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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaataaaatccttagtattccgggttgaagtcgatacttgagatgagtgaggttcttttctctacctctgagaatgtaattgcgttataaatcatgaccttggaagtgattgaacacagGTGCTGATAACAAGGAGCGTTTGCTGCGTCACGGCCGCACTTCACACATAACAGTCGTCGTCCGTGACAAAGGGTTTGGAACTGTGGAAATAGACAAAGG

Basic information

species Physcomitrella patens
transcript PP1S48_250V6.1
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|162198725|gb|FC374832.1|FC374832
EST:     TGGAGTGTTTCATCCTGGAGCGTTTTCAGCATTCCACGCATGGGGCTCCG                         GTGCTGATAACAAGGAGCGTTTGCTGCGTCACGGCCGCACTTCACACATAA
genomic: TGGAGTGTTTCATCCTGGAGCGTTTTCAGCATTCCACGCATGGGGCTCCGgtaataaaat ... ttgaacacagGTGCTGATAACAAGGAGCGTTTGCTGCGTCACGGCCGCACTTCACACATAA
EST: gi|37823578|gb|BJ581644.1|BJ581644
EST:     TGGAGTGTTTCATCCTGGAGCGTTTTCAGCATTCCACGCATGGGGCTCCG                         GTGCTGATAACAAGGAGCGTTTGCTGCGTCACGGCCGCACTTCACACATAA
genomic: TGGAGTGTTTCATCCTGGAGCGTTTTCAGCATTCCACGCATGGGGCTCCGgtaataaaat ... ttgaacacagGTGCTGATAACAAGGAGCGTTTGCTGCGTCACGGCCGCACTTCACACATAA
EST: gi|162225836|gb|FC402128.1|FC402128
EST:     TGGAGTGTTTCATCCTGGAGCGTTTTCAGCATTCCACGCATGGGGCTCCG                         GTGCTGATAACAAGGAGCGTTTGCTGCGTCACGGCCGCACTTCACACATAA
genomic: TGGAGTGTTTCATCCTGGAGCGTTTTCAGCATTCCACGCATGGGGCTCCGgtaataaaat ... ttgaacacagGTGCTGATAACAAGGAGCGTTTGCTGCGTCACGGCCGCACTTCACACATAA
EST: gi|162160718|gb|FC336422.1|FC336422
EST:     TGGAGTGTTTCATCCTGGAGCGTTTTCAGCATTCCACGCATGGGGCTCCG                         GTGCTGATAACAAGGAGCGTTTGNTGCGTCACGGCCGCACTTCACACATAA
genomic: TGGAGTGTTTCATCCTGGAGCGTTTTCAGCATTCCACGCATGGGGCTCCGgtaataaaat ... ttgaacacagGTGCTGATAACAAGGAGCGTTTGCTGCGTCACGGCCGCACTTCACACATAA
EST: gi|162256706|gb|FC433224.1|FC433224
EST:     TGGAGTGTTTCATCCTGGAGCGTTTTCAGCATTCCACGCATGGGGCTCCG                         GTGCTGATAACAAGGAGCGTTTGCTGCGTCACGGCCGCACTTCACACATAA
genomic: TGGAGTGTTTCATCCTGGAGCGTTTTCAGCATTCCACGCATGGGGCTCCGgtaataaaat ... ttgaacacagGTGCTGATAACAAGGAGCGTTTGCTGCGTCACGGCCGCACTTCACACATAA

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: 24 (upstream exon), 33 (downstream exon)
Score: 2

GCGCCTGTGAATTTTAGGAAACCCACCGAGTATGGAGGTCTTCTCGAAACTGGAGTGTTTCATCCTGGAGCGTTTTCAGCATTCCACGCATGGGGCTCCGgtaataaaat ... ttgaacacagGTGCTGATAACAAGGAGCGTTTGCTGCGTCACGGCCGCACTTCACACATAACAGTCGTCGTCCGTGACAAAGGGTTTGGAACTGTGGAAATAGACAAAGG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cctctgagaatgtaattgcgttataaatcatgaccttggaagtgattgaacacagGTGCTGATAACAAGGAGCGTTTGCTGCGTCACGGCCGCACTTCACACATAACAGTCGTCGTCCGTGACAAAGGGTTTGGAACTGTGGAAATAGACAAAGG
                    ttataaatcat  TA-rich tract