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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaaagatcatacgtcttttgggatgttaacagagtattttctgttgtagAATTTACTGTGCGTTCCATGATGAATATAATCTTCAATCATGGAGCGAAATTGACGCAAACGAAGAGGATGCTGAAGGCAGTTTGTGTTTCACACACACT

Basic information

species Selaginella moellendorffii
transcript EFJ15634
intron # 7
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|169035624|gb|FE445394.1|FE445394
EST:     GAAACAAGATTTTTGGTGCACGGTGTTGACCTCGCTGGTGCAGATACGAG                         AATTTACTGTGCGTTCCATGATGAATATAATCTTCAATCATGGAGCGAAAT
genomic: GAAACAAGATTTTTGGTGCACGGTGTTGACCTCGCTGGTGCAGATACGAGgtaaaagatc ... tctgttgtagAATTTACTGTGCGTTCCATGATGAATATAATCTTCAATCATGGAGCGAAAT
EST: gi|169032876|gb|FE438332.1|FE438332
EST:     GAAACAAGATTTTTGGTGCACGGTGTTGACCTCGCTGGTGCAGATACGAG                         AATTTACTGTGCGTTCCATGATGAATATAATCTTCAATCATGGAGCGAAAT
genomic: GAAACAAGATTTTTGGTGCACGGTGTTGACCTCGCTGGTGCAGATACGAGgtaaaagatc ... tctgttgtagAATTTACTGTGCGTTCCATGATGAATATAATCTTCAATCATGGAGCGAAAT
EST: gi|169095903|gb|FE497281.1|FE497281
EST:     GAAACAAGATTTTTGGTGCACGGTGTTGACCTCGCTGGTGCAGATACGAG                         AATTTACTGTGCGTTCCATGATGAATATAATCTTCAATCATGGAGCGAAAT
genomic: GAAACAAGATTTTTGGTGCACGGTGTTGACCTCGCTGGTGCAGATACGAGgtaaaagatc ... tctgttgtagAATTTACTGTGCGTTCCATGATGAATATAATCTTCAATCATGGAGCGAAAT
EST: gi|169032875|gb|FE438331.1|FE438331
EST:     GAAACAAGATTTNTGGTGCACGGTGTTGACCTCGCTGGTGCAGATACGAG                         AATTTACTGTGCGTTCCATGATGAATATAATCTTCAATCATGGAGCGAAAT
genomic: GAAACAAGATTTTTGGTGCACGGTGTTGACCTCGCTGGTGCAGATACGAGgtaaaagatc ... tctgttgtagAATTTACTGTGCGTTCCATGATGAATATAATCTTCAATCATGGAGCGAAAT
EST: gi|169099314|gb|FE501593.1|FE501593
EST:     GAAACAAGATTTTTGGTGCACGGTGTTGACCTCGCTGGTGCAGATACGAG                         AATTTACTGTGCGTTCCATGATGAATATAATCTTCAATCATGGAGCGAAAT
genomic: GAAACAAGATTTTTGGTGCACGGTGTTGACCTCGCTGGTGCAGATACGAGgtaaaagatc ... tctgttgtagAATTTACTGTGCGTTCCATGATGAATATAATCTTCAATCATGGAGCGAAAT
EST: gi|169058648|gb|FE466857.1|FE466857
EST:     GAAACAAGATTTTTGGTGCACGGTGTTGACCTCGCTGGTGCAGATACGAG                         AATTTACTGTGCGTTCCATGATGAATATAATCTTCAATCATGGAGCGAAAT
genomic: GAAACAAGATTTTTGGTGCACGGTGTTGACCTCGCTGGTGCAGATACGAGgtaaaagatc ... tctgttgtagAATTTACTGTGCGTTCCATGATGAATATAATCTTCAATCATGGAGCGAAAT
EST: gi|169030797|gb|FE438143.1|FE438143
EST:     GAAACAAGATTTTTGGTGCACGGTGTTGACCTCGCTGGTGCAGATACGAG                         AATTTACTGTGCGTTCCATGATGAATATAATCTTCAATCATGGAGCGAAAT
genomic: GAAACAAGATTTTTGGTGCACGGTGTTGACCTCGCTGGTGCAGATACGAGgtaaaagatc ... tctgttgtagAATTTACTGTGCGTTCCATGATGAATATAATCTTCAATCATGGAGCGAAAT
EST: gi|169103571|gb|FE507613.1|FE507613
EST:     GAAACAAGATTTTTGGTGCACGGTGTTGACCTCGCTGGTGCAGATACGAG                         AATTTACTGTGCGTTCCATGATGAATATAATCTTCAATCATGGAGCGAAAT
genomic: GAAACAAGATTTTTGGTGCACGGTGTTGACCTCGCTGGTGCAGATACGAGgtaaaagatc ... tctgttgtagAATTTACTGTGCGTTCCATGATGAATATAATCTTCAATCATGGAGCGAAAT
