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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAATTCCGCTATGGCAGCGTCCAGCTCAAGGATTTGCCCGACTCTATCGACTGGAGAGAGAAGGGGGCAGTGGTCGGGGTTAAAGATCAAGGCTCATGCGgtatgtgacacatacttctatagtctttcttccttttgtccttcgctgctggtaagttttagaatagcagtaagtccggagttcttggaaggtttactcccagcgtagtatttctagagaaggaatcgttttctttgctctgatctctaacggattttgtcttggtcggtgattcaatccag

Basic information

species Selaginella moellendorffii
transcript EFJ36576
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|169071628|gb|FE476563.1|FE476563
EST:     CTGGAGAGAGAAGGGGGCAGTGGTCGGGGTTAAAGATCAAGGCTCATGCG                         GGAGCTGCTGGGCCTTCTCGGCTGTGGCAGCGATTGAGGGCGTGAACAAGC
genomic: CTGGAGAGAGAAGGGGGCAGTGGTCGGGGTTAAAGATCAAGGCTCATGCGgtatgtgaca ... ttcaatccagGGAGCTGCTGGGCTTTCTCGGCTGTGGCAGCGATTGAGGGCGTGAACAAGC
EST: gi|169068391|gb|FE478981.1|FE478981
EST:     CTGGAGAGAGAAGGGGGCAGTGGTCGGGGTTAAAGATCAAGGCTCATGCG                         GGAGCTGCTGGGCCTTCTCGGCTGTGGCAGCGATTGAGGGCGTGAACAAGC
genomic: CTGGAGAGAGAAGGGGGCAGTGGTCGGGGTTAAAGATCAAGGCTCATGCGgtatgtgaca ... ttcaatccagGGAGCTGCTGGGCTTTCTCGGCTGTGGCAGCGATTGAGGGCGTGAACAAGC
EST: gi|70670447|gb|DN839024.1|DN839024
EST:     CTGGAGAGAGAAGGGGGCAGTGGTCGGGGTTAAAGATCAAGGCTCATGCG                         GGAGCTGCTGGGCTTTCTCGGCTGTGGCAGCGATTGAGGGCGTGAACAAGC
genomic: CTGGAGAGAGAAGGGGGCAGTGGTCGGGGTTAAAGATCAAGGCTCATGCGgtatgtgaca ... ttcaatccagGGAGCTGCTGGGCTTTCTCGGCTGTGGCAGCGATTGAGGGCGTGAACAAGC
EST: gi|169107395|gb|FE504169.1|FE504169
EST:     CTGGAGAGAGAAGGGGGCAGTGGTCGGGGTTAAAGATCAAGGCTCATGCG                         GGAGCTGCTGGGCTTTCTCGGCTGTGGCAGCGATTGAGGGCGTGAACAAGC
genomic: CTGGAGAGAGAAGGGGGCAGTGGTCGGGGTTAAAGATCAAGGCTCATGCGgtatgtgaca ... ttcaatccagGGAGCTGCTGGGCTTTCTCGGCTGTGGCAGCGATTGAGGGCGTGAACAAGC
EST: gi|169111577|gb|FE511867.1|FE511867
EST:     CTGGAGAGAGAAGGGGGCAGTGGTCGGGGTTAAAGATCAAGGCTCATGCG                         GGAGCTGCTGGGCTTTCTCGGCTGTGGCAGCGATTGAGGGCGTGAACAAGC
genomic: CTGGAGAGAGAAGGGGGCAGTGGTCGGGGTTAAAGATCAAGGCTCATGCGgtatgtgaca ... ttcaatccagGGAGCTGCTGGGCTTTCTCGGCTGTGGCAGCGATTGAGGGCGTGAACAAGC
EST: gi|169071994|gb|FE477683.1|FE477683
EST:     CTGGAGAGAGAAGGGGGCAGTGGTCGGGGTTAAAGATCAAGGCTCATGCG                         GGAGCTGCTGGGCCTTCTCGGCTGTGGCAGCGATTGAGGGCGTGAACAAGC
genomic: CTGGAGAGAGAAGGGGGCAGTGGTCGGGGTTAAAGATCAAGGCTCATGCGgtatgtgaca ... ttcaatccagGGAGCTGCTGGGCTTTCTCGGCTGTGGCAGCGATTGAGGGCGTGAACAAGC
EST: gi|70669649|gb|DN838226.1|DN838226
EST:     CTGGAGAGAGAAGGGGGCAGTGGTCGGGGTTAAAGATCAAGGCTCATGCG                         GGAGCTGCTGGGCCTTCTCGGCTGTGGCAGCGATTGAGGGCGTGAACAAGC
genomic: CTGGAGAGAGAAGGGGGCAGTGGTCGGGGTTAAAGATCAAGGCTCATGCGgtatgtgaca ... ttcaatccagGGAGCTGCTGGGCTTTCTCGGCTGTGGCAGCGATTGAGGGCGTGAACAAGC
EST: gi|169109484|gb|FE514130.1|FE514130
EST:     GGGGTTAAAGATCAAGGCTCATGCG                         GGAGCTGCTGGGCCTTCTCGGCTGTGGCAGCGATTGAGGGCGTGAACAAGC
genomic: GGGGTTAAAGATCAAGGCTCATGCGgtatgtgaca ... ttcaatccagGGAGCTGCTGGGCTTTCTCGGCTGTGGCAGCGATTGAGGGCGTGAACAAGC
EST: gi|169040444|gb|FE448444.1|FE448444
EST:     CTGGAGAGAGAAGGGGGCAGTGGTCGGGGTTAAAGATCAAGGCTCATGCG                         GGAGCTGCTGGGCCTTCTCGGCTGTGGCAGCGATTGAGGGCGTGAACAAGC
genomic: CTGGAGAGAGAAGGGGGCAGTGGTCGGGGTTAAAGATCAAGGCTCATGCGgtatgtgaca ... ttcaatccagGGAGCTGCTGGGCTTTCTCGGCTGTGGCAGCGATTGAGGGCGTGAACAAGC
EST: gi|70670124|gb|DN838701.1|DN838701
EST:     CTGGAGAGAGAAGGGGGCAGTGGTCGGGGTTAAAGATCAAGGCTCATGCG                         GGAGCTGCTGGGCCTTCTCGGCTGTGGCAGCGATTGAGGGCGTGAACAAGC
genomic: CTGGAGAGAGAAGGGGGCAGTGGTCGGGGTTAAAGATCAAGGCTCATGCGgtatgtgaca ... ttcaatccagGGAGCTGCTGGGCTTTCTCGGCTGTGGCAGCGATTGAGGGCGTGAACAAGC
EST: gi|169111834|gb|FE511214.1|FE511214
EST:     CTGGAGAGAGAAGGGGGCAGTGGTCGGGGTTAAAGATCAAGGCTCATGCG                         GGAGCTGCTGGGCCTTCTCGGCTGTGGCAGCGATTGAGGGCGTGAACAAGC
genomic: CTGGAGAGAGAAGGGGGCAGTGGTCGGGGTTAAAGATCAAGGCTCATGCGgtatgtgaca ... ttcaatccagGGAGCTGCTGGGCTTTCTCGGCTGTGGCAGCGATTGAGGGCGTGAACAAGC
EST: gi|169058162|gb|FE466592.1|FE466592
EST:     CTGGAGAGAGAAGGGGGCAGTGGTCGGGGTTAAAGATCAAGGCTCATGCG                         GGAGCTGCTGGGCCTTCTCGGCTGTGGCAGCGATTGAGGGCGTGAACAAGC
genomic: CTGGAGAGAGAAGGGGGCAGTGGTCGGGGTTAAAGATCAAGGCTCATGCGgtatgtgaca ... ttcaatccagGGAGCTGCTGGGCTTTCTCGGCTGTGGCAGCGATTGAGGGCGTGAACAAGC

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), 35 (downstream exon)
Score: 81

GAATTCCGCTATGGCAGCGTCCAGCTCAAGGATTTGCCCGACTCTATCGACTGGAGAGAGAAGGGGGCAGTGGTCGGGGTTAAAGATCAAGGCTCATGCGgtatgtgaca ... ttcaatccagGGAGCTGCTGGGCTTTCTCGGCTGTGGCAGCGATTGAGGGCGTGAACAAGCTTGCCACCGGAGAGCTCGTTTCATTGTCGGAGCAAGAGCTGGTCGACTG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAATTCCGCTATGGCAGCGTCCAGCTCAAGGATTTGCCCGACTCTATCGACTGGAGAGAGAAGGGGGCAGTGGTCGGGGTTAAAGATCAAGGCTCATGCGgtatgtgacacatacttctatagtctttcttccttttgtccttcgctgctggtaagttttagaatagcagtaagtccggagttcttggaaggtttactcccagcgtagtatttctagagaaggaatcgttttctttgctctgatctctaacggattttgtcttggtcggtgattcaatccag

- - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGATCA