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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatgaagagccatctttccagcgaaaccttcttgtgcttactgtgctcttgtacatttcttcagGTTCATGGCGACTACAGCGAGGATACCGGCGTCAAGGTTGAGCGACCAGTCGGTGATGAAGCCGAACCGGAGGCAGCAGAGGCTGAAGTAGTCGGGGCGT

Basic information

species Selaginella moellendorffii
transcript EFJ09763
intron # 6
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|169033919|gb|FE441951.1|FE441951
EST:     AGGTGAAGATTCTGAAGGCCCCAAAATTCGATCTTGGGAAGCTGATGGAG                         GTTCATGGCGACTACAGCGAGGATACCGGCGTCAAGGTTGAGCGACCAGTC
genomic: AGGTGAAGATTCTGAAGGCCCCAAAATTCGATCTTGGGAAGCTGATGGAGgtaatgaaga ... atttcttcagGTTCATGGCGACTACAGCGAGGATACCGGCGTCAAGGTTGAGCGACCAGTC
EST: gi|169098886|gb|FE502283.1|FE502283
EST:     AGGTGAAGATTCTGAAGGCCCCAAAGTTCGATCTTGGGAAGCTGATGGAG                         GTTCATGGTGACTACAGCGAGGATACTGGCGTCAAGGTTGAGCGACCAGTC
genomic: AGGTGAAGATTCTGAAGGCCCCAAAATTCGATCTTGGGAAGCTGATGGAGgtaatgaaga ... atttcttcagGTTCATGGCGACTACAGCGAGGATACCGGCGTCAAGGTTGAGCGACCAGTC
EST: gi|169022541|gb|FE429425.1|FE429425
EST:     AGGTGAAGATTCTGAAGGCCCCAAAGTTCGATCTTGGGAAGCTGATGGAG                         GTTCATGGTGACTACAGCGAGGATACTGGCGTCAAGGTTGAGCGACCAGTC
genomic: AGGTGAAGATTCTGAAGGCCCCAAAATTCGATCTTGGGAAGCTGATGGAGgtaatgaaga ... atttcttcagGTTCATGGCGACTACAGCGAGGATACCGGCGTCAAGGTTGAGCGACCAGTC
EST: gi|169020263|gb|FE430340.1|FE430340
EST:     AGGTGAAGATTCTGAAGGCCCCAAAGTTCGATCTTGGGAAGCTGATGGAG                         GTTCATGGCGACTACAGCGAGGATACTGGCGTCAAGGTTGAGCGACCAGTC
genomic: AGGTGAAGATTCTGAAGGCCCCAAAATTCGATCTTGGGAAGCTGATGGAGgtaatgaaga ... atttcttcagGTTCATGGCGACTACAGCGAGGATACCGGCGTCAAGGTTGAGCGACCAGTC
EST: gi|169051171|gb|FE460252.1|FE460252
EST:     AGGTGAAGATTCTGAAGGCCCCAAAGTTCGATCTTGGGAAGCTGATGGAG                         GTTCATGGTGACTACNGCGAGGATACTGGCGTCAAGGTTGAGCGACCAGTC
genomic: AGGTGAAGATTCTGAAGGCCCCAAAATTCGATCTTGGGAAGCTGATGGAGgtaatgaaga ... atttcttcagGTTCATGGCGACTACAGCGAGGATACCGGCGTCAAGGTTGAGCGACCAGTC
EST: gi|169103248|gb|FE504820.1|FE504820
EST:     AGGTGAAGATTCTGAAGGCCCCAAAATTCGTTCTTGGGAAGCTGATGGAG                         GTTCATGGCGACTACAGCGAGGATACCGGCGTCAAGGTTGAGCGACCAGTC
genomic: AGGTGAAGATTCTGAAGGCCCCAAAATTCGATCTTGGGAAGCTGATGGAGgtaatgaaga ... atttcttcagGTTCATGGCGACTACAGCGAGGATACCGGCGTCAAGGTTGAGCGACCAGTC
EST: gi|169065307|gb|FE473208.1|FE473208
EST:     AGGTGAAGATTCTGAAGGCCCCAAAATTCGATCTTGGGAAGCTGATGGAG                         GTTCATGGCGACTACAGCGAGGATACCGGCGTCAAGGTTGAGCGACCAGTC
genomic: AGGTGAAGATTCTGAAGGCCCCAAAATTCGATCTTGGGAAGCTGATGGAGgtaatgaaga ... atttcttcagGTTCATGGCGACTACAGCGAGGATACCGGCGTCAAGGTTGAGCGACCAGTC
EST: gi|169022540|gb|FE429424.1|FE429424
EST:     AGGTGAAGATTCTGAAGGCCCCAAAGTTCGATCTTGGGAAGCTGATGGAG                         GTTCATGGTGACTACAGCGAGGATACTGGCGTCAAGGTTGAGCGACCAGTC
genomic: AGGTGAAGATTCTGAAGGCCCCAAAATTCGATCTTGGGAAGCTGATGGAGgtaatgaaga ... atttcttcagGTTCATGGCGACTACAGCGAGGATACCGGCGTCAAGGTTGAGCGACCAGTC
EST: gi|169103224|gb|FE505628.1|FE505628
EST:     AGGTGAAGATTCTGAAGGCCCCAAAATTCGATCTTGGGAAGCTGATGGAG                         GTTCATGGCGACTACAGCGAGGATACCGGCGTCAAGGTTGAGCGACCAGTC
genomic: AGGTGAAGATTCTGAAGGCCCCAAAATTCGATCTTGGGAAGCTGATGGAGgtaatgaaga ... atttcttcagGTTCATGGCGACTACAGCGAGGATACCGGCGTCAAGGTTGAGCGACCAGTC
EST: gi|169054226|gb|FE463167.1|FE463167
EST:     AGGTGAAGATTTTGAAGGCCCCAAAGTTCGATCTTGGGAAGCTGATGGAG                         GTTCATGGTGACTACAGCGAGGATACTGGCGTCAAGGTTGAGCGACCAGTC
genomic: AGGTGAAGATTCTGAAGGCCCCAAAATTCGATCTTGGGAAGCTGATGGAGgtaatgaaga ... atttcttcagGTTCATGGCGACTACAGCGAGGATACCGGCGTCAAGGTTGAGCGACCAGTC
EST: gi|169097436|gb|FE499022.1|FE499022
EST:     AGGTGAAGATTCTGAAGGCCCCANAGTTCGATCTTGGGAAGCTGATGGAG                         GTTCATGGTGACTACAGCGAGGATACTGGCGTCAAGGTTGAGCGACCAGTC
genomic: AGGTGAAGATTCTGAAGGCCCCAAAATTCGATCTTGGGAAGCTGATGGAGgtaatgaaga ... atttcttcagGTTCATGGCGACTACAGCGAGGATACCGGCGTCAAGGTTGAGCGACCAGTC
EST: gi|169103249|gb|FE504821.1|FE504821
EST:     AGGTGAAGATTCTGAAGGCCCCAAAATTCGATCTTGGGAAGCTGATGGAG                         GTTCATGGCGACTACAGCGAGGATACCGGCGTCAAGGTTGAGCGACCAGTC
genomic: AGGTGAAGATTCTGAAGGCCCCAAAATTCGATCTTGGGAAGCTGATGGAGgtaatgaaga ... atttcttcagGTTCATGGCGACTACAGCGAGGATACCGGCGTCAAGGTTGAGCGACCAGTC
EST: gi|169097435|gb|FE499021.1|FE499021
EST:     AGGTGAAGATTCTGAAGGCCCCAAAGTTCGATCTTGGGAAGCTGATGGAG                         GTTCATGGTGACTACAGCGAGGATACTGGCGTCAAGGTTGAGCGACCAGTC
genomic: AGGTGAAGATTCTGAAGGCCCCAAAATTCGATCTTGGGAAGCTGATGGAGgtaatgaaga ... atttcttcagGTTCATGGCGACTACAGCGAGGATACCGGCGTCAAGGTTGAGCGACCAGTC
EST: gi|169098885|gb|FE502282.1|FE502282
EST:     AGGTGAAGATTCTGAAGGCCCCAAAGTTCGATCTTGGGAAGCTGATGGAG                         GTTCATGGTGACTACAGCGAGGATACTGGCGTCAAGGTTGAGCGACCAGTC
genomic: AGGTGAAGATTCTGAAGGCCCCAAAATTCGATCTTGGGAAGCTGATGGAGgtaatgaaga ... atttcttcagGTTCATGGCGACTACAGCGAGGATACCGGCGTCAAGGTTGAGCGACCAGTC
EST: gi|169065308|gb|FE473209.1|FE473209
EST:     AGGTGAAGATTCTGAAGGCCCCAAAATTCGATCTTGGGAAGCTGATGGAG                         GTTCATGGCGACTACAGCGAGGATACCCGGCGTCA-GGTTGAGCGACCAGT
