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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaggaaaaaactcttatatcatgcactgtcgctcctaattttttcatactttggtttagACAGCTTCACGACCACCAGAGCTTACTGGGCCTGGGAAATTGTTGGAAGCTGCTATCGAGGCTGGTGCTGAGGCAATCATAAAAATAAAGGACTCTTTGA

Basic information

species Selaginella moellendorffii
transcript EFJ11288
intron # 13
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|169093165|gb|FE494198.1|FE494198
EST:     CAACAACAATACCCGTCCCACTCCCTCCTGCTCCTGCAAACAATGAAACA                         ACAGCTTCACGACCACCAGAGCTTACTGGGCCTGGGAAATTGTTGGAAGCT
genomic: CAACAACAATACCCGTCCCACTCCCTCCTGCTCCTGCAAACAATGAAACAgtaaggaaaa ... tttggtttagACAGCTTCACGACCACCAGAGCTTACTGGGCCTGGGAAATTGTTGGAAGCT
EST: gi|169081724|gb|FE488182.1|FE488182
EST:     C-ACAACAATACCCGTCCCACTCCCTCCTGTTCCTGCAAACAATGAAACA                         ACAGCTTCACGACCACCAGAGCTTACTGGGCCTGGGAAATTGTTGGAAGCT
genomic: CAACAACAATACCCGTCCCACTCCCTCCTGCTCCTGCAAACAATGAAACAgtaaggaaaa ... tttggtttagACAGCTTCACGACCACCAGAGCTTACTGGGCCTGGGAAATTGTTGGAAGCT
EST: gi|169077287|gb|FE485589.1|FE485589
EST:     TGCAAACAATGAAACA                         ACAGCTTCACGACCACCAGAGCTTACTGGGCCTGGAAAATTGTTGGAAGCT
genomic: TGCAAACAATGAAACAgtaaggaaaa ... tttggtttagACAGCTTCACGACCACCAGAGCTTACTGGGCCTGGGAAATTGTTGGAAGCT
EST: gi|169029149|gb|FE439381.1|FE439381
EST:     TGCAAACAATGAAACA                         ACAGCTTCACGACCACCAGAGCTTACTGGGCCTGGGAAATTGTTGGAAGCT
genomic: TGCAAACAATGAAACAgtaaggaaaa ... tttggtttagACAGCTTCACGACCACCAGAGCTTACTGGGCCTGGGAAATTGTTGGAAGCT
EST: gi|169020101|gb|FE430880.1|FE430880
EST:     TGCAAACAATGAAACA                         ACAGCTTCACGACCACCAGAGCTTACTGGGCCTGGGAAATTGTTGGAAGCT
genomic: TGCAAACAATGAAACAgtaaggaaaa ... tttggtttagACAGCTTCACGACCACCAGAGCTTACTGGGCCTGGGAAATTGTTGGAAGCT
EST: gi|169078532|gb|FE490669.1|FE490669
EST:     TCCTGCTCCTGCAAACAATGAAACA                         ACAGCTTCACGACCACCAGAGCTTACTGGGCCTGGGAAATTGTTGGAAGCT
genomic: TCCTGCTCCTGCAAACAATGAAACAgtaaggaaaa ... tttggtttagACAGCTTCACGACCACCAGAGCTTACTGGGCCTGGGAAATTGTTGGAAGCT
EST: gi|169028495|gb|FE439104.1|FE439104
EST:     TCCTGCTCCTGCAAACAATGAAACA                         ACAGCTTCACGACCACCAGAGCTTACTGGGCCTGGGAAATTG-TGGAAGCT
genomic: TCCTGCTCCTGCAAACAATGAAACAgtaaggaaaa ... tttggtttagACAGCTTCACGACCACCAGAGCTTACTGGGCCTGGGAAATTGTTGGAAGCT

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: 141

GACCACGACCTCCAACAACAATACCCGTCCCACTCCCTCCTGCTCCTGCAAACAATGAAACAgtaaggaaaa ... tttggtttagACAGCTTCACGACCACCAGAGCTTACTGGGCCTGGGAAATTGTTGGAAGCTGCTATCGAGGCTGGTGCTGAGGCAATCATAAAAATAAAGGACTCTTTGA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaaaaactcttatatcatgcactgtcgctcctaattttttcatactttggtttagACAGCTTCACGACCACCAGAGCTTACTGGGCCTGGGAAATTGTTGGAAGCTGCTATCGAGGCTGGTGCTGAGGCAATCATAAAAATAAAGGACTCTTTGA
                            tcctaat  putative branch site (score: 141)
                                  ttttttcatacttt  CT-rich tract
                               taattttttcatactt  TA-rich tract