EST: gi|169113874|gb|FE515929.1|FE515929
EST:     GAAACAAGATTTTTGGTGCACGGTGTTGACCTCGCTGGTGCAGATACGAG                         AATTTACTGTGCGTTCCATGATGAATATAATCTTCAATCATGGAGCGAAAT
genomic: GAAACAAGATTTTTGGTGCACGGTGTTGACCTCGCTGGTGCAGATACGAGgtaaaagatc ... tctgttgtagAATTTACTGTGCGTTCCATGATGAATATAATCTTCAATCATGGAGCGAAAT
EST: gi|169052045|gb|FE460384.1|FE460384
EST:     GAAACAAGATTTTTGGTGCACGGTGTTGACCTCGCTGGTGCAGATACGAG                         AATTTACTGTGCGTTCCATGATGAATATAATCTTCAATCATGGAGCGAAAT
genomic: GAAACAAGATTTTTGGTGCACGGTGTTGACCTCGCTGGTGCAGATACGAGgtaaaagatc ... tctgttgtagAATTTACTGTGCGTTCCATGATGAATATAATCTTCAATCATGGAGCGAAAT
EST: gi|169057609|gb|FE463660.1|FE463660
EST:     GAAACAAGATTTTTGGTGCACGGTGTTGACCTCGCTGGTGCAGATACGAG                         AATTTACTGTGCGTTCCATGATGAATATAATCTTCAATCATGGAGCGAAAT
genomic: GAAACAAGATTTTTGGTGCACGGTGTTGACCTCGCTGGTGCAGATACGAGgtaaaagatc ... tctgttgtagAATTTACTGTGCGTTCCATGATGAATATAATCTTCAATCATGGAGCGAAAT
EST: gi|169024640|gb|FE432823.1|FE432823
EST:     GAAACAAGATTTTTGGTGCACGGTGTTGACCTCGCTGGTGCAGATACGAG                         AATTTACTGTGCGTTCCATGATGAATATAATCTTCAATCATGGAGCGAAAT
genomic: GAAACAAGATTTTTGGTGCACGGTGTTGACCTCGCTGGTGCAGATACGAGgtaaaagatc ... tctgttgtagAATTTACTGTGCGTTCCATGATGAATATAATCTTCAATCATGGAGCGAAAT
EST: gi|169096098|gb|FE500050.1|FE500050
EST:     GAAACAAGATTTTTGGTGCACGGTGTTGACCTCGCTGGTGCAGATACGAG                         AATTTACTGTGCGTTCCATGATGAATATAATCTTCAATCATGGAGCGAAAT
genomic: GAAACAAGATTTTTGGTGCACGGTGTTGACCTCGCTGGTGCAGATACGAGgtaaaagatc ... tctgttgtagAATTTACTGTGCGTTCCATGATGAATATAATCTTCAATCATGGAGCGAAAT
EST: gi|169037499|gb|FE445538.1|FE445538
EST:     GAAACAAGATTTTTGGTGCACGGTGTTGACCTCGCTGGTGCAGATACGAG                         AATTTACTGTGCGTTCCATGATGAATATAATCTTCAATCATGGAGCGAAAT
genomic: GAAACAAGATTTTTGGTGCACGGTGTTGACCTCGCTGGTGCAGATACGAGgtaaaagatc ... tctgttgtagAATTTACTGTGCGTTCCATGATGAATATAATCTTCAATCATGGAGCGAAAT

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: 31

ATTTTCCCGAAATTTTGGCTGTTAGACCTCTTGCAGCTGTAAGAAACGAGGAAACAAGATTTTTGGTGCACGGTGTTGACCTCGCTGGTGCAGATACGAGgtaaaagatc ... tctgttgtagAATTTACTGTGCGTTCCATGATGAATATAATCTTCAATCATGGAGCGAAATTGACGCAAACGAAGAGGATGCTGAAGGCAGTTTGTGTTTCACACACACT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtaaaagatcatacgtcttttgggatgttaacagagtattttctgttgtagAATTTACTGTGCGTTCCATGATGAATATAATCTTCAATCATGGAGCGAAATTGACGCAAACGAAGAGGATGCTGAAGGCAGTTTGTGTTTCACACACACT
                             tgttaac  putative branch site (score: 31)
                                          ttttctgtt  putative PPT
     taaaagat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaaagatcatacgtcttttgggatgttaacagagtattttctgttgtagAATTTACTGTGCGTTCCATGATGAATATAATCTTCAATCATGGAGCGAAATTGACGCAAACGAAGAGGATGCTGAAGGCAGTTTGTGTTTCACACACACT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG