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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacgtcagaacgcacgatgtccttgtcttgttgctgatccctttgtgcttgcagCTACCCCCTCAATGATACCGCTGCTACAATCAATGAGCTAGGCGGGACTATAAGGAGAGTGATGGGTGGCACTAGCGGTGTTCT

Basic information

species Selaginella moellendorffii
transcript EFJ11288
intron # 15
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|169078093|gb|FE488787.1|FE488787
EST:     ATGTGGAAAGGAGCCAATGCCGTACTCGAAGATCTGCGGAAGTG                         CTACCCCCTCAATGATACCGCTGCTACAATCAATGAGCTAGGCGGGACTAT
genomic: ATGTGGAAAGGAGCCAATGCCGTACTCGAAGATCTGCGGAAGTGgtacgtcaga ... gtgcttgcagCTACCCCCTCAATGATACCGCTGCTACAATCAATGAGCTAGGCGGGACTAT
EST: gi|169069767|gb|FE477484.1|FE477484
EST:     ATGTGGAAAGGAGCCAATGCCGTACTCGAAGATCTGCGGAAGTG                         CTACCCCCTCAATGATACCGCTGCTACAATCAATGAGCTAGGCGGGACTAT
genomic: ATGTGGAAAGGAGCCAATGCCGTACTCGAAGATCTGCGGAAGTGgtacgtcaga ... gtgcttgcagCTACCCCCTCAATGATACCGCTGCTACAATCAATGAGCTAGGCGGGACTAT
EST: gi|169093165|gb|FE494198.1|FE494198
EST:     ATGTGGAAAGGAGCCAATGCCGTACTCGAAGATCTGCGGAAGTG                         CTACCCCCTCAATGATACCGCTGCTACAATCAATGAGCTAGGCGGGACTAT
genomic: ATGTGGAAAGGAGCCAATGCCGTACTCGAAGATCTGCGGAAGTGgtacgtcaga ... gtgcttgcagCTACCCCCTCAATGATACCGCTGCTACAATCAATGAGCTAGGCGGGACTAT
EST: gi|169081724|gb|FE488182.1|FE488182
EST:     ATGTGGAAAGGAGCCAATGCCGTACTCGAAGATCTGCGGAAGTG                         CTACCCCCTCAATGATACCGCTGCTACAATCAATGAGCTAGGCGGGACTAT
genomic: ATGTGGAAAGGAGCCAATGCCGTACTCGAAGATCTGCGGAAGTGgtacgtcaga ... gtgcttgcagCTACCCCCTCAATGATACCGCTGCTACAATCAATGAGCTAGGCGGGACTAT
EST: gi|169077287|gb|FE485589.1|FE485589
EST:     ATGTGGAAAGGAGCCAATGCCGTACTCGAAGATCTGCGGAAGTG                         CTACCCCCTCAATGATACCGCTGCTACAATCAATGAGCTAGGCGGGACTAT
genomic: ATGTGGAAAGGAGCCAATGCCGTACTCGAAGATCTGCGGAAGTGgtacgtcaga ... gtgcttgcagCTACCCCCTCAATGATACCGCTGCTACAATCAATGAGCTAGGCGGGACTAT
EST: gi|169052446|gb|FE462774.1|FE462774
EST:     ATGTGGAAAGGAGCCAATGCCGTACTCGAAGATCTGCGGAAGTG                         CTACCCCCTCAATGATACCGCTGCTACAATCAATGAGCTAGGCGGGACTAT
genomic: ATGTGGAAAGGAGCCAATGCCGTACTCGAAGATCTGCGGAAGTGgtacgtcaga ... gtgcttgcagCTACCCCCTCAATGATACCGCTGCTACAATCAATGAGCTAGGCGGGACTAT
EST: gi|169076148|gb|FE485178.1|FE485178
EST:     ATGTGGAAAGGAGCCAATGCCGTACTCGAAGATCTGCGGAAGTG                         CTACCCCCTCAATGATACCGCTGCTACAATCAATGAGCTAGGCGGGACTAT
genomic: ATGTGGAAAGGAGCCAATGCCGTACTCGAAGATCTGCGGAAGTGgtacgtcaga ... gtgcttgcagCTACCCCCTCAATGATACCGCTGCTACAATCAATGAGCTAGGCGGGACTAT
EST: gi|169029149|gb|FE439381.1|FE439381
EST:     ATGTGGAAAGGAGCCAATGCCGTACTCGAAGATCTGCGGAAGTG                         CTACCCCCTCAATGATACCGCTGCTACAATCAATGAGCTAGGCGGGACTAT
genomic: ATGTGGAAAGGAGCCAATGCCGTACTCGAAGATCTGCGGAAGTGgtacgtcaga ... gtgcttgcagCTACCCCCTCAATGATACCGCTGCTACAATCAATGAGCTAGGCGGGACTAT
EST: gi|169096989|gb|FE500057.1|FE500057
EST:     ATGTGGAAAGGAGCCAATGCCGTACTCGAAGATCTGCGGAAGTG                         CTACCCCCTCAATGATACCGCTGCTACAATCAATGAGCTAGGCGGGACTAT
genomic: ATGTGGAAAGGAGCCAATGCCGTACTCGAAGATCTGCGGAAGTGgtacgtcaga ... gtgcttgcagCTACCCCCTCAATGATACCGCTGCTACAATCAATGAGCTAGGCGGGACTAT
EST: gi|169044598|gb|FE450637.1|FE450637
EST:     ACAACGATGTGGAAAGGAGCCAATGCCGTACTCGAAGATCTGCGGAAGTG                         CTACCCCCTCAATGATACCGCTGCTACAATCAATGAGCTAGGCGGGACTAT
genomic: ACAACGATGTGGAAAGGAGCCAATGCCGTACTCGAAGATCTGCGGAAGTGgtacgtcaga ... gtgcttgcagCTACCCCCTCAATGATACCGCTGCTACAATCAATGAGCTAGGCGGGACTAT
EST: gi|169040870|gb|FE447921.1|FE447921
EST:     GTACTCGAAGATATGCGGAAGTG                         CTACCCCCTCAATGATACCGCTGCTACAATCAATGAGCTAGGCGGGACTAT
genomic: GTACTCGAAGATCTGCGGAAGTGgtacgtcaga ... gtgcttgcagCTACCCCCTCAATGATACCGCTGCTACAATCAATGAGCTAGGCGGGACTAT
EST: gi|169020101|gb|FE430880.1|FE430880
EST:     ATGTGGAAAGGAGCCAATGCCGTACTCGAAGATCTGCGGAAGTG                         CTACCCCCTCAATGATACCGCTGCTACAATCAATGAGCTAGGCGGGACTAT
genomic: ATGTGGAAAGGAGCCAATGCCGTACTCGAAGATCTGCGGAAGTGgtacgtcaga ... gtgcttgcagCTACCCCCTCAATGATACCGCTGCTACAATCAATGAGCTAGGCGGGACTAT
EST: gi|169096955|gb|FE497592.1|FE497592
EST:     GATGTGGAAAGGAGCCAATGCCGTACTCGAAGATCTGCGGAAGTG                         CTACCCCCTCAATGATACCGCTGCTACAATCAATGAGCTAGGCGGGACTAT
genomic: GATGTGGAAAGGAGCCAATGCCGTACTCGAAGATCTGCGGAAGTGgtacgtcaga ... gtgcttgcagCTACCCCCTCAATGATACCGCTGCTACAATCAATGAGCTAGGCGGGACTAT
EST: gi|169096954|gb|FE497591.1|FE497591
EST:     GATGTGGAAAGGAGCCAATGCCGTACTCGAAGATCTGCGGAAGTG                         CTACCCCCTCAATGATACCGCTGCTACAATCAATGAGCTAGGCGGGACTAT
genomic: GATGTGGAAAGGAGCCAATGCCGTACTCGAAGATCTGCGGAAGTGgtacgtcaga ... gtgcttgcagCTACCCCCTCAATGATACCGCTGCTACAATCAATGAGCTAGGCGGGACTAT
EST: gi|169078532|gb|FE490669.1|FE490669
EST:     ATGTGGAAAGGAGCCAATGCCGTACTCGAAGATCTGCGGAAGTG                         CTACCCCCTCAATGATACCGCTGCTACAATCAATGAGCTAGGCGGGACTAT
