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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtcaagcttggttctctccttggttccctagcttataactttgctcgatcttgggtctctagcttataacgtttgctcgatcttccagGATCACTTTCTTCTTCGCTTTCATCCTGCTCGTCGTGGGAGCAAGCTTGAATCAGCGCCACCAGGACGATCACTGGTTCACTGGCCAGTGCTTCGTCGTC

Basic information

species Selaginella moellendorffii
transcript EFJ19063
intron # 2
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|169056931|gb|FE465469.1|FE465469
EST:     TCGTTCGTTTCCATGATCCGGCTCGCAACTTTGAGCTTGATCGCCTCCTG                         GATCACTTTCTTCTTCGCTTTCATCCTGCTCGTCGTGGGAGCAAGCTTGAA
genomic: TCGTTCGTTTCCATGATCCGGCTCGCAACTTTGAGCTTGATCGCCTCCTGgtaagtcaag ... gatcttccagGATCACTTTCTTCTTCGCTTTCATCCTGCTCGTCGTGGGAGCAAGCTTGAA
EST: gi|169056930|gb|FE465468.1|FE465468
EST:     TCGTTCGTTTCCATGATCCGGCTCGCAACTTTGAGCTTGATCGCCTCCTG                         GATCACTTTCTTCTTCGCTTTCATCCTGCTCGTCGTGGGAGCAAGCTTGAA
genomic: TCGTTCGTTTCCATGATCCGGCTCGCAACTTTGAGCTTGATCGCCTCCTGgtaagtcaag ... gatcttccagGATCACTTTCTTCTTCGCTTTCATCCTGCTCGTCGTGGGAGCAAGCTTGAA
EST: gi|169062191|gb|FE469198.1|FE469198
EST:     TCGTTCGTTTCCATGATCCGGCTCGCAACTTTGAGCTTGATCGCCTCCTG                         GATCACTTTCTTCTTCGCTTTCATCCTGCTCGTCGTGGGAGCAAGCTTGAA
genomic: TCGTTCGTTTCCATGATCCGGCTCGCAACTTTGAGCTTGATCGCCTCCTGgtaagtcaag ... gatcttccagGATCACTTTCTTCTTCGCTTTCATCCTGCTCGTCGTGGGAGCAAGCTTGAA
EST: gi|169114521|gb|FE516591.1|FE516591
EST:     TCGTTCGTTTCCATGATCCGGCTCGCAACTTTGAGCTTGATCGCCTCCTG                         GATCACTTTCTTCTTCGCTTTCATCCTGCTCGTCGTGGGAGCAAGCTTGAA
genomic: TCGTTCGTTTCCATGATCCGGCTCGCAACTTTGAGCTTGATCGCCTCCTGgtaagtcaag ... gatcttccagGATCACTTTCTTCTTCGCTTTCATCCTGCTCGTCGTGGGAGCAAGCTTGAA
EST: gi|169104530|gb|FE508130.1|FE508130
EST:     TCGTTCGTTTCCATGATCCGGCTCGCAACTTTGAGCTTGATCGCCTCCTG                         GATCACTTTCTTCTTCGCTTTCATCCTGCTCGTCGTGGGAGCAAGCTTGAA
genomic: TCGTTCGTTTCCATGATCCGGCTCGCAACTTTGAGCTTGATCGCCTCCTGgtaagtcaag ... gatcttccagGATCACTTTCTTCTTCGCTTTCATCCTGCTCGTCGTGGGAGCAAGCTTGAA
EST: gi|169058254|gb|FE464994.1|FE464994
EST:     TCGTTCGTTTCCATGATCCGGCTCGCAACTTTGAGCTTGATCGCCTCCTG                         GATCACTTTCTTCTTCGCTTTCATCCTGCTCGTCGTGGGAGCAAGCTTGAA
genomic: TCGTTCGTTTCCATGATCCGGCTCGCAACTTTGAGCTTGATCGCCTCCTGgtaagtcaag ... gatcttccagGATCACTTTCTTCTTCGCTTTCATCCTGCTCGTCGTGGGAGCAAGCTTGAA
EST: gi|169108573|gb|FE510788.1|FE510788
EST:     TCGTTCGTTTCCATGATCCGGCTCGCAACTTTGAGCTTGATCGCCTCCTG                         GATCACTTTCTTCTTCGCTTTCATCCTGCTCGTCGTGGGAGCAAGCTTGAA
genomic: TCGTTCGTTTCCATGATCCGGCTCGCAACTTTGAGCTTGATCGCCTCCTGgtaagtcaag ... gatcttccagGATCACTTTCTTCTTCGCTTTCATCCTGCTCGTCGTGGGAGCAAGCTTGAA
EST: gi|169075536|gb|FE482546.1|FE482546
EST:     TCGTTCGTTTCCATGATCCGGCTCGCAACTTTGAGCTTGATCGCCTCCTG                         GATCACTTTCTTCTTCGCTTTCATCCTGCTCGTCGTGGGAGCAAGCTTGAA
genomic: TCGTTCGTTTCCATGATCCGGCTCGCAACTTTGAGCTTGATCGCCTCCTGgtaagtcaag ... gatcttccagGATCACTTTCTTCTTCGCTTTCATCCTGCTCGTCGTGGGAGCAAGCTTGAA
EST: gi|169108574|gb|FE510789.1|FE510789
EST:     TCGTTCGTTTCCATGATCCGGCTCGCAACTTTGAGCTTGATCGCCTCCTG                         GATCACTTTCTTCTTCGCTTTCATCCTGCTCGTCGTGGGAGCAAGCTTGAA
genomic: TCGTTCGTTTCCATGATCCGGCTCGCAACTTTGAGCTTGATCGCCTCCTGgtaagtcaag ... gatcttccagGATCACTTTCTTCTTCGCTTTCATCCTGCTCGTCGTGGGAGCAAGCTTGAA

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), 32 (downstream exon)
Score: 8

TCGTTAACGTCTTTGGCGGCTGCATTTGCTGCGAGAGGAGATCGAGCTCCTCGTTCGTTTCCATGATCCGGCTCGCAACTTTGAGCTTGATCGCCTCCTGgtaagtcaag ... gatcttccagGATCACTTTCTTCTTCGCTTTCATCCTGCTCGTCGTGGGAGCAAGCTTGAATCAGCGCCACCAGGACGATCACTGGTTCACTGGCCAGTGCTTCGTCGTC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tataactttgctcgatcttgggtctctagcttataacgtttgctcgatcttccagGATCACTTTCTTCTTCGCTTTCATCCTGCTCGTCGTGGGAGCAAGCTTGAATCAGCGCCACCAGGACGATCACTGGTTCACTGGCCAGTGCTTCGTCGTC
                              ttataac  putative branch site (score: 8)
                                               tcttcc  putative PPT
                              ttataa  TA-rich tract