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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaaattcgttgcatcctttcttttgttcttccattttctacttgctaaaggactggtcttccactggattatacagGGGCAATGTTGCGCTTTCAGTTATTATGACAGCGATCAGCACATTCTTAGCAGTG

Basic information

species Selaginella moellendorffii
transcript EFJ37949
intron # 4
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|169116350|gb|FE517713.1|FE517713
EST:     GAACTGCGAGTAACGTTGTTACATACCTTGCAAG                         GNGCAATGTTGCGCTTTCAGTCATTATGACAGCGATCAGCACATTCTTAGC
genomic: GAACTGCGAGTAACGTTGTTACATACCTTGCAAGgtaaaattcg ... gattatacagGGGCAATGTTGCGCTTTCAGTTATTATGACAGCGATCAGCACATTCTTAGC
EST: gi|169111984|gb|FE510675.1|FE510675
EST:     GAACTGCGAGTAACGTTGTTACATACCTTGCAAG                         GGGCAATGTTGCGCTTTCAGTTATTATGACAGCGATCAGCACATTCTTAGC
genomic: GAACTGCGAGTAACGTTGTTACATACCTTGCAAGgtaaaattcg ... gattatacagGGGCAATGTTGCGCTTTCAGTTATTATGACAGCGATCAGCACATTCTTAGC
EST: gi|169111985|gb|FE510676.1|FE510676
EST:     GAACTGCGAGTAACGTTGTTACATACCTTGCAAG                         GGGCAATGTTGCGCTTTCAGTTATTATGACAGCGATCAGCACATTCTTAGC
genomic: GAACTGCGAGTAACGTTGTTACATACCTTGCAAGgtaaaattcg ... gattatacagGGGCAATGTTGCGCTTTCAGTTATTATGACAGCGATCAGCACATTCTTAGC

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: 33 (upstream exon), 16 (downstream exon)
Score: 2

GAACTGCGAGTAACGTTGTTACATACCTTGCAAGgtaaaattcg ... gattatacagGGGCAATGTTGCGCTTTCAGTTATTATGACAGCGATCAGCACATTCTTAGCAGTG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttgttcttccattttctacttgctaaaggactggtcttccactggattatacagGGGCAATGTTGCGCTTTCAGTTATTATGACAGCGATCAGCACATTCTTAGCAGTG
                     tgctaaa  putative branch site (score: 2)
           attttcta  TA-rich tract