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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatattaccttatctaatattgacttctttttcatactgattttgtggataaccattcttgagagctttgtttcttcgtaggaagttgctgagaatagcaatagtcggatggtttgtggtgtggtcattcggaaaaattgtgagcgattttactcctttctgaatcttactgcacgaattgttatgcagGAAGTTTGGTCTCGATGCCAACACAATTGACTTCATTGGGCATTCTTTGGCGTTGCATCGTGACGATCGTTTCTTGTCTGAGCCAGCGTTGGATACAGTG

Basic information

species Physcomitrella patens
transcript PP1S20_16V6.1
intron # 5
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|162166683|gb|FC342652.1|FC342652
EST:     ACACACGATGGAATGAACTTGCAGACAGTTACAACGAAAGAACTATTCGA                         GAAGTTTGGTCTCGATGCCAACACAATTGACTTCATTGGGCATTCTTTGGC
genomic: ACACACGATGGAATGAACTTGCAGACAGTTACAACGAAAGAACTATTCGAgtatattacc ... tgttatgcagGAAGTTTGGTCTCGATGCCAACACAATTGACTTCATTGGGCATTCTTTGGC
EST: gi|162196487|gb|FC375440.1|FC375440
EST:     ACACACGATGGAATGAACTTGCAGACAGTTACAACGAAAGAACTATTCGA                         GAAGTTTGGTCTCGATGCCAACACAATTGACTTCATTGGGCATTCTTTGGC
genomic: ACACACGATGGAATGAACTTGCAGACAGTTACAACGAAAGAACTATTCGAgtatattacc ... tgttatgcagGAAGTTTGGTCTCGATGCCAACACAATTGACTTCATTGGGCATTCTTTGGC
EST: gi|162180984|gb|FC358638.1|FC358638
EST:     ACACACGATGGAATGAACTTGCAGACAGTTACAACGAAAGAACTATTCGA                         GAAGTTTGGTCTCGATGCCAACACAATTGACTTCATTGGGCATTCTTTGGC
genomic: ACACACGATGGAATGAACTTGCAGACAGTTACAACGAAAGAACTATTCGAgtatattacc ... tgttatgcagGAAGTTTGGTCTCGATGCCAACACAATTGACTTCATTGGGCATTCTTTGGC
EST: gi|100352808|gb|BY945459.1|BY945459
EST:     ACACACGATGGAATGAACTTGCAGACAGTTACAACGAAAGAACTATTCGA                         GAAGTTTGGTCTCGATGCCAACACAATTGACTTCATTGGGCATTCTTTGGC
genomic: ACACACGATGGAATGAACTTGCAGACAGTTACAACGAAAGAACTATTCGAgtatattacc ... tgttatgcagGAAGTTTGGTCTCGATGCCAACACAATTGACTTCATTGGGCATTCTTTGGC
EST: gi|162187203|gb|FC363153.1|FC363153
EST:     ACACACGATGGAATGAACTTGCAGACAGTTACAACGAAAGAACTATTCGA                         GAAGTTTGGTCTCGATGCCAACACAATTGACTTCATTGGGCATTCTTTGGC
genomic: ACACACGATGGAATGAACTTGCAGACAGTTACAACGAAAGAACTATTCGAgtatattacc ... tgttatgcagGAAGTTTGGTCTCGATGCCAACACAATTGACTTCATTGGGCATTCTTTGGC
EST: gi|162229881|gb|FC404334.1|FC404334
EST:     ACACACGATGGAATGAACTTGCAGACAGTTACAACGAAAGAACTATTCGA                         GAAGTTTGGTCTCGATGCCAACACAATTGACTTCATTGGGCATTCTTTGGC
genomic: ACACACGATGGAATGAACTTGCAGACAGTTACAACGAAAGAACTATTCGAgtatattacc ... tgttatgcagGAAGTTTGGTCTCGATGCCAACACAATTGACTTCATTGGGCATTCTTTGGC
EST: gi|208387306|gb|DC933057.1|DC933057
EST:     ACACACGATGGAATGAACTTGCAGACAGTTACAACGAAAGAACTATTCGA                         GAAGTTTGGTCTCGATGCCAACACAATTGACTTCANTGGGCATTCTTTGGC
genomic: ACACACGATGGAATGAACTTGCAGACAGTTACAACGAAAGAACTATTCGAgtatattacc ... tgttatgcagGAAGTTTGGTCTCGATGCCAACACAATTGACTTCATTGGGCATTCTTTGGC
EST: gi|162257732|gb|FC433659.1|FC433659
EST:     ACACACGATGGAATGAACTTGCAGACAGTTACAACGAAAGAACTATTCGA                         GAAGTTTGGTCTCGATGCCAACACAATTGACTTCATTGGGCATTCTTTGGC
genomic: ACACACGATGGAATGAACTTGCAGACAGTTACAACGAAAGAACTATTCGAgtatattacc ... tgttatgcagGAAGTTTGGTCTCGATGCCAACACAATTGACTTCATTGGGCATTCTTTGGC

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: 28

CTAGGAAGTTTTTCATCTTTGTCCAGAACTACGATGAGGCAGATGCTAAAACACACGATGGAATGAACTTGCAGACAGTTACAACGAAAGAACTATTCGAgtatattacc ... tgttatgcagGAAGTTTGGTCTCGATGCCAACACAATTGACTTCATTGGGCATTCTTTGGCGTTGCATCGTGACGATCGTTTCTTGTCTGAGCCAGCGTTGGATACAGTG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaattgtgagcgattttactcctttctgaatcttactgcacgaattgttatgcagGAAGTTTGGTCTCGATGCCAACACAATTGACTTCATTGGGCATTCTTTGGCGTTGCATCGTGACGATCGTTTCTTGTCTGAGCCAGCGTTGGATACAGTG
                             atcttac  putative branch site (score: 28)
                                          aattgttat  TA-rich tract