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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttggttccattaccttgcatcgttttgtgccatgtcgtcgacctggtttctggaactggagttgcgggaagctggattggaggagacagtgaagttgctttttggtcgagggggccactgtatcatgtactgtccgcatggtttcggcaacttgccttgagattaacggcgtatttgcgcttgaatgatatgtgcagGGGAAAGATTATCAGACTCAATTACAGCTAGGCAACAATGCTTTTTACGGGTTCAATTATATTCAG

Basic information

species Physcomitrella patens
transcript PP1S367_8V6.1
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|162208677|gb|FC385074.1|FC385074
EST:     TTACAAATGAACCGCACTTTTCACAAGGAATGTTCCATTTCGACTACAGG                         GGGAAAGATTATCAGACTCAATTACAGCTAGGCAACAATGCTTTTTACGGG
genomic: TTACAAATGAACCGCACTTTTCACAAGGAATGTTCCATTTCGACTACAGGgttggttcca ... atatgtgcagGGGAAAGATTATCAGACTCAATTACAGCTAGGCAACAATGCTTTTTACGGG
EST: gi|208398286|gb|DC912299.1|DC912299
EST:     TTACAAATGAACCGCACTTTTCACAAGGAATGTTCCATTTCGACTACAGG                         GGGAAAGATTATCAGACTCAATTACAGCTAGGCAACAATGCTTTTTACGGG
genomic: TTACAAATGAACCGCACTTTTCACAAGGAATGTTCCATTTCGACTACAGGgttggttcca ... atatgtgcagGGGAAAGATTATCAGACTCAATTACAGCTAGGCAACAATGCTTTTTACGGG
EST: gi|37846861|gb|BJ604869.1|BJ604869
EST:     TTACAAATGAACCGCACTTTTCACAAGGAATGTTCCATTTCGACTACAGG                         GGGAAAGATTATCAGACTCAATTACAGCTAGGCAACAATGCTTTTTACGGG
genomic: TTACAAATGAACCGCACTTTTCACAAGGAATGTTCCATTTCGACTACAGGgttggttcca ... atatgtgcagGGGAAAGATTATCAGACTCAATTACAGCTAGGCAACAATGCTTTTTACGGG
EST: gi|162224207|gb|FC399271.1|FC399271
EST:     TTACAAATGAACCGCACTTTTCACAAGGAATGTTCCATTTCGACTACAGG                         GGGAAAGATTATCAGACTCAATTACAGCTAGGCAACAATGCTTTTTACGGG
genomic: TTACAAATGAACCGCACTTTTCACAAGGAATGTTCCATTTCGACTACAGGgttggttcca ... atatgtgcagGGGAAAGATTATCAGACTCAATTACAGCTAGGCAACAATGCTTTTTACGGG
EST: gi|208370718|gb|DC948255.1|DC948255
EST:     TTACAAATGAACCGCACTTTTCACAAGGAATGTTCCATTTCGACTACAGG                         GGGAAAGATTATCAGACTCAATTACAGCTAGGCAACAATGCTTTTTACGGG
genomic: TTACAAATGAACCGCACTTTTCACAAGGAATGTTCCATTTCGACTACAGGgttggttcca ... atatgtgcagGGGAAAGATTATCAGACTCAATTACAGCTAGGCAACAATGCTTTTTACGGG
EST: gi|208360525|gb|DC950071.1|DC950071
EST:     TTACAAATGAACCGCACTTTTCACAAGGAATGTTCCATTTCGACTACAGG                         GGGAAAGATTATCAGACTCAATTACAGCTAGGCAACAATGCTTTTTACGGG
genomic: TTACAAATGAACCGCACTTTTCACAAGGAATGTTCCATTTCGACTACAGGgttggttcca ... atatgtgcagGGGAAAGATTATCAGACTCAATTACAGCTAGGCAACAATGCTTTTTACGGG
EST: gi|18366481|gb|BJ198560.1|BJ198560
EST:     TTACAAATGAACCGCACTTTTCACAAGGAATGTTCCATTTCGACTACAGG                         GGGAAAGATTATCAGACTCAATTACAGCTAGGCAACAATGCTTTTTACGGG
genomic: TTACAAATGAACCGCACTTTTCACAAGGAATGTTCCATTTCGACTACAGGgttggttcca ... atatgtgcagGGGAAAGATTATCAGACTCAATTACAGCTAGGCAACAATGCTTTTTACGGG
EST: gi|100390127|gb|BY989207.1|BY989207
EST:     TTACAAATGAACCGCACTTTTCACAAGGAATGTTCCATTTCGACTACGGG                         GGGAAAGATTATCAGACTCAATTACAGCTAGGCNACAATGCTTTTTACGGG
genomic: TTACAAATGAACCGCACTTTTCACAAGGAATGTTCCATTTCGACTACAGGgttggttcca ... atatgtgcagGGGAAAGATTATCAGACTCAATTACAGCTAGGCAACAATGCTTTTTACGGG
EST: gi|162242295|gb|FC418872.1|FC418872
EST:     TTACAAATGAACCGCACTTTTCACAAGGAATGTTCCATTTCGACTACAGG                         GGGAAAGATTATCAGACTCAATTACAGCTAGGCAACAATGCTTTTTACGGG
genomic: TTACAAATGAACCGCACTTTTCACAAGGAATGTTCCATTTCGACTACAGGgttggttcca ... atatgtgcagGGGAAAGATTATCAGACTCAATTACAGCTAGGCAACAATGCTTTTTACGGG
EST: gi|67716961|gb|BJ967220.1|BJ967220
EST:     TTACAAATGAACCGCACTTTTCACAAGGAATGTTCCATTTCGACTACNGG                         GGGAAAGATTATCAGACTCAATTACAGCTAGGC
