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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagctttgccatctttcgctttgctttgctataagttccatcgtttgcttgttcttcgcattagttccatctttgttcttccatctttcgcttgttcttcgcatgcttgcttgtggattgttttcggagtgagtgacagtcgcatttatttttccagGCGATCGCTACCTCGACCGCTTCGTCATCCCAAACCCGGACGTCAAGTGCGTGGTGAGGAGCGACGAGGATGAGTTTCTAGTCCTGGCCAGCGATGGCTT

Basic information

species Selaginella moellendorffii
transcript EFJ23827
intron # 3
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|169114942|gb|FE515891.1|FE515891
EST:     CTGGAACGGCTACCGAGTCATGGGAATGCTGGCCATGTCCAGAGCGATCG                         GCGATCGCTACCTCGACCGCTTCGTCATCCCAAACCCGGACGTCAAGTGCG
genomic: CTGGAACGGCTACCGAGTCATGGGAATGCTGGCCATGTCCAGAGCGATTGgtgagctttg ... atttttccagGCGATCGCTACCTCGACCGCTTCGTCATCCCAAACCCGGACGTCAAGTGCG
EST: gi|169050296|gb|FE457531.1|FE457531
EST:     CTGGAACGGCTACCGAGTCATGGGAATGCTGGCCATGTCCAGAGCGATCG                         GCGATCGCTACCTCGACCGCTTCGTCATCCCAAACCCGGACGTCAAGTGCG
genomic: CTGGAACGGCTACCGAGTCATGGGAATGCTGGCCATGTCCAGAGCGATTGgtgagctttg ... atttttccagGCGATCGCTACCTCGACCGCTTCGTCATCCCAAACCCGGACGTCAAGTGCG
EST: gi|169076892|gb|FE485285.1|FE485285
EST:     CTGGAACGGCTACCGAGTCATGGGAATGCTGGCCATGTCCAGAGCGATTG                         GCGATCGCTACCTCGACCGCTTCGTCATCCCAAACCCGGACGTCAAGTGCG
genomic: CTGGAACGGCTACCGAGTCATGGGAATGCTGGCCATGTCCAGAGCGATTGgtgagctttg ... atttttccagGCGATCGCTACCTCGACCGCTTCGTCATCCCAAACCCGGACGTCAAGTGCG
EST: gi|169057915|gb|FE465513.1|FE465513
EST:     CTGGAACGGCTACCGAGTCATGGGAATGCTGGCCATGTCCAGAGCGATTG                         GCGATCGCTACCTCGACCGCTTCGTCATCCCAAACCCGGACGTCAANTGCG
genomic: CTGGAACGGCTACCGAGTCATGGGAATGCTGGCCATGTCCAGAGCGATTGgtgagctttg ... atttttccagGCGATCGCTACCTCGACCGCTTCGTCATCCCAAACCCGGACGTCAAGTGCG
EST: gi|169097547|gb|FE497989.1|FE497989
EST:     CTGGAACGGCTACCGAGTCATGGGAATGCTGGCCATGTCCAGAGCGATCG                         GCGATCGCTACCTCGACCGCTTCGTCATCC
genomic: CTGGAACGGCTACCGAGTCATGGGAATGCTGGCCATGTCCAGAGCGATTGgtgagctttg ... atttttccagGCGATCGCTACCTCGACCGCTTCGTCATCC
EST: gi|169095995|gb|FE499999.1|FE499999
EST:     GAACGGCTACCGAGTCATGGGAATGCTGGCCATGTCCAGAGCGATCG                         GCGATCGCTACCTCGACCGCTTCGTCATCCCAAACCCGGACGTCAAGTGCG
genomic: GAACGGCTACCGAGTCATGGGAATGCTGGCCATGTCCAGAGCGATTGgtgagctttg ... atttttccagGCGATCGCTACCTCGACCGCTTCGTCATCCCAAACCCGGACGTCAAGTGCG
EST: gi|169043479|gb|FE450753.1|FE450753
EST:     CTGGAACGGCTACCGAGTCATGGGAATGCTGGCCATGTCCAGAGCGATTG                         GCGATCGCTACCTCGACCGCTTCGTCATCCCAAACCCGGACGTCAAGTGCG
genomic: CTGGAACGGCTACCGAGTCATGGGAATGCTGGCCATGTCCAGAGCGATTGgtgagctttg ... atttttccagGCGATCGCTACCTCGACCGCTTCGTCATCCCAAACCCGGACGTCAAGTGCG
EST: gi|169057914|gb|FE465512.1|FE465512
EST:     CTGGAACGGCTACCGAGTCATGGGAATGCTGGCCATGTCCAGAGCGATTG                         GCGATCGCTACCTCGACCGCTTCGTCATCCCAAACCCGGACGTCAAGTGCG
genomic: CTGGAACGGCTACCGAGTCATGGGAATGCTGGCCATGTCCAGAGCGATTGgtgagctttg ... atttttccagGCGATCGCTACCTCGACCGCTTCGTCATCCCAAACCCGGACGTCAAGTGCG
