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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTTAATGACATCTCCTGCTGAGTCTTCTGGATCAACCAGCACTGGTAACTGGCTTTTTAAAAACAAAGAACATGGAAAGGCCAGCGCTACTGCCAGTTTGgtaaggcaccttgctaaagaaacctgtccactgtaacttaccggccgtaatcgttcag

Basic information

species Selaginella moellendorffii
transcript EFJ26022
intron # 13
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|169030422|gb|FE438678.1|FE438678
EST:     GGCTTTTTAAAAACAAAGAACATGGAAAGGCCAGCGCTACTGCCAGTTTG                         GGTCTTATCACCTTGTGGGATGTTGATGGAGGGCTCCCACAAATTGATAAG
genomic: GGCTTTTTAAAAACAAAGAACATGGAAAGGCCAGCGCTACTGCCAGTTTGgtaaggcacc ... aatcgttcagGGTCTTATCACCTTGTGGGATGTTGATGGAGGCCTCCCACAAATTGATAAG
EST: gi|169097110|gb|FE498956.1|FE498956
EST:     GGCTTTTTAAAAACAAAGAACATGGAAAGGCCAGCGCTACTGCCAGTTTG                         GGTCTTATCACCTTGTGGGATGTTGATGGAGGGCTCCCACAAATTGATAAG
genomic: GGCTTTTTAAAAACAAAGAACATGGAAAGGCCAGCGCTACTGCCAGTTTGgtaaggcacc ... aatcgttcagGGTCTTATCACCTTGTGGGATGTTGATGGAGGCCTCCCACAAATTGATAAG
EST: gi|169059061|gb|FE468206.1|FE468206
EST:     GGCTTTTTAAAAACAAAGAACATGGAAAGGCCAGCGCTACTGCCAGTTTG                         GGTCTTATCACCTTGTGGGATGTTGATGGAGGCCTCCCACAAATTGATAAG
genomic: GGCTTTTTAAAAACAAAGAACATGGAAAGGCCAGCGCTACTGCCAGTTTGgtaaggcacc ... aatcgttcagGGTCTTATCACCTTGTGGGATGTTGATGGAGGCCTCCCACAAATTGATAAG
EST: gi|169019958|gb|FE431023.1|FE431023
EST:     GGCTTTTTAAAAACAAAGAACATGGAAAGGCCAGCGCTACTGCCAGTTTG                         GGTCTTATCACCTTGTGGGATGTTGATGGAGGCCTCCCACAAATTGATAAG
genomic: GGCTTTTTAAAAACAAAGAACATGGAAAGGCCAGCGCTACTGCCAGTTTGgtaaggcacc ... aatcgttcagGGTCTTATCACCTTGTGGGATGTTGATGGAGGCCTCCCACAAATTGATAAG
EST: gi|169064769|gb|FE473736.1|FE473736
EST:     GGCTTTTTAAAAACAAAGAACATGGAAAGGCCAGCGCTACTGCCAGTTTG                         GGTCTTATCACCTTGTGGGATGTTGATGGAGGGCTCCCACAAATTGATAAG
genomic: GGCTTTTTAAAAACAAAGAACATGGAAAGGCCAGCGCTACTGCCAGTTTGgtaaggcacc ... aatcgttcagGGTCTTATCACCTTGTGGGATGTTGATGGAGGCCTCCCACAAATTGATAAG
EST: gi|169028509|gb|FE439924.1|FE439924
EST:     GGCTTTTTAAAAACAAAGAACATGGAAAGGCCAGCGCTACTGCCAGTTTG                         GGTCTTATCACCTTGTGGGATGTTGATGGAGGGCTCCCACAAATTGATAAG
genomic: GGCTTTTTAAAAACAAAGAACATGGAAAGGCCAGCGCTACTGCCAGTTTGgtaaggcacc ... aatcgttcagGGTCTTATCACCTTGTGGGATGTTGATGGAGGCCTCCCACAAATTGATAAG
EST: gi|169066441|gb|FE474664.1|FE474664
EST:     GGCTTTTTAAAAACAAAGAACATGGAAAGGCCAGCGCTACTGCCAGTTTG                         NGTCTTATCACCTTGT
genomic: GGCTTTTTAAAAACAAAGAACATGGAAAGGCCAGCGCTACTGCCAGTTTGgtaaggcacc ... aatcgttcagGGTCTTATCACCTTGT
EST: gi|169097981|gb|FE498778.1|FE498778
EST:     GGCTTTTTAAAAACAAAGAACATGGAAAGGCCAGCGCTACTGCCAGTTTG                         GGTCTTATCACCTTGTGGGATGTTGATGGAGGGCTCCCACAAATTGATAAG
genomic: GGCTTTTTAAAAACAAAGAACATGGAAAGGCCAGCGCTACTGCCAGTTTGgtaaggcacc ... aatcgttcagGGTCTTATCACCTTGTGGGATGTTGATGGAGGCCTCCCACAAATTGATAAG

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: 27 (upstream exon), 33 (downstream exon)
Score: 19

CTTAATGACATCTCCTGCTGAGTCTTCTGGATCAACCAGCACTGGTAACTGGCTTTTTAAAAACAAAGAACATGGAAAGGCCAGCGCTACTGCCAGTTTGgtaaggcacc ... aatcgttcagGGTCTTATCACCTTGTGGGATGTTGATGGAGGCCTCCCACAAATTGATAAGTATCTATACAGTACCGATAACCATGTTGTCGCGGGAGCTCTCTTGGCTG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTTAATGACATCTCCTGCTGAGTCTTCTGGATCAACCAGCACTGGTAACTGGCTTTTTAAAAACAAAGAACATGGAAAGGCCAGCGCTACTGCCAGTTTGgtaaggcaccttgctaaagaaacctgtccactgtaacttaccggccgtaatcgttcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA