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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgcgtaattagtctctgcttcattcaagcaattaatacgcttatcaatatgttagtgtattagtgtagtatctactctttacttatcttctagatttggtggaggtctacttcctgttgatgtacaaatggtcttccatacctcgttcacaggcgattttgtagctcactatgaggtggattggcagACTCATCGCATCAAGAAGTTTGTACTTCATACCAATTTTCCAGGTCACACGGACTTCAACTGTTATATCAAATGCAACTTCATTATTTATGTTCCCCCAA

Basic information

species Physcomitrella patens
transcript PP1S58_197V6.1
intron # 10
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|208382909|gb|DC928334.1|DC928334
EST:     ATTTTTATAATTATTTCACACGCGGCATTGATATCTTGTTCGATGGTCAG                         ACTCATCGCATCAAGAAGTTTGTACTTCATACCAATTTTCCAGGTCACACG
genomic: ATTTTTATAATTATTTCACACGCGGCATTGATATCTTGTTCGATGGTCAGgtgcgtaatt ... ggattggcagACTCATCGCATCAAGAAGTTTGTACTTCATACCAATTTTCCAGGTCACACG
EST: gi|67726513|gb|BJ976772.1|BJ976772
EST:     ATTTTTATAATTATTTCACACGCGGCATTGATATCTTGTTCGATGGTCAG                         ACTCATCGCATCAAGAAGTTTGTACTTCATACCAATTTTCCAGGTCACACG
genomic: ATTTTTATAATTATTTCACACGCGGCATTGATATCTTGTTCGATGGTCAGgtgcgtaatt ... ggattggcagACTCATCGCATCAAGAAGTTTGTACTTCATACCAATTTTCCAGGTCACACG
EST: gi|6167306|gb|AW145570.1|AW145570
EST:     ATTTTTATAATTATTTCACACGCGGCATTGATATCTTGTTCGATGGTCAG                         ACTCATCGCATCAAGAAGTTTGTACTTCATACCAATTTTCCAGGTCACACG
genomic: ATTTTTATAATTATTTCACACGCGGCATTGATATCTTGTTCGATGGTCAGgtgcgtaatt ... ggattggcagACTCATCGCATCAAGAAGTTTGTACTTCATACCAATTTTCCAGGTCACACG
EST: gi|208370963|gb|DC944338.1|DC944338
EST:     ATTTTTATAATTATTTCACACGCGGCATTGATATCTTGTTCGATGGTCAG                         ACTCATCGCATCAAGAAGTTTGTACTTCATACCAATTTTCCAGGTCACACG
genomic: ATTTTTATAATTATTTCACACGCGGCATTGATATCTTGTTCGATGGTCAGgtgcgtaatt ... ggattggcagACTCATCGCATCAAGAAGTTTGTACTTCATACCAATTTTCCAGGTCACACG
EST: gi|162176258|gb|FC352715.1|FC352715
EST:     TCACACGCGGCATTGATATCTTGTTCGATGGTCAG                         ACTCATCGCATCAAGAAGTTTGTACTTCATACCAATTTTCCAGGTCACACG
genomic: TCACACGCGGCATTGATATCTTGTTCGATGGTCAGgtgcgtaatt ... ggattggcagACTCATCGCATCAAGAAGTTTGTACTTCATACCAATTTTCCAGGTCACACG
EST: gi|37842901|gb|BJ600909.1|BJ600909
EST:     ATTTTTATAATTATTTCACACGCGGCATTGATATCTTGTTCGATGGTCAG                         ACTCATCGCATCAAGAAGTTTGTACTTCATACCAATTTTCCAGGTCACACG
genomic: ATTTTTATAATTATTTCACACGCGGCATTGATATCTTGTTCGATGGTCAGgtgcgtaatt ... ggattggcagACTCATCGCATCAAGAAGTTTGTACTTCATACCAATTTTCCAGGTCACACG
EST: gi|162155578|gb|FC331529.1|FC331529
EST:     ATTTTTATAATTATTTCACACGCGGCATTGATATCTTGTTCGATGGTCAG                         ACTCATCGCATCAAGAAGTTTGTACTTCATACCAATTTTCCAGGTCACACG
genomic: ATTTTTATAATTATTTCACACGCGGCATTGATATCTTGTTCGATGGTCAGgtgcgtaatt ... ggattggcagACTCATCGCATCAAGAAGTTTGTACTTCATACCAATTTTCCAGGTCACACG
EST: gi|37821349|gb|BJ579415.1|BJ579415
EST:     ATTTTTATAATTATTTCACACGCGGCATTGATATCTTGTTCGATGGTCAG                         ACTCATCGCATCAAGAAGTTTGTACTTCATACCAATTTTCCAGGTCACACG
genomic: ATTTTTATAATTATTTCACACGCGGCATTGATATCTTGTTCGATGGTCAGgtgcgtaatt ... ggattggcagACTCATCGCATCAAGAAGTTTGTACTTCATACCAATTTTCCAGGTCACACG

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: 33 (upstream exon), 32 (downstream exon)
Score: 4

GATCCATTCTGCCTCTGATCCAAAACCTCGCACTGCACTCTGTGGTGATTATTTTTATAATTATTTCACACGCGGCATTGATATCTTGTTCGATGGTCAGgtgcgtaatt ... ggattggcagACTCATCGCATCAAGAAGTTTGTACTTCATACCAATTTTCCAGGTCACACGGACTTCAACTGTTATATCAAATGCAACTTCATTATTTATGTTCCCCCAA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttccatacctcgttcacaggcgattttgtagctcactatgaggtggattggcagACTCATCGCATCAAGAAGTTTGTACTTCATACCAATTTTCCAGGTCACACGGACTTCAACTGTTATATCAAATGCAACTTCATTATTTATGTTCCCCCAA
                              agctcac  putative branch site (score: 4)
                       attttgta  TA-rich tract