EST: gi|169095397|gb|FE497503.1|FE497503
EST:     CTGGAACGGCTACCGAGTCATGGGAATGCTGGCCATGTCCAGAGCGATTG                         GCGATCGCTACCTCGACCGCTTCGTCATCCCAAACCCGGACGTCAAGTGCG
genomic: CTGGAACGGCTACCGAGTCATGGGAATGCTGGCCATGTCCAGAGCGATTGgtgagctttg ... atttttccagGCGATCGCTACCTCGACCGCTTCGTCATCCCAAACCCGGACGTCAAGTGCG
EST: gi|169038977|gb|FE449694.1|FE449694
EST:     CTGGAACGGCTACCGAGTCATGGGAATGCTGGCCATGTCCAGAGCGATTG                         GCGATCGCTACCTCGACCGCTTCGTCATCCCAAACCCGGACGTCAAGTGCG
genomic: CTGGAACGGCTACCGAGTCATGGGAATGCTGGCCATGTCCAGAGCGATTGgtgagctttg ... atttttccagGCGATCGCTACCTCGACCGCTTCGTCATCCCAAACCCGGACGTCAAGTGCG
EST: gi|169042207|gb|FE454250.1|FE454250
EST:     CGGCTACCGAGTCATGGGAATGCTGGCCATGTCCAGAGCGATTG                         GCGATCGCTACCTCGACCGCTTCGTCATCCCAAACCCGGACGTCAAGTGCG
genomic: CGGCTACCGAGTCATGGGAATGCTGGCCATGTCCAGAGCGATTGgtgagctttg ... atttttccagGCGATCGCTACCTCGACCGCTTCGTCATCCCAAACCCGGACGTCAAGTGCG
EST: gi|169093362|gb|FE493212.1|FE493212
EST:     TGGAACGGCTACCGAGTCATGGGAATGCTGGCCATGTCCAGAGCGATCG                         GCGATCGCTACCTCGACCGCTTCGTCATCCCAAACCCGGACGTCAAGTGCG
genomic: TGGAACGGCTACCGAGTCATGGGAATGCTGGCCATGTCCAGAGCGATTGgtgagctttg ... atttttccagGCGATCGCTACCTCGACCGCTTCGTCATCCCAAACCCGGACGTCAAGTGCG
EST: gi|169021765|gb|FE430412.1|FE430412
EST:     CTGGAACGGCTACCGAGTCATGGGAATGCTGGCCATGTCCAGAGCGATTG                         GCGATCGCTACCTCGACCGCTTCGTCATCCCAAACCCGGACGTCAAGTGCG
genomic: CTGGAACGGCTACCGAGTCATGGGAATGCTGGCCATGTCCAGAGCGATTGgtgagctttg ... atttttccagGCGATCGCTACCTCGACCGCTTCGTCATCCCAAACCCGGACGTCAAGTGCG
EST: gi|169075809|gb|FE483313.1|FE483313
EST:     CTGGAACGGCTACCGAGTCATGNGAATGCTGGCCATGTCCAGAGCGATCG                         GCGATCGCTACCTCGACCGCTTCGTCATCCCAAACCCGGACGTNCA-GTGC
genomic: CTGGAACGGCTACCGAGTCATGGGAATGCTGGCCATGTCCAGAGCGATTGgtgagctttg ... atttttccagGCGATCGCTACCTCGACCGCTTCGTCATCCCAAACCCGGACGT-CAAGTGC
EST: gi|169043478|gb|FE450752.1|FE450752
EST:     GGGAATGCTGGCCATGTCCAGAGCGATTG                         GCGATCGCTACCTCGACCGCTTCGTCATCCCAAACCCGGACGTCAAGTGCG
genomic: GGGAATGCTGGCCATGTCCAGAGCGATTGgtgagctttg ... atttttccagGCGATCGCTACCTCGACCGCTTCGTCATCCCAAACCCGGACGTCAAGTGCG
EST: gi|169042208|gb|FE454251.1|FE454251
EST:     CTGGAACGGCTACCGAGTCATGGGAATGCTGGCCATGTCCAGAGCGATTG                         GCGATCGCTACCTCGACCGCTTCGTCATCCCAAACCCGGACGTCAAGTGCG
genomic: CTGGAACGGCTACCGAGTCATGGGAATGCTGGCCATGTCCAGAGCGATTGgtgagctttg ... atttttccagGCGATCGCTACCTCGACCGCTTCGTCATCCCAAACCCGGACGTCAAGTGCG
EST: gi|169029818|gb|FE438386.1|FE438386
EST:     CTGGAACGGCTACCGAGTCATGGGAATGCTGGCCATGTCCAGAGCGATCG                         GCGATCGCTACCTCGACCGCTTCGTCATCCCAAACCCGGACGTCAAGTGCG
genomic: CTGGAACGGCTACCGAGTCATGGGAATGCTGGCCATGTCCAGAGCGATTGgtgagctttg ... atttttccagGCGATCGCTACCTCGACCGCTTCGTCATCCCAAACCCGGACGTCAAGTGCG
EST: gi|169099514|gb|FE502599.1|FE502599
EST:     GCTACCGAGTCATGGGAATGCTGGCCATGTCCAGAGCGATCG                         GCGATCGCTACCTCGACCGCTTCGTCATCCCAAACCCGGACGTCAAGTGCG
genomic: GCTACCGAGTCATGGGAATGCTGGCCATGTCCAGAGCGATTGgtgagctttg ... atttttccagGCGATCGCTACCTCGACCGCTTCGTCATCCCAAACCCGGACGTCAAGTGCG
EST: gi|169095398|gb|FE497504.1|FE497504
EST:     CTGGAACGGCTACCGAGTCATGGGAATGCTGGCCATGTCCAGAGCGATTG                         GCGATCGCTACCTCGACCGCTTCGTCATCNCAAACCCGGACGTCAAGTGCG
genomic: CTGGAACGGCTACCGAGTCATGGGAATGCTGGCCATGTCCAGAGCGATTGgtgagctttg ... atttttccagGCGATCGCTACCTCGACCGCTTCGTCATCCCAAACCCGGACGTCAAGTGCG
EST: gi|169108344|gb|FE510416.1|FE510416
EST:     GGAATGCTGGCCATGTCCAGAGCGATTG                         GCGATCGCTACCTCGACCGCTTCGTCATCCCAAACCCGGACGTCAAGTGCG
genomic: GGAATGCTGGCCATGTCCAGAGCGATTGgtgagctttg ... atttttccagGCGATCGCTACCTCGACCGCTTCGTCATCCCAAACCCGGACGTCAAGTGCG
EST: gi|169029819|gb|FE438387.1|FE438387
EST:     CTGGAACGGCTACCGAGTCATGNGAATGCTGGCCATGTCCAGAGCGATCG                         GCGATCGCTACCTCGACCGCTTCGTCA
genomic: CTGGAACGGCTACCGAGTCATGGGAATGCTGGCCATGTCCAGAGCGATTGgtgagctttg ... atttttccagGCGATCGCTACCTCGACCGCTTCGTCA
EST: gi|169026883|gb|FE434234.1|FE434234
EST:     CTGGAACGGCTACCGAGTCATGGGAATGCTGGCCATGTCCAGAGCGATTG                         GCGATCGCTACCTCGACCGCTTCGTCATCCC
genomic: CTGGAACGGCTACCGAGTCATGGGAATGCTGGCCATGTCCAGAGCGATTGgtgagctttg ... atttttccagGCGATCGCTACCTCGACCGCTTCGTCATCCC
EST: gi|169026882|gb|FE434233.1|FE434233
EST:     GGAACGGCTACCGAGTCATGGGAATGCTGGCCATGTCCAGAGCGATTG                         GCGATCGCTACCTCGACCGCTTCGTCATCCCAAACCCGGACGTCAAGTGCG
genomic: GGAACGGCTACCGAGTCATGGGAATGCTGGCCATGTCCAGAGCGATTGgtgagctttg ... atttttccagGCGATCGCTACCTCGACCGCTTCGTCATCCCAAACCCGGACGTCAAGTGCG
EST: gi|169114943|gb|FE515892.1|FE515892
EST:     CTGGAACGGCTACCGAGTCATGGGAATGCTGGCCATGTCCAGAGCGATCG                         GCGATCGCTACCTCGACCGCTTCGTCATCCCAAACCCGGACGTCAAGTGCG
genomic: CTGGAACGGCTACCGAGTCATGGGAATGCTGGCCATGTCCAGAGCGATTGgtgagctttg ... atttttccagGCGATCGCTACCTCGACCGCTTCGTCATCCCAAACCCGGACGTCAAGTGCG

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: 32 (upstream exon), 35 (downstream exon)
Score: 24

AAGGAGGATGAGATGCAACGCATCGAGGACGCCGGCGGTCGAGTCATCTTCTGGAACGGCTACCGAGTCATGGGAATGCTGGCCATGTCCAGAGCGATTGgtgagctttg ... atttttccagGCGATCGCTACCTCGACCGCTTCGTCATCCCAAACCCGGACGTCAAGTGCGTGGTGAGGAGCGACGAGGATGAGTTTCTAGTCCTGGCCAGCGATGGCTT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgcttgcttgtggattgttttcggagtgagtgacagtcgcatttatttttccagGCGATCGCTACCTCGACCGCTTCGTCATCCCAAACCCGGACGTCAAGTGCGTGGTGAGGAGCGACGAGGATGAGTTTCTAGTCCTGGCCAGCGATGGCTT
                                          tttatttttcc  CT-rich tract
                                         atttattttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagctttgccatctttcgctttgctttgctataagttccatcgtttgcttgttcttcgcattagttccatctttgttcttccatctttcgcttgttcttcgcatgcttgcttgtggattgttttcggagtgagtgacagtcgcatttatttttccagGCGATCGCTACCTCGACCGCTTCGTCATCCCAAACCCGGACGTCAAGTGCGTGGTGAGGAGCGACGAGGATGAGTTTCTAGTCCTGGCCAGCGATGGCTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGATG