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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CGCCATGTCTGTTCCTGCATCGGAGGATGCTTCCGCTGCGGCGATTGAGCAGCTGTATCGGTTCGGGGAGAGCCTGAACGAGTCCAAGGATAAGTCGAAGgtgtgtgtgtgtgtgtgctttgcctcttttgttacattagtttttatgtgtaggaagtggagttttggggatgggttggtagcgctcggattgtggttggggtgatgcaggtcattttgtaattactttttttgggtgtgagatgtgtttcatttgagtggttgggtgttgtgagtag

Basic information

species Physcomitrella patens
transcript PP1S47_196V6.1
intron # 1
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|18355356|gb|BJ187415.1|BJ187415
EST:     AGCTGTATCGGTTCGGGGAGAGCCTGAACGAGTCCAAGGATAAGTCGAAG                         AATGAAGCAGATTATCTGGGAATTATTGCTGCGGCGAAAGGAAGCGCGAAG
genomic: AGCTGTATCGGTTCGGGGAGAGCCTGAACGAGTCCAAGGATAAGTCGAAGgtgtgtgtgt ... ttgtgagtagAATGAAGCAGATTATCTGGGAATTATTGCTGCGGCGAAAGGAAGCGCGAAG
EST: gi|100361575|gb|BY984075.1|BY984075
EST:     AGCTGTATCGGTTCGGGGAGAGCCTGAACGAGTCCAAGGATAAGTCGAAG                         AATGAAGCAGATTATCTGGGAATTATTGCTGCGGCGAAAGGAAGCGCGAAG
genomic: AGCTGTATCGGTTCGGGGAGAGCCTGAACGAGTCCAAGGATAAGTCGAAGgtgtgtgtgt ... ttgtgagtagAATGAAGCAGATTATCTGGGAATTATTGCTGCGGCGAAAGGAAGCGCGAAG
EST: gi|18345792|gb|BJ177835.1|BJ177835
EST:     AGCTGTATCGGTTCGGGGAGAGCCTGAACGAGTCCAAGGATAAGTCGAAG                         AATGAAGCAGATTATCTGGGAATTATTGCTGCGGCGAAAGGAAGCGCGAAG
genomic: AGCTGTATCGGTTCGGGGAGAGCCTGAACGAGTCCAAGGATAAGTCGAAGgtgtgtgtgt ... ttgtgagtagAATGAAGCAGATTATCTGGGAATTATTGCTGCGGCGAAAGGAAGCGCGAAG
EST: gi|18326192|gb|BJ158191.1|BJ158191
EST:     AGCTGTATCGGTTCGGGGAGAGCCTGAACGAGTCCAAGGATAAGTCGAAG                         AATGAAGCAGATTATCTGGGAATTATTGCTGCGGCGAAAGGAAGCGCGAAG
genomic: AGCTGTATCGGTTCGGGGAGAGCCTGAACGAGTCCAAGGATAAGTCGAAGgtgtgtgtgt ... ttgtgagtagAATGAAGCAGATTATCTGGGAATTATTGCTGCGGCGAAAGGAAGCGCGAAG
EST: gi|208383270|gb|DC907244.1|DC907244
EST:     AGCTGTATCGGTTCGGGGAGAGCCTGAACGAGTCCAAGGATAAGTCGAAG                         AATGAAGCAGATTATCTGGGAATTATTGCTGCGGCGAAAGGAAGCGCGAAG
genomic: AGCTGTATCGGTTCGGGGAGAGCCTGAACGAGTCCAAGGATAAGTCGAAGgtgtgtgtgt ... ttgtgagtagAATGAAGCAGATTATCTGGGAATTATTGCTGCGGCGAAAGGAAGCGCGAAG
EST: gi|162177459|gb|FC353720.1|FC353720
EST:     AGCTGTATCGGTTCGGGGAGAGCCTGAACGAGTCCAAGGATAAGTCGAAG                         AATGAAGCAGATTATCTGGGAATTATTGCTGCGGCGAAAGGAAGCGCGAAG
genomic: AGCTGTATCGGTTCGGGGAGAGCCTGAACGAGTCCAAGGATAAGTCGAAGgtgtgtgtgt ... ttgtgagtagAATGAAGCAGATTATCTGGGAATTATTGCTGCGGCGAAAGGAAGCGCGAAG
EST: gi|18325198|gb|BJ157194.1|BJ157194
EST:     AGCTGTATCGGTTCGGGGAGAGCCTGAACGAGTCCAAGGATAAGTCGAAG                         AATGAAGCAGATTATCTGGGAATTATTGCTGCGGCGAAAGGAAGCGCGAAG
genomic: AGCTGTATCGGTTCGGGGAGAGCCTGAACGAGTCCAAGGATAAGTCGAAGgtgtgtgtgt ... ttgtgagtagAATGAAGCAGATTATCTGGGAATTATTGCTGCGGCGAAAGGAAGCGCGAAG
EST: gi|100363091|gb|BY984352.1|BY984352
EST:     AGCTGTATCGGTTCGGGGAGAGCCTGAACGAGTCCAAGGATAAGTCGAAG                         AATGAAGCAGATTATCTGGGAATTATTGCTGCGGCGAAAGGAAGCGCGAAG
genomic: AGCTGTATCGGTTCGGGGAGAGCCTGAACGAGTCCAAGGATAAGTCGAAGgtgtgtgtgt ... ttgtgagtagAATGAAGCAGATTATCTGGGAATTATTGCTGCGGCGAAAGGAAGCGCGAAG
EST: gi|100386966|gb|BY988235.1|BY988235
EST:     AGCTGTATCGGTTCGGGGAGAGCCTGAACGAGTCCAAGGATAAGTCGAAG                         AATGAAGCAGATTATCTGGGAATTATTGCTGCGGCGAAAGGAAGCGCGAAG
genomic: AGCTGTATCGGTTCGGGGAGAGCCTGAACGAGTCCAAGGATAAGTCGAAGgtgtgtgtgt ... ttgtgagtagAATGAAGCAGATTATCTGGGAATTATTGCTGCGGCGAAAGGAAGCGCGAAG
EST: gi|18325679|gb|BJ157676.1|BJ157676
EST:     AGCTGTATCGGTTCGGGGAGAGCCTGAACGAGTCCAAGGATAAGTCGAAG                         AATGAAGCAGATTATCTGGGAATTATTGCTGCGGCGAAAGGAAGCGCGAAG
genomic: AGCTGTATCGGTTCGGGGAGAGCCTGAACGAGTCCAAGGATAAGTCGAAGgtgtgtgtgt ... ttgtgagtagAATGAAGCAGATTATCTGGGAATTATTGCTGCGGCGAAAGGAAGCGCGAAG
EST: gi|18352423|gb|BJ184477.1|BJ184477
EST:     AGCTGTATCGGTTCGGGGAGAGCCTGAACGAGTCCAAGGATAAGTCGAAG                         AATGAAGCAGATTATCTGGGAATTATTGCTGCGGCGAAAGGAAGCGCGAAG
genomic: AGCTGTATCGGTTCGGGGAGAGCCTGAACGAGTCCAAGGATAAGTCGAAGgtgtgtgtgt ... ttgtgagtagAATGAAGCAGATTATCTGGGAATTATTGCTGCGGCGAAAGGAAGCGCGAAG
EST: gi|100359470|gb|BY984270.1|BY984270
EST:     AGCTGTATCGGTTCGGGGAGAGCCTGAACGAGTCCAAGGATAAGTCGAAG                         AATGAAGCAGATTATCTGGGAATTATTGCTGCGGCGAAAGGAAGCGCGAAG
genomic: AGCTGTATCGGTTCGGGGAGAGCCTGAACGAGTCCAAGGATAAGTCGAAGgtgtgtgtgt ... ttgtgagtagAATGAAGCAGATTATCTGGGAATTATTGCTGCGGCGAAAGGAAGCGCGAAG

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), 33 (downstream exon)
Score: 19

CGCCATGTCTGTTCCTGCATCGGAGGATGCTTCCGCTGCGGCGATTGAGCAGCTGTATCGGTTCGGGGAGAGCCTGAACGAGTCCAAGGATAAGTCGAAGgtgtgtgtgt ... ttgtgagtagAATGAAGCAGATTATCTGGGAATTATTGCTGCGGCGAAAGGAAGCGCGAAGTCGAAGCAGCTAGCCGCACAGCTCATCCCTCGATTTTTCAAGCATTTTC




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