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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgggtcgtctaatatgcttcttcagatcaccttgtcaaattgtagaggtgacatgggtgtcgttgtagtgttccatgcagaaattgtgcctgaatatgaatgtgtttggcagGATGTGTGGGCAGAGTTAGGTCGGCCATGTGGTATTCACCAGAAACAG

Basic information

species Physcomitrella patens
transcript PP1S58_197V6.1
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|208382909|gb|DC928334.1|DC928334
EST:     TGTGGTTTACTGGTGGTGGCCAGCATCTTTTATTCGGTGCATCTCCACAG                         GATGTGTGGGCAGAGTTAGGTCGGCCATGTGGTATTCACCAGAAACAG
genomic: TGTGGTTTACTGGTGGTGGCCAGCATCTTTTATTCGGTGCATCTCCACAGgtgggtcgtc ... tgtttggcagGATGTGTGGGCAGAGTTAGGTCGGCCATGTGGTATTCACCAGAAACAG
EST: gi|67726513|gb|BJ976772.1|BJ976772
EST:     TGGCCAGCATCTTTTATTCGGTGCATCTCCACAG                         GATGTGTGGGCAGAGTTAGGTCGGCCATGTGGTATTCACCAGAAACAG
genomic: TGGCCAGCATCTTTTATTCGGTGCATCTCCACAGgtgggtcgtc ... tgtttggcagGATGTGTGGGCAGAGTTAGGTCGGCCATGTGGTATTCACCAGAAACAG
EST: gi|6167306|gb|AW145570.1|AW145570
EST:     CAGCATCTTTTATTCGGTGCATCTCCACAG                         GATGTGTGGGCAGAGTTAGGTCGGCCATGTGGTATTCACCAGAAACAG
genomic: CAGCATCTTTTATTCGGTGCATCTCCACAGgtgggtcgtc ... tgtttggcagGATGTGTGGGCAGAGTTAGGTCGGCCATGTGGTATTCACCAGAAACAG
EST: gi|67718012|gb|BJ968271.1|BJ968271
EST:     TGTGGTTTACTGGTGGTGGCCAGCATCTTTTATTCGGTGCATCTCCACAG                         GATGTGTGGGCAGAGTTAGGTCGGCCATGTG
genomic: TGTGGTTTACTGGTGGTGGCCAGCATCTTTTATTCGGTGCATCTCCACAGgtgggtcgtc ... tgtttggcagGATGTGTGGGCAGAGTTAGGTCGGCCATGTG

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: 26 (upstream exon), 31 (downstream exon)
Score: 12

TTGGCAGAGGAATTGTGGTTTACTGGTGGTGGCCAGCATCTTTTATTCGGTGCATCTCCACAGgtgggtcgtc ... tgtttggcagGATGTGTGGGCAGAGTTAGGTCGGCCATGTGGTATTCACCAGAAACAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtcgttgtagtgttccatgcagaaattgtgcctgaatatgaatgtgtttggcagGATGTGTGGGCAGAGTTAGGTCGGCCATGTGGTATTCACCAGAAACAG
                                   aatatgaat  TA-rich tract