genomic: AGGTGAAGATTCTGAAGGCCCCAAAATTCGATCTTGGGAAGCTGATGGAGgtaatgaaga ... atttcttcagGTTCATGGCGACTACAGCGAGGATACC-GGCGTCAAGGTTGAGCGACCAGT
EST: gi|169055046|gb|FE462961.1|FE462961
EST:     AGGTGAAGATTCTGAAGGCCCCAAAGTTCGATCTTGGGAAGCTGATGGAG                         GTTCATGGCGACTACAGCGAGGATACTGGCGTCAAGGTTGAGCGACCAGTC
genomic: AGGTGAAGATTCTGAAGGCCCCAAAATTCGATCTTGGGAAGCTGATGGAGgtaatgaaga ... atttcttcagGTTCATGGCGACTACAGCGAGGATACCGGCGTCAAGGTTGAGCGACCAGTC
EST: gi|169069101|gb|FE476740.1|FE476740
EST:     AGGTGAAGATTCTGAAGGCCCCAAAGTTCGATCTTGGGAAGCTGATGGAG                         GTTCATGGTGACTACAGCGAGGATACTGGCGTCAAGGTTGAGCGACCAGTC
genomic: AGGTGAAGATTCTGAAGGCCCCAAAATTCGATCTTGGGAAGCTGATGGAGgtaatgaaga ... atttcttcagGTTCATGGCGACTACAGCGAGGATACCGGCGTCAAGGTTGAGCGACCAGTC
EST: gi|169048875|gb|FE456655.1|FE456655
EST:     AGGTGAAGATTCTGAAGGCCCCAAAGTTCGATCTTGGGAAGCTGATGGAG                         GTTCATGGCGACTACAGCGAGGATACTGGCGTCAAGGTTGAGCGACCAGTC
genomic: AGGTGAAGATTCTGAAGGCCCCAAAATTCGATCTTGGGAAGCTGATGGAGgtaatgaaga ... atttcttcagGTTCATGGCGACTACAGCGAGGATACCGGCGTCAAGGTTGAGCGACCAGTC
EST: gi|169056434|gb|FE467013.1|FE467013
EST:     AGGTGAAGATCCTGAAGGCCCCAAAGTTCGATCTTGGGAAGCTGATGGAG                         GTTCATGGTGACTACAGCGAGGATACTGGCGTCAAGGTTGAGCGACCAGTT
genomic: AGGTGAAGATTCTGAAGGCCCCAAAATTCGATCTTGGGAAGCTGATGGAGgtaatgaaga ... atttcttcagGTTCATGGCGACTACAGCGAGGATACCGGCGTCAAGGTTGAGCGACCAGTC

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: 25 (upstream exon), 33 (downstream exon)
Score: 28

CGAGAAAGTGACTGCGGGAATCTATCCCCTGCAGAACACTTACATTCGTAAGGTGAAGATTCTGAAGGCCCCAAAATTCGATCTTGGGAAGCTGATGGAGgtaatgaaga ... atttcttcagGTTCATGGCGACTACAGCGAGGATACCGGCGTCAAGGTTGAGCGACCAGTCGGTGATGAAGCCGAACCGGAGGCAGCAGAGGCTGAAGTAGTCGGGGCGT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccatctttccagcgaaaccttcttgtgcttactgtgctcttgtacatttcttcagGTTCATGGCGACTACAGCGAGGATACCGGCGTCAAGGTTGAGCGACCAGTCGGTGATGAAGCCGAACCGGAGGCAGCAGAGGCTGAAGTAGTCGGGGCGT
                         tgcttac  putative branch site (score: 28)
                                            catttcttc  putative PPT
                                          tacattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaatgaagagccatctttccagcgaaaccttcttgtgcttactgtgctcttgtacatttcttcagGTTCATGGCGACTACAGCGAGGATACCGGCGTCAAGGTTGAGCGACCAGTCGGTGATGAAGCCGAACCGGAGGCAGCAGAGGCTGAAGTAGTCGGGGCGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG