTTGGACCCGTGATGCGGAGGCAGAGATTATTCCTACGTGCAGgttggtctcaacccaagctctttttatcaagatcatgttcttactagagttcttccatttttctcaactttctcgcag

Basic information

species Selaginella moellendorffii
transcript EFJ24149
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ24149 (Selaginella moellendorffii), 5'ss of exon 4
lower sequence: LOC_Os01g43090.1 (Oryza sativa), 5'ss of exon 4
CCATCCGGCGAGCTCATGTGGTGCATCCGATCACTGCTGTTCAGCTGGAGTGGTCACTTTGGACCCGTGATGCGGAGGCAGAGATTATTCCTACGTGCAGgttggtctca-acccaagctctttttatcaagatcatgttcttactag--agttcttccatttttctcaactttctcgcag
||||| ||||||||||||  ||||| || |||||||| |||||| |||||||||| || ||| | |||||    ||  | || ||| | ||    |||||||   |  |  | |  || | ||  ||   |     || || | | ||  |  || ||    |   |  |||   |  |||
CCATCAGGCGAGCTCATGCCGTGCACCCAATCACTGCAGTTCAGATGGAGTGGTCTCTCTGGGCTCGTGACATTGAACCCGAAATTGTGCCGCTCTGCAGgtgaattccgcatcgcaggttttactaatgattgattgctcatgcaagtaaactcatcgcaatccatggactccattccag
















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|169064037|gb|FE472224.1|FE472224
EST:     TGGTCACTTTGGACCCGTGATGCGGAGGCAGAGATTATTCCTACGTGCAG                         AGAGCTTGGCATCGGAATAGTTCCATACAGCCCTCTCGGACGAGGCTTCTT
genomic: TGGTCACTTTGGACCCGTGATGCGGAGGCAGAGATTATTCCTACGTGCAGgttggtctca ... tttctcgcagAGAGCTTGGCATCGGAATAGTTCCATACAGCCCTCTCGGACGAGGCTTCTT
EST: gi|169033794|gb|FE442138.1|FE442138
EST:     TGGTCACTTTGGACCCGTGATGCGGAGGCAGAGATTATTCCTACGTGCAG                         AGAGCTTGGCATCGGAATAGTTCCATACAGCCCTCTCGGACGAGGCTTCTT
genomic: TGGTCACTTTGGACCCGTGATGCGGAGGCAGAGATTATTCCTACGTGCAGgttggtctca ... tttctcgcagAGAGCTTGGCATCGGAATAGTTCCATACAGCCCTCTCGGACGAGGCTTCTT
EST: gi|169064038|gb|FE472225.1|FE472225
EST:     TGGTCACTTTGGACCCGTGATGCGGAGGCAGAGATTATTCCTACGTGCAG                         AGAGCTTGGCATCGGAATAGTTCCATACAGCCCTCTCGGACGAGGCTTCTT
genomic: TGGTCACTTTGGACCCGTGATGCGGAGGCAGAGATTATTCCTACGTGCAGgttggtctca ... tttctcgcagAGAGCTTGGCATCGGAATAGTTCCATACAGCCCTCTCGGACGAGGCTTCTT
EST: gi|169052709|gb|FE463531.1|FE463531
EST:     TGGTCACTTTGGACCCGTGATGCGGAGGCAGAGATTATTCCTACGTGCAG                         AGAGCTTGGCATCGGAATAGTTCCATACAGCCCTCTCGGACGAGGCTTCTT
genomic: TGGTCACTTTGGACCCGTGATGCGGAGGCAGAGATTATTCCTACGTGCAGgttggtctca ... tttctcgcagAGAGCTTGGCATCGGAATAGTTCCATACAGCCCTCTCGGACGAGGCTTCTT
EST: gi|169060887|gb|FE469282.1|FE469282
EST:     TGGTCACTTTGGACCCGTGATGCGGAGGCAGAGATTATTCCTACGTGCAG                         AGAGCTTGGCATCGGAATAGTTCCATACAGCCCTCTCGGACGAGGCTTCTT
genomic: TGGTCACTTTGGACCCGTGATGCGGAGGCAGAGATTATTCCTACGTGCAGgttggtctca ... tttctcgcagAGAGCTTGGCATCGGAATAGTTCCATACAGCCCTCTCGGACGAGGCTTCTT
EST: gi|169100363|gb|FE501160.1|FE501160
EST:     TGGTCACTTTGGACCCGTGATGCGGAGGCAGAGATTATTCCTACGTGCAG                         AGAGCTTGGCATCGGAATAGTTCCATACAGCCCTCTCGGACGAGGCTTCTT
genomic: TGGTCACTTTGGACCCGTGATGCGGAGGCAGAGATTATTCCTACGTGCAGgttggtctca ... tttctcgcagAGAGCTTGGCATCGGAATAGTTCCATACAGCCCTCTCGGACGAGGCTTCTT
EST: gi|169033793|gb|FE442137.1|FE442137
EST:     TGGTCACTTTGGACCCGTGATGCGGAGGCAGAGATTATTCCTACGTGCAG                         AGAGCTTGGCATCGGAATAGTTCCATACAGCCCTCTCGGACGAGGCTTCTT
genomic: TGGTCACTTTGGACCCGTGATGCGGAGGCAGAGATTATTCCTACGTGCAGgttggtctca ... tttctcgcagAGAGCTTGGCATCGGAATAGTTCCATACAGCCCTCTCGGACGAGGCTTCTT
EST: gi|169100364|gb|FE501161.1|FE501161
EST:     TGGTCACTTTGGACCCGTGATGCGGAGGCAGAGATTATTCCTACGTGCAG                         AGAGCTTGGCATCGGAATAGTTCCATACAGCCCTCTCGGACGAGGCTTCTT
genomic: TGGTCACTTTGGACCCGTGATGCGGAGGCAGAGATTATTCCTACGTGCAGgttggtctca ... tttctcgcagAGAGCTTGGCATCGGAATAGTTCCATACAGCCCTCTCGGACGAGGCTTCTT
EST: gi|169052708|gb|FE463530.1|FE463530
EST:     TGGTCACTTTGGACCCGTGATGCGGAGGCAGAGATTATTCCTACGTGCAG                         AGAGCTTGGCATCGGAATAGTTCCATACAGCCCTCTCGGACGAGGCTTCTT
genomic: TGGTCACTTTGGACCCGTGATGCGGAGGCAGAGATTATTCCTACGTGCAGgttggtctca ... tttctcgcagAGAGCTTGGCATCGGAATAGTTCCATACAGCCCTCTCGGACGAGGCTTCTT
EST: gi|169060886|gb|FE469281.1|FE469281
EST:     TGGTCACTTTGGACCCGTGATGCGGAGGCAGAGATTATTCCTACGTGCAG                         AGAGCTTGGCATCGGAATAGTTCCATACAGCCCTCTCGGACGAGGCTTCTT
genomic: TGGTCACTTTGGACCCGTGATGCGGAGGCAGAGATTATTCCTACGTGCAGgttggtctca ... tttctcgcagAGAGCTTGGCATCGGAATAGTTCCATACAGCCCTCTCGGACGAGGCTTCTT

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: 22

CCATCCGGCGAGCTCATGTGGTGCATCCGATCACTGCTGTTCAGCTGGAGTGGTCACTTTGGACCCGTGATGCGGAGGCAGAGATTATTCCTACGTGCAGgttggtctca ... tttctcgcagAGAGCTTGGCATCGGAATAGTTCCATACAGCCCTCTCGGACGAGGCTTCTTCTCCGGCAAAGCGATTGTTGAGAAGCTACAAAGCGATGATTCCCGTCTT




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