genomic: TTACAAATGAACCGCACTTTTCACAAGGAATGTTCCATTTCGACTACAGGgttggttcca ... atatgtgcagGGGAAAGATTATCAGACTCAATTACAGCTAGGC
EST: gi|162242296|gb|FC418873.1|FC418873
EST:     TTACAAATGAACCGCACTTTTCACAAGGAATGTTCCATTTCGACTACAGG                         GGGAAAGATTATCAGACTCAATTACAGCTAGGCAACAATGCTTTTTACGGG
genomic: TTACAAATGAACCGCACTTTTCACAAGGAATGTTCCATTTCGACTACAGGgttggttcca ... atatgtgcagGGGAAAGATTATCAGACTCAATTACAGCTAGGCAACAATGCTTTTTACGGG
EST: gi|208357650|gb|DC934116.1|DC934116
EST:     TTACAAATGAACCGCACTTTTCACAAGGAATGTTCCATTTCGACTACAGG                         GGGAAAGATTATCAGACTCAATTACAGCTAGGCAACAATGCTTTTTACGGG
genomic: TTACAAATGAACCGCACTTTTCACAAGGAATGTTCCATTTCGACTACAGGgttggttcca ... atatgtgcagGGGAAAGATTATCAGACTCAATTACAGCTAGGCAACAATGCTTTTTACGGG
EST: gi|162208676|gb|FC385073.1|FC385073
EST:     TTACAAATGAACCGCACTTTTCACAAGGAATGTTCCATTTCGACTACAGG                         GGGAAAGATTATCAGACTCAATTACAGCTAGGCAACAATGCTTTTTACGGG
genomic: TTACAAATGAACCGCACTTTTCACAAGGAATGTTCCATTTCGACTACAGGgttggttcca ... atatgtgcagGGGAAAGATTATCAGACTCAATTACAGCTAGGCAACAATGCTTTTTACGGG
EST: gi|67726076|gb|BJ976335.1|BJ976335
EST:     TTACAAATGAACCGCACTTTTCACAAGGAATGTTCCATTTCGACTACAGG                         GGGAAAGATTATCAGACTCAATTACAGCTAGGCAACAATGCTTTTTACGGG
genomic: TTACAAATGAACCGCACTTTTCACAAGGAATGTTCCATTTCGACTACAGGgttggttcca ... atatgtgcagGGGAAAGATTATCAGACTCAATTACAGCTAGGCAACAATGCTTTTTACGGG
EST: gi|208344796|gb|DC912630.1|DC912630
EST:     TTACAAATGAACCGCACTTTTCACAAGGAATGTTCCATTTCGACTACAGG                         GGGAAAGATTATCAGACTCAATTACAGCTAGGCAACAATGCTTTTTACGGG
genomic: TTACAAATGAACCGCACTTTTCACAAGGAATGTTCCATTTCGACTACAGGgttggttcca ... atatgtgcagGGGAAAGATTATCAGACTCAATTACAGCTAGGCAACAATGCTTTTTACGGG
EST: gi|208348734|gb|DC926409.1|DC926409
EST:     TTACAAATGAACCGCACTTTTCACAAGGAATGTTCCATTTCGACTACAGG                         GGGAAAGATTATCAGACTCAATTACAGCTAGGCAACAATGCTTTTTACGGG
genomic: TTACAAATGAACCGCACTTTTCACAAGGAATGTTCCATTTCGACTACAGGgttggttcca ... atatgtgcagGGGAAAGATTATCAGACTCAATTACAGCTAGGCAACAATGCTTTTTACGGG
EST: gi|37823603|gb|BJ581669.1|BJ581669
EST:     CAAGGAATGTTCCATTTCGACTACAGG                         GGGAAAGATTATCAGACTCAATTACAGCTAGGCAACAATGCTTTTTACGGG
genomic: CAAGGAATGTTCCATTTCGACTACAGGgttggttcca ... atatgtgcagGGGAAAGATTATCAGACTCAATTACAGCTAGGCAACAATGCTTTTTACGGG
EST: gi|208374571|gb|DC940760.1|DC940760
EST:     TTACAAATGAACCGCACTTTTCACAAGGAATGTTCCATTTCGACTACAGG                         GGGAAAGATTATCAGACTCAATTACAGCTAGGCAACAATGCTTTTTACGGG
genomic: TTACAAATGAACCGCACTTTTCACAAGGAATGTTCCATTTCGACTACAGGgttggttcca ... atatgtgcagGGGAAAGATTATCAGACTCAATTACAGCTAGGCAACAATGCTTTTTACGGG
EST: gi|100413081|gb|BY992578.1|BY992578
EST:     TTACAAATGAACCGCACTTTTCACAAGGAATGTTCCATTTCGACTACNGG                         GGGAAAGATTATCAGACTCAATTACAGCTAGGCAACAATGCTNTTTACGGG
genomic: TTACAAATGAACCGCACTTTTCACAAGGAATGTTCCATTTCGACTACAGGgttggttcca ... atatgtgcagGGGAAAGATTATCAGACTCAATTACAGCTAGGCAACAATGCTTTTTACGGG

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: 7

CTTACAAATGAACCGCACTTTTCACAAGGAATGTTCCATTTCGACTACAGGgttggttcca ... atatgtgcagGGGAAAGATTATCAGACTCAATTACAGCTAGGCAACAATGCTTTTTACGGGTTCAATTATATTCAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcggcaacttgccttgagattaacggcgtatttgcgcttgaatgatatgtgcagGGGAAAGATTATCAGACTCAATTACAGCTAGGCAACAATGCTTTTTACGGGTTCAATTATATTCAG
                  gattaac  putative branch site (score: 7)
                                         aatgatat  TA-rich tract