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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaactgtttttactctgtgcttgttagcaatctaaattactatcttgtgtgacagTATGCATTGCGGAAGCTGTATCACGAAAGCCCTCGTCTCATTGCTGTTCTCTACACATCACCAACGTGTGGCCCTTGCAGAACACTAAAGCCAATCTTCA

Basic information

species Selaginella moellendorffii
transcript EFJ06429
intron # 8
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|169063332|gb|FE472166.1|FE472166
EST:     AGGATGTCGAGATGGGATTTGATATCACTGCGACCAAGCACAAAGGCCAG                         TATGCATTGCGGAAGCTGTATCACGAAAGCCCTCGTCTCATTGCTGTTCTC
genomic: AGGATGTCGAGATGGGATTTGATATCACTGCGACCAAGCACAAAGGCCAGgtaaactgtt ... tgtgtgacagTATGCATTGCGGAAGCTGTATCACGAAAGCCCTCGTCTCATTGCTGTTCTC
EST: gi|169021677|gb|FE428894.1|FE428894
EST:     AGGATGTCGAGATGGGATTCGATATCACTGCGACCAAGCACAAAGGCCAG                         TATGCATTGCGGAAGCTGTACCACGAAAGCCCTCGTCTCATTGCTGTTCTC
genomic: AGGATGTCGAGATGGGATTTGATATCACTGCGACCAAGCACAAAGGCCAGgtaaactgtt ... tgtgtgacagTATGCATTGCGGAAGCTGTATCACGAAAGCCCTCGTCTCATTGCTGTTCTC
EST: gi|169031595|gb|FE439060.1|FE439060
EST:     AGGATGTCGAGATGGGATTTGATATCACTGCGACCAAGCACAAAGGCCAG                         TATGCATTGCGGAAGCTGTATCACGAAAGCCCTCGTCTCATTGCTGTTCTC
genomic: AGGATGTCGAGATGGGATTTGATATCACTGCGACCAAGCACAAAGGCCAGgtaaactgtt ... tgtgtgacagTATGCATTGCGGAAGCTGTATCACGAAAGCCCTCGTCTCATTGCTGTTCTC

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: 30 (upstream exon), 32 (downstream exon)
Score: 9

CCAAAACAGGAAGAAACTAAGAAGGAGCTCACAAGCGAGGATGTCGAGATGGGATTTGATATCACTGCGACCAAGCACAAAGGCCAGgtaaactgtt ... tgtgtgacagTATGCATTGCGGAAGCTGTATCACGAAAGCCCTCGTCTCATTGCTGTTCTCTACACATCACCAACGTGTGGCCCTTGCAGAACACTAAAGCCAATCTTCA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaactgtttttactctgtgcttgttagcaatctaaattactatcttgtgtgacagTATGCATTGCGGAAGCTGTATCACGAAAGCCCTCGTCTCATTGCTGTTCTCTACACATCACCAACGTGTGGCCCTTGCAGAACACTAAAGCCAATCTTCA
                             atctaaa  putative branch site (score: 9)
                                       ctatctt  putative PPT
                            aatctaaattactat  TA-rich tract