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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtcatcacgaaaaaccatcgcttctagcgctctaatgtttcttctttccttgcagAGGCTCTTGGGAGTGAAAATGGCTCCCTTTAGAATGAGCGTTTTGTGTCGCTGGAGTCCCAATGGATTTAAAGTTTTGAAAGCTCCCGAGAGCCAAAAAG

Basic information

species Selaginella moellendorffii
transcript EFJ31600
intron # 5
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|169039866|gb|FE447552.1|FE447552
EST:     CCGTGTGTCGAGAAGGCGAAGCAATCTCGCCAGAAGCATCGCGGATACTT                         AGGCTCTTGGGAGTGAAAATGGCTCCCTTTANAATGAGCCTTTTGTGTCGC
genomic: CCGTGTGTCGAGAAGGCGAAGCAATCTCGCCAGAAGCATCGCGGATACTTgtgagtcatc ... ttccttgcagAGGCTCTTGGGAGTGAAAATGGCTCCCTTTAGAATGAGCGTTTTGTGTCGC
EST: gi|169039865|gb|FE447551.1|FE447551
EST:     CCGTGTGTCGAGAAGGCGAAGCAATCTCGCCAGAAGCATCGCGGATACTT                         AGGCTCTTGGGAGTGAAAATGGCTCCCTTTAGAATGAGCCTTTTGTGTCGC
genomic: CCGTGTGTCGAGAAGGCGAAGCAATCTCGCCAGAAGCATCGCGGATACTTgtgagtcatc ... ttccttgcagAGGCTCTTGGGAGTGAAAATGGCTCCCTTTAGAATGAGCGTTTTGTGTCGC
EST: gi|169028147|gb|FE432152.1|FE432152
EST:     CCGTGTGTCGAGAAGGCGAAGCAATCTCGCCAGAAGCATCGCGGATACTT                         AGGCTCTTGGGAGTGAAAATGGCTCCCTTTAAAATGAGCCTTTTGTGTCGC
genomic: CCGTGTGTCGAGAAGGCGAAGCAATCTCGCCAGAAGCATCGCGGATACTTgtgagtcatc ... ttccttgcagAGGCTCTTGGGAGTGAAAATGGCTCCCTTTAGAATGAGCGTTTTGTGTCGC

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), 25 (downstream exon)
Score: 4

GCGTTGTGGAGCTGGTCGGCGATTACACCGTGTGTCGAGAAGGCGAAGCAATCTCGCCAGAAGCATCGCGGATACTTgtgagtcatc ... ttccttgcagAGGCTCTTGGGAGTGAAAATGGCTCCCTTTAGAATGAGCGTTTTGTGTCGCTGGAGTCCCAATGGATTTAAAGTTTTGAAAGCTCCCGAGAGCCAAAAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtcatcacgaaaaaccatcgcttctagcgctctaatgtttcttctttccttgcagAGGCTCTTGGGAGTGAAAATGGCTCCCTTTAGAATGAGCGTTTTGTGTCGCTGGAGTCCCAATGGATTTAAAGTTTTGAAAGCTCCCGAGAGCCAAAAAG
                             ctctaat  putative branch site (score: 4)
                             ctctaatgtttcttct  CT-rich tract
                                taatgttt  TA-rich tract