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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGGACAATCACTTGTGCAAgtaagtttccatacacattcagtgttaatagaatacctaagaaatttaagatcatcaaattttcttgtgactttactgcacgtttataaccgtaatttatttttctcgacatagcacgtactttgcgtttaagaaaacttcacgactgagaatgcctagctgaggtgattgatttggaaatcttgcgacacag

Basic information

species Physcomitrella patens
transcript PP1S52_245V6.1
intron # 2
splice site 5'
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|18348574|gb|BJ180623.1|BJ180623
EST:     CAGCAGGGGACAATCACTTGTGCAA                         GCATGTAGATTGCAGTCAGCTCGCAAATTCTCTGGGAAGGATATCAGGTTC
genomic: CAGCAGGGGACAATCACTTGTGCAAgtaagtttcc ... tgcgacacagGCATGTAGATTGCAGTCAGCTCGCAAATTCTCTGGGAAGGATATCAGGTTC
EST: gi|18354034|gb|BJ186089.1|BJ186089
EST:     CAGCAGGGGACAATCACTTGTGCAA                         GCATGTAGATTGCAGTCAGCTCGCAAATTCTCTGGGAAGGATATCAGGTTC
genomic: CAGCAGGGGACAATCACTTGTGCAAgtaagtttcc ... tgcgacacagGCATGTAGATTGCAGTCAGCTCGCAAATTCTCTGGGAAGGATATCAGGTTC
EST: gi|162277342|gb|FC453148.1|FC453148
EST:     CAGCAGGGGACAATCACTTGTGCAA                         GCATGTAGATTGCAGTCAGCTCGCAAATTCTCTGGGAAGGATATCAGGTTC
genomic: CAGCAGGGGACAATCACTTGTGCAAgtaagtttcc ... tgcgacacagGCATGTAGATTGCAGTCAGCTCGCAAATTCTCTGGGAAGGATATCAGGTTC
EST: gi|18373050|gb|BJ204652.1|BJ204652
EST:     CAGCAGGGGACAATCACTTGTGCAA                         GCATGTAGATTGCAGTCAGCTCGCAAATTCTCTGGGAAGGATATCAGGTTC
genomic: CAGCAGGGGACAATCACTTGTGCAAgtaagtttcc ... tgcgacacagGCATGTAGATTGCAGTCAGCTCGCAAATTCTCTGGGAAGGATATCAGGTTC

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: 29 (upstream exon), 31 (downstream exon)
Score: 6

GGGACAATCACTTGTGCAAgtaagtttcc ... tgcgacacagGCATGTAGATTGCAGTCAGCTCGCAAATTCTCTGGGAAGGATATCAGGTTCGGAGTTGAGGCTCGAGCTCTTATGTTGCAAGGTGTGGAGCAACTTGCAG




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