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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctaacattcttctggccgtctctctccactttgaagcaaaattcctggacgaataaggtgaacacctaacatatgtttggccttgttggtggacttgtagGTTTATTCATCACATACGTTGCACTGAATGCCATGAATGGGAGCGGGCAACCCGCACTCCTTTACATCGTGCCTTGTACTCTAG

Basic information

species Physcomitrella patens
transcript PP1S1_478V6.1
intron # 12
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|162277631|gb|FC453262.1|FC453262
EST:     GAGTTTGTTCAGAGGCTACTTCCTATGGTCCACAGTTGGTTATGGCCTAG                         GTTTATTCATCACATACGTTGCACTGAATGCCATGAATGGGAGCGGGCAAC
genomic: GAGTTTGTTCAGAGGCTACTTCCTATGGTCCACAGTTGGTTATGGCCTAGgtaggcgcaa ... ggacttgtagGTTTATTCATCACATACGTTGCACTGAATGCCATGAATGGGAGCGGGCAAC
EST: gi|37850157|gb|BJ608165.1|BJ608165
EST:     GAGTTTGTTCAGAGGCTACTTCCTATGGTCCACAGTTGGTTATGGCCTAG                         GTTTATTCATCACATACGTTGCACTGAATGCCATGAATGGGAGCGGGCAAC
genomic: GAGTTTGTTCAGAGGCTACTTCCTATGGTCCACAGTTGGTTATGGCCTAGgtaggcgcaa ... ggacttgtagGTTTATTCATCACATACGTTGCACTGAATGCCATGAATGGGAGCGGGCAAC
EST: gi|162160845|gb|FC337667.1|FC337667
EST:     GAGTTTGTTCAGAGGCTACTTCCTATGGTCCACAGTTGGTTATGGCCTAG                         GTTTATTCATCACATACGTTGCACTGAATGCCATGAATGGGAGCGGGCAAC
genomic: GAGTTTGTTCAGAGGCTACTTCCTATGGTCCACAGTTGGTTATGGCCTAGgtaggcgcaa ... ggacttgtagGTTTATTCATCACATACGTTGCACTGAATGCCATGAATGGGAGCGGGCAAC
EST: gi|37841043|gb|BJ599051.1|BJ599051
EST:     GAGTTTGTTCAGAGGCTACTTCCTATGGTCCACAGTTGGTTATGGCCTAG                         GTTTATTCATCACATACGTTGCACTGAATGCCATGAATGGGAGCGGGCAAC
genomic: GAGTTTGTTCAGAGGCTACTTCCTATGGTCCACAGTTGGTTATGGCCTAGgtaggcgcaa ... ggacttgtagGTTTATTCATCACATACGTTGCACTGAATGCCATGAATGGGAGCGGGCAAC
EST: gi|37853139|gb|BJ611147.1|BJ611147
EST:     GAGTTTGTTCAGAGGCTACTTCCTATGGTCCACAGTTGGTTATGGCCTAG                         GTTTATTCATCACATACGTTGCACTGAATGCCATGAATGGGAGCGGGCAAC
genomic: GAGTTTGTTCAGAGGCTACTTCCTATGGTCCACAGTTGGTTATGGCCTAGgtaggcgcaa ... ggacttgtagGTTTATTCATCACATACGTTGCACTGAATGCCATGAATGGGAGCGGGCAAC
EST: gi|208385472|gb|DC953091.1|DC953091
EST:     GAGTTTGTTCAGAGGCTACTTCCTATGGTCCACAGTTGGTTATGGCCTAG                         GTTTATTCATCACATACGTTGCACTGAATGCCATGAATGGGAGCGGGCAAC
genomic: GAGTTTGTTCAGAGGCTACTTCCTATGGTCCACAGTTGGTTATGGCCTAGgtaggcgcaa ... ggacttgtagGTTTATTCATCACATACGTTGCACTGAATGCCATGAATGGGAGCGGGCAAC
EST: gi|208370567|gb|DC951603.1|DC951603
EST:     GAGTTTGTTCAGAGGCTACTTCCTATGGTCCACAGTTGGTTATGGCCTAG                         GTTTATTCATCACATACGTTGCACTGAATGCCATGAATGGGAGCGGGCAAC
genomic: GAGTTTGTTCAGAGGCTACTTCCTATGGTCCACAGTTGGTTATGGCCTAGgtaggcgcaa ... ggacttgtagGTTTATTCATCACATACGTTGCACTGAATGCCATGAATGGGAGCGGGCAAC
EST: gi|162163486|gb|FC340020.1|FC340020
EST:     GAGTTTGTTCAGAGGCTACTTCCTATGGTCCACAGTTGGTTATGGCCTAG                         GTTTATTCATCACATACGTTGCACTGAATGCCATGAATGGGAGCGGGCAAC
genomic: GAGTTTGTTCAGAGGCTACTTCCTATGGTCCACAGTTGGTTATGGCCTAGgtaggcgcaa ... ggacttgtagGTTTATTCATCACATACGTTGCACTGAATGCCATGAATGGGAGCGGGCAAC
EST: gi|208394841|gb|DC915634.1|DC915634
EST:     GAGTTTGTTCAGAGGCTACTTCCTATGGTCCACAGTTGGTTATGGCCTAG                         GTTTATTCATCACATACGTTGCACTGAATGCCATGAATGGGAGCGGGCAAC
genomic: GAGTTTGTTCAGAGGCTACTTCCTATGGTCCACAGTTGGTTATGGCCTAGgtaggcgcaa ... ggacttgtagGTTTATTCATCACATACGTTGCACTGAATGCCATGAATGGGAGCGGGCAAC
EST: gi|67725738|gb|BJ975997.1|BJ975997
EST:     GAGTTTGTTCAGAGGCTACTTCCTATGGTCCACAGTTGGTTATGGCCTAG                         GTTTATTCATCACATACGTTGCACTGAATGCCATGAATGGGAGCGGGCAAC
genomic: GAGTTTGTTCAGAGGCTACTTCCTATGGTCCACAGTTGGTTATGGCCTAGgtaggcgcaa ... ggacttgtagGTTTATTCATCACATACGTTGCACTGAATGCCATGAATGGGAGCGGGCAAC
EST: gi|162212457|gb|FC388705.1|FC388705
EST:     GAGTTTGTTCAGAGGCTACTTCCTATGGTCCACAGTTGGTTATGGCCTAG                         GTTTATTCATCACATACGTTGCACTGAATGCCATGAATGGGAGCGGGCAAC
genomic: GAGTTTGTTCAGAGGCTACTTCCTATGGTCCACAGTTGGTTATGGCCTAGgtaggcgcaa ... ggacttgtagGTTTATTCATCACATACGTTGCACTGAATGCCATGAATGGGAGCGGGCAAC

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: 25 (upstream exon), 34 (downstream exon)
Score: 9

GTATGACTGGACAGCAAGAAAGAGTTTGTTCAGAGGCTACTTCCTATGGTCCACAGTTGGTTATGGCCTAGgtaggcgcaa ... ggacttgtagGTTTATTCATCACATACGTTGCACTGAATGCCATGAATGGGAGCGGGCAACCCGCACTCCTTTACATCGTGCCTTGTACTCTAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tggacgaataaggtgaacacctaacatatgtttggccttgttggtggacttgtagGTTTATTCATCACATACGTTGCACTGAATGCCATGAATGGGAGCGGGCAACCCGCACTCCTTTACATCGTGCCTTGTACTCTAG
                  acctaac  putative branch site (score: 9)
                     taacatat  TA-rich tract