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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacgtggagctccatagctttcacacaagctttcaaagaaaagactaaaatttctgatgatatcgcagGGGTTAAGTAGCTCGGAGTACAATGACAAGAAGGAGGCTGTGGCCGATGTGATCGTTAAGAGACTGGAAGCGAAACTGTTTCCCGGTCTCAAGGACGCAA

Basic information

species Selaginella moellendorffii
transcript EFJ21638
intron # 9
splice site 3'
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|169040804|gb|FE447855.1|FE447855
EST:     ATCGCCATATTCTTCACATATTTACCACCGCATGGGCCGATGATTGGCAA                         GGGTTAAGTAGCTCGGAGTACAATGACAAGAAGGAGGCTGTGGCCGATGTG
genomic: ATCGCCATATTCTTCACATATTTACCACCGCATGGGCCGATGATTGGCAAgtacgtggag ... gatatcgcagGGGTTAAGTAGCTCGGAGTACAATGACAAGAAGGAGGCTGTGGCCGATGTG
EST: gi|169103946|gb|FE508404.1|FE508404
EST:     ATCGCCATATTCTTCACATATTTACCACCGCATGGGCCGATGATTGGCAA                         GGGTTAAGTAGCTCGGAGTACAATGACAAGAAGGAGGCTGTGGCCGATGTG
genomic: ATCGCCATATTCTTCACATATTTACCACCGCATGGGCCGATGATTGGCAAgtacgtggag ... gatatcgcagGGGTTAAGTAGCTCGGAGTACAATGACAAGAAGGAGGCTGTGGCCGATGTG
EST: gi|169045741|gb|FE453053.1|FE453053
EST:     ATCGCCATATTCTTCACATATTTACCACCGCATGGGCCGATGATTGGCAA                         GGGTTAAGTAGCTCGGAGTACAATGACAAGAAGGAGGCTGTGGCCGATGTG
genomic: ATCGCCATATTCTTCACATATTTACCACCGCATGGGCCGATGATTGGCAAgtacgtggag ... gatatcgcagGGGTTAAGTAGCTCGGAGTACAATGACAAGAAGGAGGCTGTGGCCGATGTG
EST: gi|169027210|gb|FE435081.1|FE435081
EST:     ATCGCCATATTCTTCACATATTTACCACCGCATGGGCCGATGATTGGCAA                         GGGTTAAGTAGCTCGGAGTACAATGACAAGAAGGAGGCTGTGGCCGATGTG
genomic: ATCGCCATATTCTTCACATATTTACCACCGCATGGGCCGATGATTGGCAAgtacgtggag ... gatatcgcagGGGTTAAGTAGCTCGGAGTACAATGACAAGAAGGAGGCTGTGGCCGATGTG
EST: gi|169096608|gb|FE499520.1|FE499520
EST:     ATCGCCATATTCTTCACATATTTACCACCGCATGGGCCGATGATTGGCAA                         GGGTTAAGTAGCTCGGAGTACAATGACAAGAAGGAGGCTGTGGCCGATGTG
genomic: ATCGCCATATTCTTCACATATTTACCACCGCATGGGCCGATGATTGGCAAgtacgtggag ... gatatcgcagGGGTTAAGTAGCTCGGAGTACAATGACAAGAAGGAGGCTGTGGCCGATGTG
EST: gi|169040805|gb|FE447856.1|FE447856
EST:     ATCGCCATATTCTTCACATATTTACCACCGCATGGGCCGATGATTGGCAA                         GGGTTAAGTAGCTCGGAGTACAATGACAAGAAGGAGGCTGTGGCCGATGTG
genomic: ATCGCCATATTCTTCACATATTTACCACCGCATGGGCCGATGATTGGCAAgtacgtggag ... gatatcgcagGGGTTAAGTAGCTCGGAGTACAATGACAAGAAGGAGGCTGTGGCCGATGTG
EST: gi|169048503|gb|FE455737.1|FE455737
EST:     ATCGCCATATTCTTCACATATTTACCACCGCATGGGCCGATGATTGGCAA                         GGGTTAAGTAGCTCGGAGTACAATGACAAGAAGGAGGCTGTGGCCGATGTG
genomic: ATCGCCATATTCTTCACATATTTACCACCGCATGGGCCGATGATTGGCAAgtacgtggag ... gatatcgcagGGGTTAAGTAGCTCGGAGTACAATGACAAGAAGGAGGCTGTGGCCGATGTG
EST: gi|169048502|gb|FE455736.1|FE455736
EST:     ATCGCCATATTCTTCACATATTTACCACCGCATGGGCCGATGATTGGCAA                         GGGTTAAGTAGCTCGGAGTACAATGACAAGAAGGAGGCTGTGGCCGATGTG
genomic: ATCGCCATATTCTTCACATATTTACCACCGCATGGGCCGATGATTGGCAAgtacgtggag ... gatatcgcagGGGTTAAGTAGCTCGGAGTACAATGACAAGAAGGAGGCTGTGGCCGATGTG

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: 21 (upstream exon), 31 (downstream exon)
Score: 4

GATCTTCTTGAGCATTCCCACTGTTTTGGATCCCTCGCTAGCTCCAGAGGATCGCCATATTCTTCACATATTTACCACCGCATGGGCCGATGATTGGCAAgtacgtggag ... gatatcgcagGGGTTAAGTAGCTCGGAGTACAATGACAAGAAGGAGGCTGTGGCCGATGTGATCGTTAAGAGACTGGAAGCGAAACTGTTTCCCGGTCTCAAGGACGCAA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atagctttcacacaagctttcaaagaaaagactaaaatttctgatgatatcgcagGGGTTAAGTAGCTCGGAGTACAATGACAAGAAGGAGGCTGTGGCCGATGTGATCGTTAAGAGACTGGAAGCGAAACTGTTTCCCGGTCTCAAGGACGCAA
                         aaaagactaaaattt  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacgtggagctccatagctttcacacaagctttcaaagaaaagactaaaatttctgatgatatcgcagGGGTTAAGTAGCTCGGAGTACAATGACAAGAAGGAGGCTGTGGCCGATGTGATCGTTAAGAGACTGGAAGCGAAACTGTTTCCCGGTCTCAAGGACGCAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG