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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaccacacttgtccctcattttggcaaggtttgaatgaatcgtagttgtgtcttatgcacatttacttcgtttcaatttgaatttaacatgattctttagcttatagagacaaggctcgtctttctgatacatgaaaacctgaggtctcattcctcagGTACAATGTCGTTGGGCAATGGGCGGTGACAACTAGCGTAGACTTCTCGTTGGCCCAACTGATAGCGGTCATGGTTCTTCTTGGCACCGGCGGGGCAAAT

Basic information

species Physcomitrella patens
transcript PP1S47_191V6.1
intron # 3
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|100446803|gb|CJ971102.1|CJ971102
EST:     CAATTAGCTGGTCCAAGATGGGGCCCCTTTGCATCCTGGATTACTGGCTG                         GTACAATGTCGTTGGGCAATGGGCGGTGACAACTAGCGTAGACTTCTCGTT
genomic: CAATTAGCTGGTCCAAGATGGGGCCCCTTTGCATCCTGGATTACTGGCTGgtaccacact ... cattcctcagGTACAATGTCGTTGGGCAATGGGCGGTGACAACTAGCGTAGACTTCTCGTT
EST: gi|100371010|gb|BY985893.1|BY985893
EST:     CAATTAGCTGGTCCAAGATGGGGCCCCTTTGCATCCTGGATTACTGGCTG                         GTACAATGTCGTTGGGCAATGGGCGGTGACAACTAGCGTAGACTTCTCG
genomic: CAATTAGCTGGTCCAAGATGGGGCCCCTTTGCATCCTGGATTACTGGCTGgtaccacact ... cattcctcagGTACAATGTCGTTGGGCAATGGGCGGTGACAACTAGCGTAGACTTCTCG
EST: gi|162279639|gb|FC455885.1|FC455885
EST:     CAATTAGCTGGTCCAAGATGGGGCCCCTTTGCATCCTGGATTACTGGCTG                         GTACAATGTCGTTGGGCAATGGGCGGTGACAACTAGCGTAGACTTCTCGTT
genomic: CAATTAGCTGGTCCAAGATGGGGCCCCTTTGCATCCTGGATTACTGGCTGgtaccacact ... cattcctcagGTACAATGTCGTTGGGCAATGGGCGGTGACAACTAGCGTAGACTTCTCGTT

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: 21 (upstream exon), 15 (downstream exon)
Score: 1

AGATTTGCTCAGCATTCCCAACATCAGGAGGGCTTTATTACTGGAGTTCACAATTAGCTGGTCCAAGATGGGGCCCCTTTGCATCCTGGATTACTGGCTGgtaccacact ... cattcctcagGTACAATGTCGTTGGGCAATGGGCGGTGACAACTAGCGTAGACTTCTCGTTGGCCCAACTGATAGCGGTCATGGTTCTTCTTGGCACCGGCGGGGCAAAT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atagagacaaggctcgtctttctgatacatgaaaacctgaggtctcattcctcagGTACAATGTCGTTGGGCAATGGGCGGTGACAACTAGCGTAGACTTCTCGTTGGCCCAACTGATAGCGGTCATGGTTCTTCTTGGCACCGGCGGGGCAAAT
                   ttctgat  putative branch site (score: 1)
                                          tctcattcctc  putative PPT
                            atgaaaa  TA-rich tract