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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtactctaacgggatcgcggccacaaaaatttcagctctcatggatcaatttccccccagGTGTCGGCTCTAGGTCTGGGATGCATGGGCCTCTCCACCTTCTATGGCACGCCGACGAGCGATGACGCTGGGATCGCGCTCATACACCACGCTTTCAATT

Basic information

species Selaginella moellendorffii
transcript EFJ24149
intron # 1
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|169033794|gb|FE442138.1|FE442138
EST:     CGACGGCTATGGAGTGGAGGCGCACGAAGCTGGGCTCGCAGGGGCTAGAG                         GTGTCGGCTCTAGGTCTGGGATGCATGGGCCTCTCCACCTTCTATGGCACG
genomic: CGACGGCTATGGAGTGGAGGCGCACGAAGCTGGGCTCGCAGGGGCTAGAGgtactctaac ... ttccccccagGTGTCGGCTCTAGGTCTGGGATGCATGGGCCTCTCCACCTTCTATGGCACG
EST: gi|169064038|gb|FE472225.1|FE472225
EST:     GGAGTGGAGGCGCACGAAGCTGGGCTCGCAGGGGCTAGAG                         GTGTCGGCTCTAGGTCTGGGATGCATGGGCCTCTCCACCTTCTATGGCACG
genomic: GGAGTGGAGGCGCACGAAGCTGGGCTCGCAGGGGCTAGAGgtactctaac ... ttccccccagGTGTCGGCTCTAGGTCTGGGATGCATGGGCCTCTCCACCTTCTATGGCACG
EST: gi|169052709|gb|FE463531.1|FE463531
EST:     GGAGTGGAGGCGCACGAAGCTGGGCTCGCAGGGGCTAGAG                         GTGTCGGCTCTAGGTCTGGGATGCATGGGCCTCTCCACCTTCTATGGCACG
genomic: GGAGTGGAGGCGCACGAAGCTGGGCTCGCAGGGGCTAGAGgtactctaac ... ttccccccagGTGTCGGCTCTAGGTCTGGGATGCATGGGCCTCTCCACCTTCTATGGCACG
EST: gi|169060887|gb|FE469282.1|FE469282
EST:     CTATGGAGTGGAGGCGCACGAAGCTGGGCTCGCAGGGGCTAGAG                         GTGTCGGCTCTAGGTCTGGGATGCATGGGCCTCTCCACCTTCTATGGCACG
genomic: CTATGGAGTGGAGGCGCACGAAGCTGGGCTCGCAGGGGCTAGAGgtactctaac ... ttccccccagGTGTCGGCTCTAGGTCTGGGATGCATGGGCCTCTCCACCTTCTATGGCACG
EST: gi|169100364|gb|FE501161.1|FE501161
EST:     GGCGCACGAAGCTGGGCTCGCAGGGGCTAGAG                         GTGTCGGCTCTAGGTCTGGGATGCATGGGCCTCTCCACCTTCTATGGCACG
genomic: GGCGCACGAAGCTGGGCTCGCAGGGGCTAGAGgtactctaac ... ttccccccagGTGTCGGCTCTAGGTCTGGGATGCATGGGCCTCTCCACCTTCTATGGCACG

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: 32 (upstream exon), 35 (downstream exon)
Score: 15

AATTTTGTCTAGAGTATTCAAACAGTCGACGGCTATGGAGTGGAGGCGCACGAAGCTGGGCTCGCAGGGGCTAGAGgtactctaac ... ttccccccagGTGTCGGCTCTAGGTCTGGGATGCATGGGCCTCTCCACCTTCTATGGCACGCCGACGAGCGATGACGCTGGGATCGCGCTCATACACCACGCTTTCAATT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctaacgggatcgcggccacaaaaatttcagctctcatggatcaatttccccccagGTGTCGGCTCTAGGTCTGGGATGCATGGGCCTCTCCACCTTCTATGGCACGCCGACGAGCGATGACGCTGGGATCGCGCTCATACACCACGCTTTCAATT
 ctctaac  putative branch site (score: 15)
                                            tttcccccc  putative PPT
                 acaaaaattt  TA-rich tract