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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtattcgcatccgtctatttttttaggtttactgtaaatttggagttaaattttgaagttggtatatgcatcgtgtacatatagagaaactcgctctgcatatttctaggtttagaggattcaagtgaccgagcaccaatgttgatgtctctacgcggatgatatgcagGCAGATTTTGTACTCAACAAAGTTTGTAAGATCTCTGGCGATTCGCTTTGCAGAAATGAGGACATCTCATGG

Basic information

species Physcomitrella patens
transcript PP1S6_218V6.1
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|162201494|gb|FC378234.1|FC378234
EST:     GCGCTCTATGTGTTCCTGACAAACAGATTGATCGAAATGCTCAAAACCTG                         GCAGATTTTGTACTCAACAAAGTTTGTAAGATCTCTGGCGATTCGCTTTGC
genomic: GCGCTCTATGTGTTCCTGACAAACAGATTGATCGAAATGCTCAAAACCTGgtattcgcat ... tgatatgcagGCAGATTTTGTACTCAACAAAGTTTGTAAGATCTCTGGCGATTCGCTTTGC
EST: gi|100352152|gb|BY983062.1|BY983062
EST:     GCGCTCTATGTGTTCCTGACAAACAGATTGATCGAAATGCTCAAAACCTG                         GCAGATTTTGTACTCCACAAAATTTTGTA-GATCTCTGGCGATTCGCTTTG
genomic: GCGCTCTATGTGTTCCTGACAAACAGATTGATCGAAATGCTCAAAACCTGgtattcgcat ... tgatatgcagGCAGATTTTGTACTCAACAAAGTTT-GTAAGATCTCTGGCGATTCGCTTTG

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: 35 (upstream exon), 35 (downstream exon)
Score: 13

GATCTGTCGGGGCGGAGAATTGCGCTGTATTCCAGGTTTTCGACGTCAAGGCGCTCTATGTGTTCCTGACAAACAGATTGATCGAAATGCTCAAAACCTGgtattcgcat ... tgatatgcagGCAGATTTTGTACTCAACAAAGTTTGTAAGATCTCTGGCGATTCGCTTTGCAGAAATGAGGACATCTCATGG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaggattcaagtgaccgagcaccaatgttgatgtctctacgcggatgatatgcagGCAGATTTTGTACTCAACAAAGTTTGTAAGATCTCTGGCGATTCGCTTTGCAGAAATGAGGACATCTCATGG
                         tgttgat  putative branch site (score: 13)
                                            atgatat  TA-rich tract