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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ccactcgtagatgtatgaactcgcacagaaacaaagtacttatgatcacttgacttgcggttctcaacctaatgtgttgtatgttgtgtttactttacagGGGCCGCGCACTAGTACAA

Basic information

species Physcomitrella patens
transcript PP1S149_289V6.1
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|162276485|gb|FC452683.1|FC452683
EST:     TCGGCTACCATGTATCGTGCGGCGGCTACGTTGTCGGCCCGTATCAACAG                         GGGCCGCGCACTAGTACAA
genomic: TCGGCTACCATGTATCGTGCGGCGGCTACGTTGTCGGCCCGTATCAACAGgtgctcttct ... tactttacagGGGCCGCGCACTAGTACAA
EST: gi|208390363|gb|DC933408.1|DC933408
EST:     TCGGCTACCATGTATCGTGCGGCGGCTACGTTGTCGGCCCGTATCAACAG                         GGGCCGCGCACTAGTACAA
genomic: TCGGCTACCATGTATCGTGCGGCGGCTACGTTGTCGGCCCGTATCAACAGgtgctcttct ... tactttacagGGGCCGCGCACTAGTACAA

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), 23 (downstream exon)
Score: 4

GTCGGTGTGGGTGGTATCGGAGGTTTAAGGTTTAAGAAAAAAACAGGGGTTCGGCTACCATGTATCGTGCGGCGGCTACGTTGTCGGCCCGTATCAACAGgtgctcttct ... tactttacagGGGCCGCGCACTAGTACAA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcacttgacttgcggttctcaacctaatgtgttgtatgttgtgtttactttacagGGGCCGCGCACTAGTACAA
                     acctaat  putative branch site (score: 4)
                                           tttacttt  putative PPT
                                           tttacttta  TA-rich tract