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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGCCTGCTATGGTGTTCTCAGGTTCATCATGGAGTCTGGAGCCAAGGGTTGTGAGgtatggacgaactctcggcattttgctcttcaggttgtaacttcattcctggctcctttcag

Basic information

species Selaginella moellendorffii
transcript EFJ34304
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ34304 (Selaginella moellendorffii), 5'ss of exon 4
lower sequence: PP1S31_178V6.1 (Physcomitrella patens), 5'ss of exon 4
GGCCTGCTATGGTGTTCTCAGGTTCATCATGGAGTCTGGAGCCAAGGGTTGTGAGgtatggacgaactct-cggcattttgctcttcaggttgtaacttcattcctggctcct---ttcag-----------------------------------
||| |||||||| || || |||||||||||||||   || |||||||||||||||||||||   | |||| | | || | | |       ||| ||| |  |   |  ||  |      ||                                   
GGCTTGCTATGGAGTGCTGAGGTTCATCATGGAGAGCGGTGCCAAGGGTTGTGAGgtatgg-taacctctactggatgtagtttgagccattgaaacgttttgtttaactgatggacctagtggacagtcgtatgaatgtatttttgcgaaatatc

upper sequence: EFJ34304 (Selaginella moellendorffii), 5'ss of exon 4
lower sequence: PP1S136_175V6.1 (Physcomitrella patens), 5'ss of exon 4
GGCCTGCTATGGTGTTCTCAGGTTCATCATGGAGTCTGGAGCCAAGGGTTGTGAGgta---tggacgaactctcggcattttgctcttcaggttgtaacttcattcctggctcctttcag---------------------------------------
||| |||||||| || || |||||||||||||||   || ||||||||||||||||||   ||  |     || |  ||||||     ||  |||||  ||| ||   |  | | || ||                                       
GGCTTGCTATGGAGTGCTGAGGTTCATCATGGAGAGCGGTGCCAAGGGTTGTGAGgtactgtgaccatgtgcttgatattttggaagcca--ttgta--ttcctttgggtattcatttagtgatatgtcattccggacgccctaaaaaactccaagcat
















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|169072227|gb|FE479359.1|FE479359
EST:     GCTATGGTGTTCTCAGGTTCATCATGGAGTCTGGAGCCAAGGGTTGTGAG                         GTGATTGTGAGCGGCAAGCTCCGAGCCCAACGCGCCAAGTCGATGAAGTTC
genomic: GCTATGGTGTTCTCAGGTTCATCATGGAGTCTGGAGCCAAGGGTTGTGAGgtatggacga ... ctcctttcagGTGATTGTGAGCGGCAAGCTCCGAGCCCAACGCGCCAAGTCGATGAAGTTC
EST: gi|169038060|gb|FE446658.1|FE446658
EST:     GCTATGGTGTTCTCAGGTTCATCATGGAGTCTGGAGCCAAGGGTTGTGAG                         GTGATTGTGAGCGGCAAGCTCCGAGCCCAACGCGCCAAGTCGATGAAGTTC
genomic: GCTATGGTGTTCTCAGGTTCATCATGGAGTCTGGAGCCAAGGGTTGTGAGgtatggacga ... ctcctttcagGTGATTGTGAGCGGCAAGCTCCGAGCCCAACGCGCCAAGTCGATGAAGTTC
EST: gi|169043108|gb|FE454022.1|FE454022
EST:     GCTATGGTGTTCTCAGGTTCATCATGGAGTCTGGAGCCAAGGGTTGTGAG                         GTGATTGTGAGCGGCAAGCTCCGAGCCCAACGCGCCAAGTCGATGAAGTTC
genomic: GCTATGGTGTTCTCAGGTTCATCATGGAGTCTGGAGCCAAGGGTTGTGAGgtatggacga ... ctcctttcagGTGATTGTGAGCGGCAAGCTCCGAGCCCAACGCGCCAAGTCGATGAAGTTC
EST: gi|70671143|gb|DN839720.1|DN839720
EST:     GCTATGGTGTTCTCAAGTTCATCATGGAGTCTGGAGCCAAGGGTTGTGAG                         GTGATTGTGAGCGGCGAGCTCCGAGCCCAACGCGCCAAGTCGATGAAGTTC
genomic: GCTATGGTGTTCTCAGGTTCATCATGGAGTCTGGAGCCAAGGGTTGTGAGgtatggacga ... ctcctttcagGTGATTGTGAGCGGCAAGCTCCGAGCCCAACGCGCCAAGTCGATGAAGTTC
EST: gi|169038061|gb|FE446659.1|FE446659
EST:     GCTATGGTGTTCTCAGGTTCATCATGGAGTCTGGAGCCAAGGGTTGTGAG                         GTGATTGTGAGCGGCAAGCTCCGAGCCCAACGCGCCAAGTCGATGAAGTTC
genomic: GCTATGGTGTTCTCAGGTTCATCATGGAGTCTGGAGCCAAGGGTTGTGAGgtatggacga ... ctcctttcagGTGATTGTGAGCGGCAAGCTCCGAGCCCAACGCGCCAAGTCGATGAAGTTC
EST: gi|169103365|gb|FE507342.1|FE507342
EST:     GCTATGGTGTTCTCAGGTTCATCATGGAGTCTGGAGCCAAGGGTTGTGAG                         GTGATTGTGAGCGGCAAGCTCCGAGCCCAACGCGCCAAGTCGATGAAGTTC
genomic: GCTATGGTGTTCTCAGGTTCATCATGGAGTCTGGAGCCAAGGGTTGTGAGgtatggacga ... ctcctttcagGTGATTGTGAGCGGCAAGCTCCGAGCCCAACGCGCCAAGTCGATGAAGTTC
EST: gi|169044789|gb|FE454104.1|FE454104
EST:     GCTATGGTGTTCTCAGGTTCATCATGGAGTCTGGAGCCAAGGGTTGTGAG                         GTGATTGTGAGCGGCAAGCTCCGAGCCCAACGCGCCAAGTCGATGAAGTTC
genomic: GCTATGGTGTTCTCAGGTTCATCATGGAGTCTGGAGCCAAGGGTTGTGAGgtatggacga ... ctcctttcagGTGATTGTGAGCGGCAAGCTCCGAGCCCAACGCGCCAAGTCGATGAAGTTC
EST: gi|169073958|gb|FE481670.1|FE481670
EST:     GCTATGGTGTTCTCAGGTTCATCATGGAGTCTGGAGCCAAGGGTTGTGAG                         GTGATTGTGAGCGGCAAGCTCCGAGCCCAACGCGCCAAGTCGATGAAGTTC
genomic: GCTATGGTGTTCTCAGGTTCATCATGGAGTCTGGAGCCAAGGGTTGTGAGgtatggacga ... ctcctttcagGTGATTGTGAGCGGCAAGCTCCGAGCCCAACGCGCCAAGTCGATGAAGTTC
EST: gi|169067196|gb|FE474964.1|FE474964
EST:     GCTATGGTGTTCTCAGGTTCATCATGGAGTCTGGAGCCAAGGGTTGTGAG                         GTGATTGTGAGCGGCAAGCTCCGAGCCCAACGCGCCAAGTCGATGAAGTTC
genomic: GCTATGGTGTTCTCAGGTTCATCATGGAGTCTGGAGCCAAGGGTTGTGAGgtatggacga ... ctcctttcagGTGATTGTGAGCGGCAAGCTCCGAGCCCAACGCGCCAAGTCGATGAAGTTC
EST: gi|169034020|gb|FE444210.1|FE444210
EST:     GCTATGGTGTTCTCAGGTTCATCATGGAGTCTGGAGCCAAGGGTTGTGAG                         GTGATTGTGAGCGGCAAGCTCCGAGCCCAACGCGCCAAGTCGATGAAGTTC
genomic: GCTATGGTGTTCTCAGGTTCATCATGGAGTCTGGAGCCAAGGGTTGTGAGgtatggacga ... ctcctttcagGTGATTGTGAGCGGCAAGCTCCGAGCCCAACGCGCCAAGTCGATGAAGTTC
EST: gi|169073959|gb|FE481671.1|FE481671
EST:     GCTATGGTGTTCTCAGGTTCATCATGGAGTCTGGAGCCAAGGGTTGTGAG                         GTGATTGTGAGCGGCAAGCTCCGAGCCCAACGCGCCAAGTCGATGAAGTTC
genomic: GCTATGGTGTTCTCAGGTTCATCATGGAGTCTGGAGCCAAGGGTTGTGAGgtatggacga ... ctcctttcagGTGATTGTGAGCGGCAAGCTCCGAGCCCAACGCGCCAAGTCGATGAAGTTC
EST: gi|169034021|gb|FE444211.1|FE444211
EST:     GCTATGGTGTTCTCAGGTTCATCATGGAGTCTGGAGCCAAGGGTTGTGAG                         GTGATTGTGAGCGGCAAGCTCCGAGCCCAACGCGCCAAGTCGATGAAGTTC
genomic: GCTATGGTGTTCTCAGGTTCATCATGGAGTCTGGAGCCAAGGGTTGTGAGgtatggacga ... ctcctttcagGTGATTGTGAGCGGCAAGCTCCGAGCCCAACGCGCCAAGTCGATGAAGTTC
EST: gi|169055910|gb|FE465111.1|FE465111
EST:     GCTATGGTGTTCTCAGGTTCATCATGGAGTCTGGAGCCAAGGGTTGTGAG                         GTGATTGTGAGCGGCAAGCTCCGAGCCCAACGCGCCAAGTCGATGAAGTTC
genomic: GCTATGGTGTTCTCAGGTTCATCATGGAGTCTGGAGCCAAGGGTTGTGAGgtatggacga ... ctcctttcagGTGATTGTGAGCGGCAAGCTCCGAGCCCAACGCGCCAAGTCGATGAAGTTC
EST: gi|169055911|gb|FE465112.1|FE465112
EST:     GCTATGGTGTTCTCAGGTTCATCATGGAGTCTGGAGCCAAGGGTTGTGAG                         GTGATTGTGAGCGGCAAGCTCCGAGCCCAACGCGCCAAGTCGATGAAGTTC
genomic: GCTATGGTGTTCTCAGGTTCATCATGGAGTCTGGAGCCAAGGGTTGTGAGgtatggacga ... ctcctttcagGTGATTGTGAGCGGCAAGCTCCGAGCCCAACGCGCCAAGTCGATGAAGTTC
EST: gi|169043107|gb|FE454021.1|FE454021
EST:     GCTATGGTGTTCTCAGGTTCATCATGGAGTCTGGAGCCAAGGGTTGTGAG                         GTGATTGTGAGCGGCAAGCTCCGAGCCCAACGCGCCAAGTCGATGAAGTTC
genomic: GCTATGGTGTTCTCAGGTTCATCATGGAGTCTGGAGCCAAGGGTTGTGAGgtatggacga ... ctcctttcagGTGATTGTGAGCGGCAAGCTCCGAGCCCAACGCGCCAAGTCGATGAAGTTC

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: 149

GGCCTGCTATGGTGTTCTCAGGTTCATCATGGAGTCTGGAGCCAAGGGTTGTGAGgtatggacga ... ctcctttcagGTGATTGTGAGCGGCAAGCTCCGAGCCCAACGCGCCAAGTCGATGAAGTTCAAGGACGGATACATGATCTCGTCTGGCAGCCCCGTGAACGAGTTCATTG




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Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGCCTGCTATGGTGTTCTCAGGTTCATCATGGAGTCTGGAGCCAAGGGTTGTGAGgtatggacgaactctcggcattttgctcttcaggttgtaacttcattcctggctcctttcag

- - - - - - - - - - - - -  CATGGA