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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCGGCGCAGCAGCCGTGGAGGCTCAGCCTCCGCCGCCCCGATCGCGTCGATGTGGCGCCTGATTCGCCGCGGAATTCCATGCACGATTGCCTCAAGAAGTgtaagctatcgattgatttggtagttcttttggttctttctggcgaaatcgctcacacatcgcgatatttcggcag

Basic information

species Selaginella moellendorffii
transcript EFJ22209
intron # 1
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|169092881|gb|FE493745.1|FE493745
EST:     TGTGGCGCCTGATTCGCCGCGGAATTCCATGCACGATTGCCTCAAGAAGT                         GGTCGACCACTCCAGTGGATGAGTTCTATCAGCAGCAGCTCGAAATGCTCG
genomic: TGTGGCGCCTGATTCGCCGCGGAATTCCATGCACGATTGCCTCAAGAAGTgtaagctatc ... atttcggcagGGTCGACCACTCCAGTGGATGAGTTCTATCAGCAGCAGCTCGAAATGCTCG
EST: gi|169115734|gb|FE517320.1|FE517320
EST:     TGTGGCGCCTGATTCGCCGCGGAATTCCATGCACGATTGCCTCAAGAAGT                         GGTCGACCACTCCAGTGGATGAGTTCTATCAGCAGCAGCTCGAAATGCTCG
genomic: TGTGGCGCCTGATTCGCCGCGGAATTCCATGCACGATTGCCTCAAGAAGTgtaagctatc ... atttcggcagGGTCGACCACTCCAGTGGATGAGTTCTATCAGCAGCAGCTCGAAATGCTCG
EST: gi|169094521|gb|FE494499.1|FE494499
EST:     TGTGGCGCCTGATTCGCCGCGGAATTCCATGCACGATTGCCTCAAGAAGT                         GGTCGACCACTCCAGTGGATGAGTTCTATCAGCAGCAGCTCGAAATGCTCG
genomic: TGTGGCGCCTGATTCGCCGCGGAATTCCATGCACGATTGCCTCAAGAAGTgtaagctatc ... atttcggcagGGTCGACCACTCCAGTGGATGAGTTCTATCAGCAGCAGCTCGAAATGCTCG
EST: gi|169101381|gb|FE502524.1|FE502524
EST:     TGTGGCGCCTGATTCGCCGCGGAATTCCATGCACGATTGCCTCAAGAAGT                         GGTCGACCACTCCAGTGGATGAGTTCTATCAGCAGCAGCTCGAAATGCTCG
genomic: TGTGGCGCCTGATTCGCCGCGGAATTCCATGCACGATTGCCTCAAGAAGTgtaagctatc ... atttcggcagGGTCGACCACTCCAGTGGATGAGTTCTATCAGCAGCAGCTCGAAATGCTCG
EST: gi|169018701|gb|FE426678.1|FE426678
EST:     TGTGGCGCCTGATTCGCCGCGGAATTCCATGCACGATTGCCTCAAGAAGT                         GGTCGACCACTCCAGTGGATGAGTTCTATCAGCAGCAGCTCGAAATGCTCG
genomic: TGTGGCGCCTGATTCGCCGCGGAATTCCATGCACGATTGCCTCAAGAAGTgtaagctatc ... atttcggcagGGTCGACCACTCCAGTGGATGAGTTCTATCAGCAGCAGCTCGAAATGCTCG
EST: gi|169103985|gb|FE504296.1|FE504296
EST:     TGTGGCGCCTGATTCGCCGCGGAATTCCATGCACGATTGCCTCAAGAAGT                         GGTCGACCACTCCAGTGGATGAGTTCTATCAGCAGCAGCTCGAAATGCTCG
genomic: TGTGGCGCCTGATTCGCCGCGGAATTCCATGCACGATTGCCTCAAGAAGTgtaagctatc ... atttcggcagGGTCGACCACTCCAGTGGATGAGTTCTATCAGCAGCAGCTCGAAATGCTCG
EST: gi|169056828|gb|FE465418.1|FE465418
EST:     TGTGGCGCCTGATTCGCCGCGGAATTCCATGCACGATTGCCTCAAGAAGT                         GGTCGACCACTCCAGTGGATGAGTTCTATCAGCAGCAGCTCGAAATGCTCG
genomic: TGTGGCGCCTGATTCGCCGCGGAATTCCATGCACGATTGCCTCAAGAAGTgtaagctatc ... atttcggcagGGTCGACCACTCCAGTGGATGAGTTCTATCAGCAGCAGCTCGAAATGCTCG
EST: gi|169052822|gb|FE461200.1|FE461200
EST:     TGTGGCGCCTGATTCGCCGCGGAATTCCATGCACGATTGCCTCAAGAAGT                         GGTCGACCACTCCAGTGGATGAGTTCTATCAGCAGCAGCTCGAAATGCTCG
genomic: TGTGGCGCCTGATTCGCCGCGGAATTCCATGCACGATTGCCTCAAGAAGTgtaagctatc ... atttcggcagGGTCGACCACTCCAGTGGATGAGTTCTATCAGCAGCAGCTCGAAATGCTCG
EST: gi|169068129|gb|FE476886.1|FE476886
EST:     TGTGGCGCCTGATTCGCCGCGGAATTCCATGCACGATTGCCTCAAGAAGT                         GGTCGACCACTCCAGTGGATGAGTTCTATCAGCAGCAGCTCGAAATGCTCG
genomic: TGTGGCGCCTGATTCGCCGCGGAATTCCATGCACGATTGCCTCAAGAAGTgtaagctatc ... atttcggcagGGTCGACCACTCCAGTGGATGAGTTCTATCAGCAGCAGCTCGAAATGCTCG
EST: gi|169054285|gb|FE460730.1|FE460730
EST:     TGTGGCGCCTGATTCGCCGCGGAATTCCATGCACGATTGCCTCAAGAAGT                         GGTCGACCACTCCAGTGGATGAGTTCTACCAGCAGCAGCTCGAAATGCTCG
genomic: TGTGGCGCCTGATTCGCCGCGGAATTCCATGCACGATTGCCTCAAGAAGTgtaagctatc ... atttcggcagGGTCGACCACTCCAGTGGATGAGTTCTATCAGCAGCAGCTCGAAATGCTCG
EST: gi|169022152|gb|FE430981.1|FE430981
EST:     TGTGGCGCCTGATTCGCCGCGGAATTCCATGCACGATTGCCTCAAGAAGT                         GGTCGACCACTCCAGTGGATGAGTTCTACCAGCAGCAGCTCGAAATGCTCG
genomic: TGTGGCGCCTGATTCGCCGCGGAATTCCATGCACGATTGCCTCAAGAAGTgtaagctatc ... atttcggcagGGTCGACCACTCCAGTGGATGAGTTCTATCAGCAGCAGCTCGAAATGCTCG
EST: gi|169042485|gb|FE453670.1|FE453670
EST:     TGTGGCGCCTGATTCGCCGCGGAATTCCATGCACGATTGCCTCAAGAAGT                         GGTCGACCACTCCAGTGGATGAGTTCTATCAGCAGCAGCTCGAAATGCTCG
genomic: TGTGGCGCCTGATTCGCCGCGGAATTCCATGCACGATTGCCTCAAGAAGTgtaagctatc ... atttcggcagGGTCGACCACTCCAGTGGATGAGTTCTATCAGCAGCAGCTCGAAATGCTCG
EST: gi|169028596|gb|FE440739.1|FE440739
EST:     TGTGGCGCCTGATTCGCCGCGGAATTCCATGCACGATTGCCTCAAGAAGT                         GGTCGACCACTCCAGTGGATGAGTTCTACCAGCAGCAGCTCGAAATGCTCG
genomic: TGTGGCGCCTGATTCGCCGCGGAATTCCATGCACGATTGCCTCAAGAAGTgtaagctatc ... atttcggcagGGTCGACCACTCCAGTGGATGAGTTCTATCAGCAGCAGCTCGAAATGCTCG
EST: gi|169109635|gb|FE510069.1|FE510069
EST:     TGTGGCGCCTGATTCGCCGCGGAATTCCATGCACGATTGCCTCAAGAAGT                         GGTCGACCACTCCAGTGGATGAGTTCTATCAGCAGCAGCTCGAAATGCTCG
genomic: TGTGGCGCCTGATTCGCCGCGGAATTCCATGCACGATTGCCTCAAGAAGTgtaagctatc ... atttcggcagGGTCGACCACTCCAGTGGATGAGTTCTATCAGCAGCAGCTCGAAATGCTCG

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: 34 (upstream exon), 34 (downstream exon)
Score: 33

GCGGCGCAGCAGCCGTGGAGGCTCAGCCTCCGCCGCCCCGATCGCGTCGATGTGGCGCCTGATTCGCCGCGGAATTCCATGCACGATTGCCTCAAGAAGTgtaagctatc ... atttcggcagGGTCGACCACTCCAGTGGATGAGTTCTATCAGCAGCAGCTCGAAATGCTCGATTCCTTCTCGGAGCTGGACAGCATTCAAGACCGAGGGCCAATGTCCGC




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCGGCGCAGCAGCCGTGGAGGCTCAGCCTCCGCCGCCCCGATCGCGTCGATGTGGCGCCTGATTCGCCGCGGAATTCCATGCACGATTGCCTCAAGAAGTgtaagctatcgattgatttggtagttcttttggttctttctggcgaaatcgctcacacatcgcgatatttcggcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT