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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatttttttctcttcggatttggaggctgtcattaagtagcgtgaacaagcttgtcttactgaaaatgccaaagttgagttcctttgccttaataaattcagcaattttggaattttggcagGTTGAAGAAGTTGCTGCCCACAAGTCACATAAAAAGAACCAAGCCCGCCTCCGTAGCGGTACTACTTCAGCCGCTAATGTTGCTTAGATCTACACTTTGG

Basic information

species Physcomitrella patens
transcript PP1S97_74V6.1
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|18341219|gb|BJ173252.1|BJ173252
EST:     GTCACATTGAGCTCATCCTCTCTGAGAAGGAGACTCCAGTCAAGAAAGAG                         GTTGAAGAAGTTGCTGCCCACAAGTCACATAAAAAGAACCAAGCCCGCCTC
genomic: GTCACATTGAGCTCATCCTCTCTGAGAAGGAGACTCCAGTCAAGAAAGAGgtattttttt ... attttggcagGTTGAAGAAGTTGCTGCCCACAAGTCACATAAAAAGAACCAAGCCCGCCTC
EST: gi|37850662|gb|BJ608670.1|BJ608670
EST:     GTCACATTGAGCTCATCCTCTCTGAGAAGGAGACTCCAGTCAAGAAAGAG                         GTTGAAGAAGTTGCTGCCCACAAGTCACATAAAAAGAACCAAGCCCGCCTC
genomic: GTCACATTGAGCTCATCCTCTCTGAGAAGGAGACTCCAGTCAAGAAAGAGgtattttttt ... attttggcagGTTGAAGAAGTTGCTGCCCACAAGTCACATAAAAAGAACCAAGCCCGCCTC
EST: gi|162250608|gb|FC428199.1|FC428199
EST:     GTCACATTGAGCTCATCCTCTCTGAGAAGGAGACTCCAGTCAAGAAAGAG                         GTTGAAGAAGTTGCTGCCCACAAGTCACATAAAAAGAACCAAGCCCGCCTC
genomic: GTCACATTGAGCTCATCCTCTCTGAGAAGGAGACTCCAGTCAAGAAAGAGgtattttttt ... attttggcagGTTGAAGAAGTTGCTGCCCACAAGTCACATAAAAAGAACCAAGCCCGCCTC
EST: gi|37829134|gb|BJ587146.1|BJ587146
EST:     GTCACATTGAGCTCATCCTCTCTGAGAAGGAGACTCCAGTCAAGAAAGAG                         GTTGAAGAAGTTGCTGCCCACAAGTCACATAAAAAGAACCAAGCCCGCCTC
genomic: GTCACATTGAGCTCATCCTCTCTGAGAAGGAGACTCCAGTCAAGAAAGAGgtattttttt ... attttggcagGTTGAAGAAGTTGCTGCCCACAAGTCACATAAAAAGAACCAAGCCCGCCTC
EST: gi|162274404|gb|FC450431.1|FC450431
EST:     GTCACATTGAGCTCATCCTCTCTGAGAAGGAGACTCCAGTCAAGAAAGAG                         GTTGAAGAAGTTGCTGCCCACAAGTCACATAAAAAGAACCAAGCCCGCCTC
genomic: GTCACATTGAGCTCATCCTCTCTGAGAAGGAGACTCCAGTCAAGAAAGAGgtattttttt ... attttggcagGTTGAAGAAGTTGCTGCCCACAAGTCACATAAAAAGAACCAAGCCCGCCTC
EST: gi|162274878|gb|FC451113.1|FC451113
EST:     GTCACATTGAGCTCATCCTCTCTGAGAAGGAGACTCCAGTCAAGAAAGAG                         GTTGAAGAAGTTGCTGCCCACAAGTCACATAAAAAGAACCAAGCCCGCCTC
genomic: GTCACATTGAGCTCATCCTCTCTGAGAAGGAGACTCCAGTCAAGAAAGAGgtattttttt ... attttggcagGTTGAAGAAGTTGCTGCCCACAAGTCACATAAAAAGAACCAAGCCCGCCTC
EST: gi|162262677|gb|FC438472.1|FC438472
EST:     GTCACATTGAGCTCATCCTCTCTGAGAAGGAGACTCCAGTCAAGAAAGAG                         GTTGAAGAAGTTGCTGCCCACAAGTCACATAAAAAGAACCAAGCCCGCCTC
genomic: GTCACATTGAGCTCATCCTCTCTGAGAAGGAGACTCCAGTCAAGAAAGAGgtattttttt ... attttggcagGTTGAAGAAGTTGCTGCCCACAAGTCACATAAAAAGAACCAAGCCCGCCTC
EST: gi|162235235|gb|FC412111.1|FC412111
EST:     GTCACATTGAGCTCATCCTCTCTGAGAAGGAGACTCCAGTCAAGAAAGAG                         GTTGAAGAAGTTGCTGCCCACAAGTCACATAAAAAGAACCAAGCCCGCCTC
genomic: GTCACATTGAGCTCATCCTCTCTGAGAAGGAGACTCCAGTCAAGAAAGAGgtattttttt ... attttggcagGTTGAAGAAGTTGCTGCCCACAAGTCACATAAAAAGAACCAAGCCCGCCTC
EST: gi|37844465|gb|BJ602473.1|BJ602473
EST:     GTCACATTGAGCTCATCCTCTCTGAGAAGGAGACTCCAGTCAAGAAAGAG                         GTTGAAGAAGTTGCTGCCCACAAGTCACATAAAAAGAACCAAGCCCGCCTC
genomic: GTCACATTGAGCTCATCCTCTCTGAGAAGGAGACTCCAGTCAAGAAAGAGgtattttttt ... attttggcagGTTGAAGAAGTTGCTGCCCACAAGTCACATAAAAAGAACCAAGCCCGCCTC
EST: gi|162274403|gb|FC450430.1|FC450430
EST:     GTCACATTGAGCTCATCCTCTCTGAGAAGGAGACTCCAGTCAAGAAAGAG                         GTTGAAGAAGTTGCTGCCCACAAGTCACATAAAAAGAACCAAGCCCGCCTC
genomic: GTCACATTGAGCTCATCCTCTCTGAGAAGGAGACTCCAGTCAAGAAAGAGgtattttttt ... attttggcagGTTGAAGAAGTTGCTGCCCACAAGTCACATAAAAAGAACCAAGCCCGCCTC
EST: gi|37823916|gb|BJ581982.1|BJ581982
EST:     GTCACATTGAGCTCATCCTCTCTGAGAAGGAGACTCCAGTCAAGAAAGAG                         GTTGAAGAAGTTGCTGCCCACAAGTCACATAAAAAGAACCAAGCCCGCCTC
genomic: GTCACATTGAGCTCATCCTCTCTGAGAAGGAGACTCCAGTCAAGAAAGAGgtattttttt ... attttggcagGTTGAAGAAGTTGCTGCCCACAAGTCACATAAAAAGAACCAAGCCCGCCTC
EST: gi|162266465|gb|FC442501.1|FC442501
EST:     GTCACATTGAGCTCATCCTCTCTGAGAAGGAGACTCCAGTCAAGAAAGAG                         GTTGAAGAAGTTGCTGCCCACAAGTCACATAAAAAGAACCAAGCCCGCCTC
genomic: GTCACATTGAGCTCATCCTCTCTGAGAAGGAGACTCCAGTCAAGAAAGAGgtattttttt ... attttggcagGTTGAAGAAGTTGCTGCCCACAAGTCACATAAAAAGAACCAAGCCCGCCTC
EST: gi|18327847|gb|BJ159851.1|BJ159851
EST:     GTCACATTGAGCTCATCCTCTCTGAGAAGGAGACTCCAGTCAAGAAAGAG                         GTTGAAGAAGTTGCTGCCCACAAGTCACATAAAAAGAACCAAGCCCGCCTC
genomic: GTCACATTGAGCTCATCCTCTCTGAGAAGGAGACTCCAGTCAAGAAAGAGgtattttttt ... attttggcagGTTGAAGAAGTTGCTGCCCACAAGTCACATAAAAAGAACCAAGCCCGCCTC
EST: gi|37822217|gb|BJ580283.1|BJ580283
EST:     GTCACATTGAGCTCATCCTCTCTGAGAAGGAGACTCCAGTCAAGAAAGAG                         GTTGAAGAAGTTGCTGCCCACAAGTCACATAAAAAGAACCAAGCCCGCCTC
genomic: GTCACATTGAGCTCATCCTCTCTGAGAAGGAGACTCCAGTCAAGAAAGAGgtattttttt ... attttggcagGTTGAAGAAGTTGCTGCCCACAAGTCACATAAAAAGAACCAAGCCCGCCTC
EST: gi|18360908|gb|BJ192972.1|BJ192972
EST:     GTCACATTGAGCTCATCCTCTCTGAGAAGGAGACTCCAGTCAAGAAAGAG                         GTTGAAGAAGTTGCT
genomic: GTCACATTGAGCTCATCCTCTCTGAGAAGGAGACTCCAGTCAAGAAAGAGgtattttttt ... attttggcagGTTGAAGAAGTTGCT
EST: gi|37847619|gb|BJ605627.1|BJ605627
EST:     GTCACATTGAGCTCATCCTCTCTGAGAAGGAGACTCCAGTCAAGAAAGAG                         GTTGAAGAAGTTGCTGCCCACAAGTCACATAAAAAGAACCAAGCCCGCCTC
genomic: GTCACATTGAGCTCATCCTCTCTGAGAAGGAGACTCCAGTCAAGAAAGAGgtattttttt ... attttggcagGTTGAAGAAGTTGCTGCCCACAAGTCACATAAAAAGAACCAAGCCCGCCTC
EST: gi|37827543|gb|BJ585555.1|BJ585555
EST:     GTCACATTGAGCTCATCCTCTCTGAGAAGGAGACTCCAGTCAAGAAAGAG                         GTTGAAGAAGTTGCTGCCCACAAGTCACATAAAAAGAACCAAGCCCGCCTC
genomic: GTCACATTGAGCTCATCCTCTCTGAGAAGGAGACTCCAGTCAAGAAAGAGgtattttttt ... attttggcagGTTGAAGAAGTTGCTGCCCACAAGTCACATAAAAAGAACCAAGCCCGCCTC
EST: gi|162272845|gb|FC448820.1|FC448820
EST:     GTCACATTGAGCTCATCCTCTCTGAGAAGGAGACTCCAGTCAAGAAAGAG                         GTTGAAGAAGTTGCTGCCCACAAGTCACATAAAAAGAACCAAGCCCGCCTC
genomic: GTCACATTGAGCTCATCCTCTCTGAGAAGGAGACTCCAGTCAAGAAAGAGgtattttttt ... attttggcagGTTGAAGAAGTTGCTGCCCACAAGTCACATAAAAAGAACCAAGCCCGCCTC
EST: gi|37849153|gb|BJ607161.1|BJ607161
EST:     GTCACATTGAGCTCATCCTCTCTGAGAAGGAGACTCCAGTCAAGAAAGAG                         GTTGAAGAAGTTGCTGCCCACAAGTCACATAAAAAGAACCAAGCCCGCCTC
genomic: GTCACATTGAGCTCATCCTCTCTGAGAAGGAGACTCCAGTCAAGAAAGAGgtattttttt ... attttggcagGTTGAAGAAGTTGCTGCCCACAAGTCACATAAAAAGAACCAAGCCCGCCTC
EST: gi|37852997|gb|BJ611005.1|BJ611005
EST:     GTCACATTGAGCTCATCCTCTCTGAGAAGGAGACTCCAGTCAAGAAAGAG                         GTTGAAGAAGTTGCTGCCCACAAGTCACATAAAAAGCAACGCAAGCCCGCC
genomic: GTCACATTGAGCTCATCCTCTCTGAGAAGGAGACTCCAGTCAAGAAAGAGgtattttttt ... attttggcagGTTGAAGAAGTTGCTGCCCACAAGTCACATAAAAAG-AAC-CAAGCCCGCC
EST: gi|37835375|gb|BJ593387.1|BJ593387
EST:     GTCACATTGAGCTCATCCTCTCTGAGAAGGAGACTCCAGTCAAGAAAGAG                         GTTGAAGAAGTTGCTGCCCACAAGTCACATAAAAAGAACCAAGCCCGCCTC
genomic: GTCACATTGAGCTCATCCTCTCTGAGAAGGAGACTCCAGTCAAGAAAGAGgtattttttt ... attttggcagGTTGAAGAAGTTGCTGCCCACAAGTCACATAAAAAGAACCAAGCCCGCCTC
EST: gi|37838798|gb|BJ596806.1|BJ596806
EST:     GTCACATTGAGCTCATCCTCTCTGAGAAGGAGACTCCAGTCAAGAAAGAG                         GTTGAAGAAGTTGCTGCCCACAAGTCACATAAAAAGAACCAAGCCCGCCTC
genomic: GTCACATTGAGCTCATCCTCTCTGAGAAGGAGACTCCAGTCAAGAAAGAGgtattttttt ... attttggcagGTTGAAGAAGTTGCTGCCCACAAGTCACATAAAAAGAACCAAGCCCGCCTC
EST: gi|162203338|gb|FC378785.1|FC378785
EST:     GTCACATTGAGCTCATCCTCTCTGAGAAGGAGACTCCAGTCAAGAAAGAG                         GTTGAAGAAGTTGCTGCCCACAAGTCACATAAAAAGAACCAAGCCCGCCTC
genomic: GTCACATTGAGCTCATCCTCTCTGAGAAGGAGACTCCAGTCAAGAAAGAGgtattttttt ... attttggcagGTTGAAGAAGTTGCTGCCCACAAGTCACATAAAAAGAACCAAGCCCGCCTC
EST: gi|162266464|gb|FC442500.1|FC442500
EST:     GTCACATTGAGCTCATCCTCTCTGAGAAGGAGACTCCAGTCAAGAAAGAG                         GTTGAAGAAGTTGCTGCCCACAAGTCACATAAAAAGAACCAAGCCCGCCTC
genomic: GTCACATTGAGCTCATCCTCTCTGAGAAGGAGACTCCAGTCAAGAAAGAGgtattttttt ... attttggcagGTTGAAGAAGTTGCTGCCCACAAGTCACATAAAAAGAACCAAGCCCGCCTC
EST: gi|18367163|gb|BJ199244.1|BJ199244
EST:     GTCACATTGAGCTCATCCTCTCTGAGAAGGAGACTCCAGTCAAGAAAGAG                         GTTGAAGAAGTTGCTGCCCACAAGTCACATAAAAAGAACCA
genomic: GTCACATTGAGCTCATCCTCTCTGAGAAGGAGACTCCAGTCAAGAAAGAGgtattttttt ... attttggcagGTTGAAGAAGTTGCTGCCCACAAGTCACATAAAAAGAACCA
EST: gi|37825964|gb|BJ584030.1|BJ584030
EST:     GTCACATTGAGCTCATCCTCTCTGAGAAGGAGACTCCAGTCAAGAAAGAG                         GTTGAAGAAGTTGCTGCCCACAAGTCACATAAAAAGAACCAAGCCCGCCTC
genomic: GTCACATTGAGCTCATCCTCTCTGAGAAGGAGACTCCAGTCAAGAAAGAGgtattttttt ... attttggcagGTTGAAGAAGTTGCTGCCCACAAGTCACATAAAAAGAACCAAGCCCGCCTC
EST: gi|162272844|gb|FC448819.1|FC448819
EST:     GTCACATTGAGCTCATCCTCTCTGAGAAGGAGACTCCAGTCAAGAAAGAG                         GTTGAAGAAGTTGCTGCCCACAAGTCACATAAAAAGAACCAAGCCCGCCTC
genomic: GTCACATTGAGCTCATCCTCTCTGAGAAGGAGACTCCAGTCAAGAAAGAGgtattttttt ... attttggcagGTTGAAGAAGTTGCTGCCCACAAGTCACATAAAAAGAACCAAGCCCGCCTC
EST: gi|18350164|gb|BJ182215.1|BJ182215
EST:     GTCACATTGAGCTCATCCTCTCTGAGAAGGAGACTCCAGTCAAGAAAGAG                         GTTGAAGAAGTTGCTGCCCACAAGTCACATAAAAAGAACCAAGCCCGCC
genomic: GTCACATTGAGCTCATCCTCTCTGAGAAGGAGACTCCAGTCAAGAAAGAGgtattttttt ... attttggcagGTTGAAGAAGTTGCTGCCCACAAGTCACATAAAAAGAACCAAGCCCGCC
EST: gi|162235236|gb|FC412112.1|FC412112
EST:     GTCACATTGAGCTCATCCTCTCTGAGAAGGAGACTCCAGTCAAGAAAGAG                         GTTGAAGAAGTTGCTGCCCACAAGTCACATAAAAAGAACCAAGCCCGCCTC
genomic: GTCACATTGAGCTCATCCTCTCTGAGAAGGAGACTCCAGTCAAGAAAGAGgtattttttt ... attttggcagGTTGAAGAAGTTGCTGCCCACAAGTCACATAAAAAGAACCAAGCCCGCCTC
EST: gi|162230491|gb|FC407406.1|FC407406
EST:     GTCACATTGAGCTCATCCTCTCTGAGAAGGAGACTCCAGTCAAGAAAGAG                         GTTGAAGAAGTTGCTGCCCACAAGTCACATAAAAAGAACCAAGCCCGCCTC
genomic: GTCACATTGAGCTCATCCTCTCTGAGAAGGAGACTCCAGTCAAGAAAGAGgtattttttt ... attttggcagGTTGAAGAAGTTGCTGCCCACAAGTCACATAAAAAGAACCAAGCCCGCCTC
EST: gi|162203337|gb|FC378784.1|FC378784
EST:     GTCACATTGAGCTCATCCTCTCTGAGAAGGAGACTCCAGTCAAGAAAGAG                         GTTGAAGAAGTTGCTGCCCACAAGTCACATAAAAAGAACCAAGCCCGCCTC
genomic: GTCACATTGAGCTCATCCTCTCTGAGAAGGAGACTCCAGTCAAGAAAGAGgtattttttt ... attttggcagGTTGAAGAAGTTGCTGCCCACAAGTCACATAAAAAGAACCAAGCCCGCCTC
EST: gi|162201673|gb|FC377477.1|FC377477
EST:     GTCACATTGAGCTCATCCTCTCTGAGAAGGAGACTCCAGTCAAGAAAGAG                         GTTGAAGAAGTTGCTGCCCACAAGTCACATAAAAAGAACCAAGCCCGCCTC
genomic: GTCACATTGAGCTCATCCTCTCTGAGAAGGAGACTCCAGTCAAGAAAGAGgtattttttt ... attttggcagGTTGAAGAAGTTGCTGCCCACAAGTCACATAAAAAGAACCAAGCCCGCCTC
EST: gi|162201674|gb|FC377478.1|FC377478
EST:     GTCACATTGAGCTCATCCTCTCTGAGAAGGAGACTCCAGTCAAGAAAGAG                         GTTGAAGAAGTTGCTGCCCACAAGTCACATAAAAAGAACCAAGCCCGCCTC
genomic: GTCACATTGAGCTCATCCTCTCTGAGAAGGAGACTCCAGTCAAGAAAGAGgtattttttt ... attttggcagGTTGAAGAAGTTGCTGCCCACAAGTCACATAAAAAGAACCAAGCCCGCCTC
EST: gi|18336082|gb|BJ168104.1|BJ168104
EST:     GTCACATTGAGCTCATCCTCTCTGAGAAGGAGACTCCAGTCAAGAAAGAG                         GTTGAAGAAGTTGCTGCCCACAAGTCACATAAAAAGAACCAAGCCCGCCTC
genomic: GTCACATTGAGCTCATCCTCTCTGAGAAGGAGACTCCAGTCAAGAAAGAGgtattttttt ... attttggcagGTTGAAGAAGTTGCTGCCCACAAGTCACATAAAAAGAACCAAGCCCGCCTC
EST: gi|162262676|gb|FC438471.1|FC438471
EST:     GTCACATTGAGCTCATCCTCTCTGAGAAGGAGACTCCAGTCAAGAAAGAG                         GTTGAAGAAGTTGCTGCCCACAAGTCACATAAAAAGAACCAAGCCCGCCTC
genomic: GTCACATTGAGCTCATCCTCTCTGAGAAGGAGACTCCAGTCAAGAAAGAGgtattttttt ... attttggcagGTTGAAGAAGTTGCTGCCCACAAGTCACATAAAAAGAACCAAGCCCGCCTC
EST: gi|162179935|gb|FC356006.1|FC356006
EST:     GTCACATTGAGCTCATCCTCTCTGAGAAGGAGACTCCAGTCAAGAAAGAG                         GTTGAAGAAGTTGCTGCCCACAAGTCACATAAAAAGAACCAAGCCCGCCTC
genomic: GTCACATTGAGCTCATCCTCTCTGAGAAGGAGACTCCAGTCAAGAAAGAGgtattttttt ... attttggcagGTTGAAGAAGTTGCTGCCCACAAGTCACATAAAAAGAACCAAGCCCGCCTC

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), 33 (downstream exon)
Score: 23

CTTACATGTCCTCACCTTGTCACATTGAGCTCATCCTCTCTGAGAAGGAGACTCCAGTCAAGAAAGAGgtattttttt ... attttggcagGTTGAAGAAGTTGCTGCCCACAAGTCACATAAAAAGAACCAAGCCCGCCTCCGTAGCGGTACTACTTCAGCCGCTAATGTTGCTTAGATCTACACTTTGG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gccaaagttgagttcctttgccttaataaattcagcaattttggaattttggcagGTTGAAGAAGTTGCTGCCCACAAGTCACATAAAAAGAACCAAGCCCGCCTCCGTAGCGGTACTACTTCAGCCGCTAATGTTGCTTAGATCTACACTTTGG
                    ccttaat  putative branch site (score: 23)
                                    aattttggaatttt  TA-rich tract