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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTCCCGTCGTGAGCTTCTCGTCTCTCAAAGGTGCTGCCGAGCTCAAGTTTTACCTCGAGGATACTAACAACTTCGACACCATTTCGACCGTTTTTAACAGgtgagttgaatggtagaatggttttggagcattcctgtagtcctgctgctgagctgatggctattcttttttgatcgcag

Basic information

species Selaginella moellendorffii
transcript EFJ10313
intron # 1
splice site 5'
intron type U2

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|169097569|gb|FE499220.1|FE499220
EST:     TACCTCGAGGATACTAACAACTTCGACACTATTTCGACCGTTTTTAACAG                         GACGAGTAGATTCGCCAGGTTGCANAGTGTTAAATGCTTGCTGGCTGGTCG
genomic: TACCTCGAGGATACTAACAACTTCGACACCATTTCGACCGTTTTTAACAGgtgagttgaa ... ttgatcgcagGACGAGTAGATTCGCCAGGTTGCAAAGTGTTAAATGCTTGCTGGCTGGTCG
EST: gi|169082494|gb|FE490031.1|FE490031
EST:     TACCTCGAGGATACTAACAACTTCGACACCATTTCGACCGTTTTTAACAG                         GACGAGTAGATTCGCCAGGTTGCAAAGTGTTAAATGCTTGCTGGCTGGTCG
genomic: TACCTCGAGGATACTAACAACTTCGACACCATTTCGACCGTTTTTAACAGgtgagttgaa ... ttgatcgcagGACGAGTAGATTCGCCAGGTTGCAAAGTGTTAAATGCTTGCTGGCTGGTCG
EST: gi|169029369|gb|FE439770.1|FE439770
EST:     ACCTCGAGGATACTAAACA-CTTCGACACTATTTCGACCGTTTTTAACAG                         GACGAGTAGATTCGCC
genomic: ACCTCGAGGATACTAA-CAACTTCGACACCATTTCGACCGTTTTTAACAGgtgagttgaa ... ttgatcgcagGACGAGTAGATTCGCC
EST: gi|169025721|gb|FE433631.1|FE433631
EST:     TACCTCGAGGATACTAACAACTTCGACACTATTTCGACCGTTTTTAACAG                         GACGAGTAGATTCGCCAGGTTGCAAAGTGTTAAATGCTTGCTGGCTGGTCG
genomic: TACCTCGAGGATACTAACAACTTCGACACCATTTCGACCGTTTTTAACAGgtgagttgaa ... ttgatcgcagGACGAGTAGATTCGCCAGGTTGCAAAGTGTTAAATGCTTGCTGGCTGGTCG
EST: gi|169044245|gb|FE452975.1|FE452975
EST:     TACCTCGAGGATACTAACAACTTCGACACCATTTCGACCGTTTTTAACAG                         GACGAGTAGATTCGCCAGGTTGCAAAGTGTTAAATGCTTGCTGGCTGGTCG
genomic: TACCTCGAGGATACTAACAACTTCGACACCATTTCGACCGTTTTTAACAGgtgagttgaa ... ttgatcgcagGACGAGTAGATTCGCCAGGTTGCAAAGTGTTAAATGCTTGCTGGCTGGTCG

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: 19 (upstream exon), 35 (downstream exon)
Score: 4

CTCCCGTCGTGAGCTTCTCGTCTCTCAAAGGTGCTGCCGAGCTCAAGTTTTACCTCGAGGATACTAACAACTTCGACACCATTTCGACCGTTTTTAACAGgtgagttgaa ... ttgatcgcagGACGAGTAGATTCGCCAGGTTGCAAAGTGTTAAATGCTTGCTGGCTGGTCGAAACGCATACATTAGATTCTGTTGCTCCACTGGTGACGCAATGGGGATG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTCCCGTCGTGAGCTTCTCGTCTCTCAAAGGTGCTGCCGAGCTCAAGTTTTACCTCGAGGATACTAACAACTTCGACACCATTTCGACCGTTTTTAACAGgtgagttgaatggtagaatggttttggagcattcctgtagtcctgctgctgagctgatggctattcttttttgatcgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT