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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgtcaggtcacctatcgcttgttgttcgtgttcgaacagggcagttgacgcactggtgcaagcggagtatcttatctgaggaaacatcttgggtttgaacagGTGGAGAGGTCATCTGGCTACAACGAGCACAGGCCCCGTCGGCCACCTCCTGACCTTCCTTCATTGCTCTTGAATAGCAGAATTGTGTACATTGGAATGC

Basic information

species Physcomitrella patens
transcript PP1S37_54V6.1
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|18352066|gb|BJ184119.1|BJ184119
EST:     CGTTGTTGGATATTTTGTCGAACCCGGTGATGATGGCAGCTCCAGCTCAN                         GTGGAGAGGTCATCTGGCTACAACGAGCACAGGCCCCGTCGGCCACCTCCT
genomic: CGTTGTTGGATATTTTGTCGAACCCGGTGATGATGGCAGCTCCAGCTCAGgtttgtcagg ... gtttgaacagGTGGAGAGGTCATCTGGCTACAACGAGCACAGGCCCCGTCGGCCACCTCCT




















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: 27 (upstream exon), 9 (downstream exon)
Score: 2

AATGGGGAAAGCTCAATTGGCTGGCGCGAGCGGTGTTTCTGATGGCCCCCCGTTGTTGGATATTTTGTCGAACCCGGTGATGATGGCAGCTCCAGCTCAGgtttgtcagg ... gtttgaacagGTGGAGAGGTCATCTGGCTACAACGAGCACAGGCCCCGTCGGCCACCTCCTGACCTTCCTTCATTGCTCTTGAATAGCAGAATTGTGTACATTGGAATGC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acgcactggtgcaagcggagtatcttatctgaggaaacatcttgggtttgaacagGTGGAGAGGTCATCTGGCTACAACGAGCACAGGCCCCGTCGGCCACCTCCTGACCTTCCTTCATTGCTCTTGAATAGCAGAATTGTGTACATTGGAATGC
 agttgac  putative branch site (score: 2)
                    tatcttat  TA-rich tract