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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTCTTCGAAGGGACTACTGGAATTGATAACAAGCACACGACTGTTGAGTTCACTGGAGAGgtggcttgctctttcttcctacagtgattttgactctactgtatgctttccag

Basic information

species Selaginella moellendorffii
transcript EFJ11911
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ11911 (Selaginella moellendorffii), 5'ss of exon 4
lower sequence: PP1S85_75V6.1 (Physcomitrella patens), 5'ss of exon 5
GTCTTCGAAGGGACTACTGGAATTGATAACAAGCACACGACTGTTGAGTTCACTGGAGAGgtggcttgctctttct------tcctacagtgattt-tg-actctact-gtatgctttccag--------------------------------------
|| || ||||| ||  | || || |||||||||||||| ||  |||||||||||||||||||  |||| |  ||||      |  | ||||  ||| || |||  |||   |||| | | |                                       
GTTTTTGAAGGAACCTCGGGTATCGATAACAAGCACACTACCATTGAGTTCACTGGAGAGgtaacttgattcttctcacatcttttccagtcctttatgtacttcacttaaatgcatccgactataattgattgtaacttactttgtatggcttgcttta

upper sequence: EFJ11911 (Selaginella moellendorffii), 5'ss of exon 4
lower sequence: PP1S425_12V6.1 (Physcomitrella patens), 5'ss of exon 4
GTCTTCGAAGGGACTACTGGAATTGATAACAAGCACACGACTGTTGAGTTCACTGGAGAGgtggcttgctctttcttcctacagtgattttgactctactgtatgctttccag--------------------------------------------------
||||| || || ||| ||||||| |||||||||||||| ||  |||| ||||||||||||||   ||| |  |||||  || | |  |  ||| |    | | | |||  |                                                    
GTCTTTGAGGGAACTTCTGGAATCGATAACAAGCACACCACCATTGAATTCACTGGAGAGgtaatttgat--ttcttagtatactt-tcgtgagttctttatttacttaacgtgaatgcatctggcctcgacggaccctaccctctagtttgcaaactacttt
















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|169049346|gb|FE458244.1|FE458244
EST:     GGACTACTGGAATTGATAACAAGCACACGACTGTTGAGTTCACTGGAGAG                         GTGTTGAAAACCCCGGTGTCCATAGATATGCTCGGTAGAATCTTTAATGGT
genomic: GGACTACTGGAATTGATAACAAGCACACGACTGTTGAGTTCACTGGAGAGgtggcttgct ... tgctttccagGTGTTGAAAACCCCGGTGTCCATAGATATGCTCGGTAGAATCTTTAATGGT
EST: gi|169092669|gb|FE496263.1|FE496263
EST:     GGACTACTGGAATTGATAACAAGCACACGACTGTTGAGTTCACTGGAGAG                         GTGTTGAAAACCCCGGTGTCCATAGATATGCTCGGTAGAATCTTTAATGGT
genomic: GGACTACTGGAATTGATAACAAGCACACGACTGTTGAGTTCACTGGAGAGgtggcttgct ... tgctttccagGTGTTGAAAACCCCGGTGTCCATAGATATGCTCGGTAGAATCTTTAATGGT
EST: gi|169108146|gb|FE512519.1|FE512519
EST:     GGACTACTGGAATTGATAACAAGCACACGACTGTTGAGTTCACTGGAGAG                         GTGTTGAAAACCCCGGTGTCCATAGATATGCTCGGTAGAATCTTTAATGGT
genomic: GGACTACTGGAATTGATAACAAGCACACGACTGTTGAGTTCACTGGAGAGgtggcttgct ... tgctttccagGTGTTGAAAACCCCGGTGTCCATAGATATGCTCGGTAGAATCTTTAATGGT
EST: gi|169035381|gb|FE444319.1|FE444319
EST:     GGACTACTGGAATTGATAACAAGCACACGACTGTTGAGTTCACTGGAGAG                         GTGTTGAAAACCCCGGTGTCCATAGATATGCTCGGTAGAATCTTTAATGGT
genomic: GGACTACTGGAATTGATAACAAGCACACGACTGTTGAGTTCACTGGAGAGgtggcttgct ... tgctttccagGTGTTGAAAACCCCGGTGTCCATAGATATGCTCGGTAGAATCTTTAATGGT
EST: gi|169104894|gb|FE509038.1|FE509038
EST:     GGACTACTGGAATTGATAACAAGCACACGACTGTTGAGTTCACTGGAGAG                         GTGTTGAAAACCCCGGTGTCCATAGATATGCTCGGTAGAATCTTTAATGGT
genomic: GGACTACTGGAATTGATAACAAGCACACGACTGTTGAGTTCACTGGAGAGgtggcttgct ... tgctttccagGTGTTGAAAACCCCGGTGTCCATAGATATGCTCGGTAGAATCTTTAATGGT
EST: gi|169049517|gb|FE458740.1|FE458740
EST:     GGACTACTGGAATTGATAACAAGCACACGACTGTTGAGTTCACTGGAGAG                         GTGTTGAAAACCCCGGTGTCCATAGATATGCTCGGTAGAATCTTTAATGGT
genomic: GGACTACTGGAATTGATAACAAGCACACGACTGTTGAGTTCACTGGAGAGgtggcttgct ... tgctttccagGTGTTGAAAACCCCGGTGTCCATAGATATGCTCGGTAGAATCTTTAATGGT
EST: gi|169059085|gb|FE468230.1|FE468230
EST:     GGACTACTGGAATTGATAACAAGCACACGACTGTTGAGTTCACTGGAGAG                         GTGTTGAAAACCCCGGTGTCCATAGATATGCTCGGTAGAATCTTTAATGGT
genomic: GGACTACTGGAATTGATAACAAGCACACGACTGTTGAGTTCACTGGAGAGgtggcttgct ... tgctttccagGTGTTGAAAACCCCGGTGTCCATAGATATGCTCGGTAGAATCTTTAATGGT
EST: gi|169088665|gb|FE491525.1|FE491525
EST:     GGACTACTGGAATTGATAACAAGCACACGACTGTTGAGTTCACTGGAGAG                         GTGTTGAAAACCCCGGTGTCCATAGATATGCTCGGTAGAATCTTTAATGGT
genomic: GGACTACTGGAATTGATAACAAGCACACGACTGTTGAGTTCACTGGAGAGgtggcttgct ... tgctttccagGTGTTGAAAACCCCGGTGTCCATAGATATGCTCGGTAGAATCTTTAATGGT
EST: gi|169057426|gb|FE465730.1|FE465730
EST:     GGACTACTGGAATTGATAACAAGCACACGACTGTTGAGTTCACTGGAGAG                         GTGTTGAAAACCCCGGTGTCCATAGATATGCTCGGTAGAATCTTTAATGGT
genomic: GGACTACTGGAATTGATAACAAGCACACGACTGTTGAGTTCACTGGAGAGgtggcttgct ... tgctttccagGTGTTGAAAACCCCGGTGTCCATAGATATGCTCGGTAGAATCTTTAATGGT

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), 34 (downstream exon)
Score: 11

GTCTTCGAAGGGACTACTGGAATTGATAACAAGCACACGACTGTTGAGTTCACTGGAGAGgtggcttgct ... tgctttccagGTGTTGAAAACCCCGGTGTCCATAGATATGCTCGGTAGAATCTTTAATGGTTCTGGGAAGCCTATCGATAACGGGCCCCCGATCTTGGCAGAAGCTTACC




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTCTTCGAAGGGACTACTGGAATTGATAACAAGCACACGACTGTTGAGTTCACTGGAGAGgtggcttgctctttcttcctacagtgattttgactctactgtatgctttccag

- - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA