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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cggtcttacgatagtttgcacttatttcaatgggtaaattgatgtgactccagcgtaataatatttctaaccctgtagcagcattgtttcttctggacagTACATACTGCATGACTGGGACGACGAAAGCTGTATCAAACTTTTGAAGAACTGTCACAAGGTGTTACCTGCAAACGGCAAGGTGATTGCTGTGGACAGCG

Basic information

species Physcomitrella patens
transcript PP1S56_71V6.1
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|162176424|gb|FC353817.1|FC353817
EST:     GAGACATGTTTGAGTCCATCCCATCTGGAGGCGATGCCATCTTCTTGAAG                         TACATACTGCATGACTGGGACGACGAAAGCTGTATCANACTTTTGAAGAAC
genomic: GAGACATGTTTGAGTCCATCCCATCTGGAGGCGATGCCATCTTCTTGAAGgtcagtcctc ... ttctggacagTACATACTGCATGACTGGGACGACGAAAGCTGTATCAAACTTTTGAAGAAC
EST: gi|37843419|gb|BJ601427.1|BJ601427
EST:     GGCGATGCCATCTTCTTGAAG                         TACATACTGCATGACTGGGACGACGAAAGCTGTATCAAACTTTTGAAGAAC
genomic: GGCGATGCCATCTTCTTGAAGgtcagtcctc ... ttctggacagTACATACTGCATGACTGGGACGACGAAAGCTGTATCAAACTTTTGAAGAAC
EST: gi|18334012|gb|BJ166028.1|BJ166028
EST:     GCGATGCCATCTTCTTGAAG                         TACATACTGCATGACTGGGACGACGAAAGCTGTATCAAACTTTTGAAGAAC
genomic: GCGATGCCATCTTCTTGAAGgtcagtcctc ... ttctggacagTACATACTGCATGACTGGGACGACGAAAGCTGTATCAAACTTTTGAAGAAC
EST: gi|162153286|gb|FC329068.1|FC329068
EST:     GAGACATGTTTGAGTCCATCCCATCTGGAGGCGATGCCATCTTCTTGAAG                         TACATACTGCATGACTGGGACGACGAAAGCTGTATCAAACTTTTGAAGAAC
genomic: GAGACATGTTTGAGTCCATCCCATCTGGAGGCGATGCCATCTTCTTGAAGgtcagtcctc ... ttctggacagTACATACTGCATGACTGGGACGACGAAAGCTGTATCAAACTTTTGAAGAAC
EST: gi|162259570|gb|FC435497.1|FC435497
EST:     GAGACATGTTTGAGTCCATCCCATCTGGAGGCGATGCCATCTTCTTGAAG                         TACATACTGCATGACTGGGACGACGAAAGCTGTATCAAACTTTTGAAGAAC
genomic: GAGACATGTTTGAGTCCATCCCATCTGGAGGCGATGCCATCTTCTTGAAGgtcagtcctc ... ttctggacagTACATACTGCATGACTGGGACGACGAAAGCTGTATCAAACTTTTGAAGAAC
EST: gi|37835723|gb|BJ593735.1|BJ593735
EST:     AGGCGATGCCATNTTCTTGAAG                         TACATACTGCATGACTGGGACGACGAAAGCTGTATCAAACTTTTGAAGAAC
genomic: AGGCGATGCCATCTTCTTGAAGgtcagtcctc ... ttctggacagTACATACTGCATGACTGGGACGACGAAAGCTGTATCAAACTTTTGAAGAAC
EST: gi|162244129|gb|FC419806.1|FC419806
EST:     GAGACATGTTTGAGTCCATCCCATCTGGAGGCGATGCCATCTTCTTGAAG                         TACATACTGCATGACTGGGACGACGAAAGCTGTATCAAACTTTTGAAGAAC
genomic: GAGACATGTTTGAGTCCATCCCATCTGGAGGCGATGCCATCTTCTTGAAGgtcagtcctc ... ttctggacagTACATACTGCATGACTGGGACGACGAAAGCTGTATCAAACTTTTGAAGAAC
EST: gi|37837845|gb|BJ595853.1|BJ595853
EST:     TGGAGGCGATGCCATCTTCTTGAAG                         TACATACTGCATGACTGGGACGACGAAAGCTGTATCAAACTTTTGAAGAAC
genomic: TGGAGGCGATGCCATCTTCTTGAAGgtcagtcctc ... ttctggacagTACATACTGCATGACTGGGACGACGAAAGCTGTATCAAACTTTTGAAGAAC
EST: gi|162172204|gb|FC348769.1|FC348769
EST:     GAGACATGTTTGAGTCCATCCCATCTGGAGGCGATGCCATCTTCTTGAAG                         TACATACTGCATGACTGGGACGACGAAAGCTGTATCAAACTTTTGAAGAAC
genomic: GAGACATGTTTGAGTCCATCCCATCTGGAGGCGATGCCATCTTCTTGAAGgtcagtcctc ... ttctggacagTACATACTGCATGACTGGGACGACGAAAGCTGTATCAAACTTTTGAAGAAC
EST: gi|37843068|gb|BJ601076.1|BJ601076
EST:     GAGACATGTTTGAGTCCATCCCATCTGGAGGCGATGCCATCTTCTTGAAG                         TACATACTGCATGACTGGGACGACGAAAGCTGTATCAAACTTTTGAAGAAC
genomic: GAGACATGTTTGAGTCCATCCCATCTGGAGGCGATGCCATCTTCTTGAAGgtcagtcctc ... ttctggacagTACATACTGCATGACTGGGACGACGAAAGCTGTATCAAACTTTTGAAGAAC

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: 34 (upstream exon), 35 (downstream exon)
Score: 7

GAGTGGAGCACATGAGTGGAGACATGTTTGAGTCCATCCCATCTGGAGGCGATGCCATCTTCTTGAAGgtcagtcctc ... ttctggacagTACATACTGCATGACTGGGACGACGAAAGCTGTATCAAACTTTTGAAGAACTGTCACAAGGTGTTACCTGCAAACGGCAAGGTGATTGCTGTGGACAGCG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gactccagcgtaataatatttctaaccctgtagcagcattgtttcttctggacagTACATACTGCATGACTGGGACGACGAAAGCTGTATCAAACTTTTGAAGAACTGTCACAAGGTGTTACCTGCAAACGGCAAGGTGATTGCTGTGGACAGCG
                   ttctaac  putative branch site (score: 7)
                                      ttgtttcttct  putative PPT
          taataatatttctaa  TA-rich tract