genomic: ATGTGGAAAGGAGCCAATGCCGTACTCGAAGATCTGCGGAAGTGgtacgtcaga ... gtgcttgcagCTACCCCCTCAATGATACCGCTGCTACAATCAATGAGCTAGGCGGGACTAT
EST: gi|169028495|gb|FE439104.1|FE439104
EST:     ATGTGGAAAGGAGCCAATGCCGTACTCGAAGATCTGCGGAAGTG                         CTACCCCCTCAATGATACCGCTGCTACAATCAATGAGCTAGGCGGGACTAT
genomic: ATGTGGAAAGGAGCCAATGCCGTACTCGAAGATCTGCGGAAGTGgtacgtcaga ... gtgcttgcagCTACCCCCTCAATGATACCGCTGCTACAATCAATGAGCTAGGCGGGACTAT
EST: gi|169066803|gb|FE473635.1|FE473635
EST:     ATGTGGAAAGGAGCCAATGCCGTACTCGAAGATCTGCGGAAGTG                         CTACCCCCTCAATGATACCGCTGCTACAATCAATGAGCTAGGCGGGACTAT
genomic: ATGTGGAAAGGAGCCAATGCCGTACTCGAAGATCTGCGGAAGTGgtacgtcaga ... gtgcttgcagCTACCCCCTCAATGATACCGCTGCTACAATCAATGAGCTAGGCGGGACTAT
EST: gi|169029649|gb|FE437320.1|FE437320
EST:     TGCCGTACTCGAAGATCTGCGGAAGTG                         CTACCCCCTCAATGATACCGCTGCTACAATCAATGAGCTAGGCGGGACTAT
genomic: TGCCGTACTCGAAGATCTGCGGAAGTGgtacgtcaga ... gtgcttgcagCTACCCCCTCAATGATACCGCTGCTACAATCAATGAGCTAGGCGGGACTAT
EST: gi|169033716|gb|FE441644.1|FE441644
EST:     ATGTGGAAAGGAGCCAATGCCGTACTCGAAGATCTGCGGAAGTG                         CTACCCCCTCAATGATACCGCTGCTACAATCAATGAGCTAGGCGGGACTAT
genomic: ATGTGGAAAGGAGCCAATGCCGTACTCGAAGATCTGCGGAAGTGgtacgtcaga ... gtgcttgcagCTACCCCCTCAATGATACCGCTGCTACAATCAATGAGCTAGGCGGGACTAT
EST: gi|169110787|gb|FE512637.1|FE512637
EST:     ATGTGGAAAGGAGCCAATGCCGTACTCGAAGATCTGCGGAAGTG                         CTACCCCCTCAATGATACCGCTGCTACAATCAATGAGCTAGGCGGGACTAT
genomic: ATGTGGAAAGGAGCCAATGCCGTACTCGAAGATCTGCGGAAGTGgtacgtcaga ... gtgcttgcagCTACCCCCTCAATGATACCGCTGCTACAATCAATGAGCTAGGCGGGACTAT

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), 33 (downstream exon)
Score: 75

ATGTGGAAAGGAGCCAATGCCGTACTCGAAGATCTGCGGAAGTGgtacgtcaga ... gtgcttgcagCTACCCCCTCAATGATACCGCTGCTACAATCAATGAGCTAGGCGGGACTATAAGGAGAGTGATGGGTGGCACTAGCGGTGTTCT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtacgtcagaacgcacgatgtccttgtcttgttgctgatccctttgtgcttgcagCTACCCCCTCAATGATACCGCTGCTACAATCAATGAGCTAGGCGGGACTATAAGGAGAGTGATGGGTGGCACTAGCGGTGTTCT
                                tgctgat  putative branch site (score: 75)
                                      tccctttgt  CT-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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacgtcagaacgcacgatgtccttgtcttgttgctgatccctttgtgcttgcagCTACCCCCTCAATGATACCGCTGCTACAATCAATGAGCTAGGCGGGACTATAAGGAGAGTGATGGGTGGCACTAGCGGTGTTCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA