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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagttcgcaacgttggtgtgcttgctgtctgtaatggctgttattagtgcactattgaggcaatgatctctgatcaatatgtgcatctcgttatagtggatgaggcgaacatgatgtgaacttggtgattattactgtatgcagAACTCGTCCTCTATATCGAGTGCTGCCTATTTTGACCGTGAAGAAGTTGGCTCTCCCGGCAGTTCTTCTATTGACGTTACGGCGAGTGAGCTCATGTCTA

Basic information

species Physcomitrella patens
transcript PP1S795_4V6.1
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|208370166|gb|DC951765.1|DC951765
EST:     AATATAAAAACAATGATCAGGGAAATTCTGGGCGTCTAGAGAAATTCGCT                         AACTCGTCCTCTATATCGAGTGCTGCCTATTTTGACCGTGAAGAAGTTGGC
genomic: AATATAAAAACAATGATCAGGGAAATTCTGGGCGTCTAGAGAAATTCGCTgtaagttcgc ... ctgtatgcagAACTCGTCCTCTATATCGAGTGCTGCCTATTTTGACCGTGAAGAAGTTGGC
EST: gi|208368245|gb|DC951511.1|DC951511
EST:     AATATAAAAACAATGATCAGGGAAATTCTGGGCGTCTAGAGAAATTCGCT                         AACTCGTCCTCTATTTCGAGTGCTGCCTATTTTGACCGTGAAGAAGTTGGC
genomic: AATATAAAAACAATGATCAGGGAAATTCTGGGCGTCTAGAGAAATTCGCTgtaagttcgc ... ctgtatgcagAACTCGTCCTCTATATCGAGTGCTGCCTATTTTGACCGTGAAGAAGTTGGC
EST: gi|208358641|gb|DC949976.1|DC949976
EST:     AATATAAAAACAATGATCAGGGAAATTCTGGGCGTCTAGAGAAATTCGCT                         AACTCGTCCTCTATATCGAGTGCTGCCTATTTTGACCGTGAAGAAGTTGGC
genomic: AATATAAAAACAATGATCAGGGAAATTCTGGGCGTCTAGAGAAATTCGCTgtaagttcgc ... ctgtatgcagAACTCGTCCTCTATATCGAGTGCTGCCTATTTTGACCGTGAAGAAGTTGGC
EST: gi|67696742|gb|BJ956975.1|BJ956975
EST:     AATATAAAAACAATGATCAGGGAAATTCTGGGCGTCTAGAGAAATTCGCT                         AACTCGTCCTCTATATCGAGTGCTGCCTATTTTGACCGTGAAGAAGTTGGC
genomic: AATATAAAAACAATGATCAGGGAAATTCTGGGCGTCTAGAGAAATTCGCTgtaagttcgc ... ctgtatgcagAACTCGTCCTCTATATCGAGTGCTGCCTATTTTGACCGTGAAGAAGTTGGC
EST: gi|208396541|gb|DC915853.1|DC915853
EST:     AATATAAAAACAATGATCAGGGAAATTCTGGGCGTCTAGAGAAATTCGCT                         AACTCGTCCTCTATATCGAGTGCTGCCTATTTTGACCGTGAAGAAGTTGGC
genomic: AATATAAAAACAATGATCAGGGAAATTCTGGGCGTCTAGAGAAATTCGCTgtaagttcgc ... ctgtatgcagAACTCGTCCTCTATATCGAGTGCTGCCTATTTTGACCGTGAAGAAGTTGGC
EST: gi|162221477|gb|FC397286.1|FC397286
EST:     AATATAAAAACAATGATCAGGGAAATTCTGGGCGTCTAGAGAAATTCGCT                         AACTCGTCCTCTATATCGAGTGCTGCCTATTTTGACCGTGAAGAAGTTGGC
genomic: AATATAAAAACAATGATCAGGGAAATTCTGGGCGTCTAGAGAAATTCGCTgtaagttcgc ... ctgtatgcagAACTCGTCCTCTATATCGAGTGCTGCCTATTTTGACCGTGAAGAAGTTGGC
EST: gi|67720059|gb|BJ970318.1|BJ970318
EST:     AATATAAAAACAATGATCAGGGAAATTCTGGGCGTCTAGAGAAATTCGCT                         AACTCGTCCTCTATATCGAGTGCTGCCTATTTTGACCGTGAAGAAGTTGGC
genomic: AATATAAAAACAATGATCAGGGAAATTCTGGGCGTCTAGAGAAATTCGCTgtaagttcgc ... ctgtatgcagAACTCGTCCTCTATATCGAGTGCTGCCTATTTTGACCGTGAAGAAGTTGGC
EST: gi|208362683|gb|DC947174.1|DC947174
EST:     AATATAAAAACAATGATCAGGGAAATTCTGGGCGTCTAGAGAAATTCGCT                         AACTCGTCCTCTATATCGAGTGCTGCCTATTTTGACCGTGAAGAAGTTGGC
genomic: AATATAAAAACAATGATCAGGGAAATTCTGGGCGTCTAGAGAAATTCGCTgtaagttcgc ... ctgtatgcagAACTCGTCCTCTATATCGAGTGCTGCCTATTTTGACCGTGAAGAAGTTGGC
EST: gi|162200943|gb|FC377346.1|FC377346
EST:     AATATAAAAACAATGATCAGGGAAATTCTGGGCGTCTAGAGAAATTCGCT                         AACTCGTCCTCTATATCGAGTGCTGCCTATTTTGACCGTGAAGAAGTTGGC
genomic: AATATAAAAACAATGATCAGGGAAATTCTGGGCGTCTAGAGAAATTCGCTgtaagttcgc ... ctgtatgcagAACTCGTCCTCTATATCGAGTGCTGCCTATTTTGACCGTGAAGAAGTTGGC
EST: gi|67695640|gb|BJ955873.1|BJ955873
EST:     AATATAAAAACAATGATCAGGGAAATTCTGGGCGTCTAGAGAAATTCGCT                         AACTCGTCCTCTATATCGAGTGCTGCCTATTTTGACCGTGAAGAAGTTGGC
genomic: AATATAAAAACAATGATCAGGGAAATTCTGGGCGTCTAGAGAAATTCGCTgtaagttcgc ... ctgtatgcagAACTCGTCCTCTATATCGAGTGCTGCCTATTTTGACCGTGAAGAAGTTGGC
EST: gi|67698195|gb|BJ958428.1|BJ958428
EST:     AATATAAAAACAATGATCAGGGAAATTCTGGGCGTCTAGAGAAATTCGCT                         AACTCGTCCTCTATATCGAGTGCTGCCTATTTTGACCGTGAAGAAGTTGGC
genomic: AATATAAAAACAATGATCAGGGAAATTCTGGGCGTCTAGAGAAATTCGCTgtaagttcgc ... ctgtatgcagAACTCGTCCTCTATATCGAGTGCTGCCTATTTTGACCGTGAAGAAGTTGGC
EST: gi|18334153|gb|BJ166169.1|BJ166169
EST:     AATATAAAAACAATGATCAGGGAAATTCTGGGCGTCTAGAGAAATTCGCT                         AACTCGTCCTCTATATCGAGTGCTGCCTATTTTGACCGTGAAGAAGTTGGC
genomic: AATATAAAAACAATGATCAGGGAAATTCTGGGCGTCTAGAGAAATTCGCTgtaagttcgc ... ctgtatgcagAACTCGTCCTCTATATCGAGTGCTGCCTATTTTGACCGTGAAGAAGTTGGC
EST: gi|162194335|gb|FC368518.1|FC368518
EST:     AATATAAAAACAATGATCAGGGAAATTCTGGGCGTCTAGAGAAATTCGCT                         AACTCGTCCTCTATATCGAGTGCTGCCTATTTTGACCGTGAAGAAGTTGGC
genomic: AATATAAAAACAATGATCAGGGAAATTCTGGGCGTCTAGAGAAATTCGCTgtaagttcgc ... ctgtatgcagAACTCGTCCTCTATATCGAGTGCTGCCTATTTTGACCGTGAAGAAGTTGGC
EST: gi|67572272|gb|BJ945096.1|BJ945096
EST:     AATATAAAAACAATGATCAGGGAAATTCTGGGCGTCTAGAGAAATTCGCT                         AACTCGTCCTCTATATCGAGTGCTGCCTATTTTGACCGTGAAGAAGTTGGC
genomic: AATATAAAAACAATGATCAGGGAAATTCTGGGCGTCTAGAGAAATTCGCTgtaagttcgc ... ctgtatgcagAACTCGTCCTCTATATCGAGTGCTGCCTATTTTGACCGTGAAGAAGTTGGC
EST: gi|37830194|gb|BJ588206.1|BJ588206
EST:     AATATAAAAACAATGATCAGGGAAATTCTGGGCGTCTAGAGAAATTCGCT                         AACTCGTCCTCTATATCGAGTGCTGCCTATTTTGACCGTGAAGAAGTTGGC
genomic: AATATAAAAACAATGATCAGGGAAATTCTGGGCGTCTAGAGAAATTCGCTgtaagttcgc ... ctgtatgcagAACTCGTCCTCTATATCGAGTGCTGCCTATTTTGACCGTGAAGAAGTTGGC
EST: gi|18335952|gb|BJ167973.1|BJ167973
EST:     AATATAAAAACAATGATCAGGGAAATTCTGGGCGTCTAGAGAAATTCGCT                         AACTCGTCCTCTATATCGAGTGCTGCCTATTTTGACCGTGAAGAAGTTGGC
genomic: AATATAAAAACAATGATCAGGGAAATTCTGGGCGTCTAGAGAAATTCGCTgtaagttcgc ... ctgtatgcagAACTCGTCCTCTATATCGAGTGCTGCCTATTTTGACCGTGAAGAAGTTGGC
EST: gi|18335829|gb|BJ167850.1|BJ167850
EST:     AATATAAAAACAATGATCAGGGAAATTCTGGGCGTCTAGAGAAATTCGCT                         AACTCGTCCTCTATATCGAGTGCTGCCTATTTTGACCGTGAAGAAGTTGGC
genomic: AATATAAAAACAATGATCAGGGAAATTCTGGGCGTCTAGAGAAATTCGCTgtaagttcgc ... ctgtatgcagAACTCGTCCTCTATATCGAGTGCTGCCTATTTTGACCGTGAAGAAGTTGGC
EST: gi|37823009|gb|BJ581075.1|BJ581075
EST:     AATATAAAAACAATGATCAGGGAAATTCTGGGCGTCTAGAGAAATTCGCT                         AACTCGTCCTCTATATCGAGTGCTGCCTATTTTGACCGTGAAGAAGTTGGC
genomic: AATATAAAAACAATGATCAGGGAAATTCTGGGCGTCTAGAGAAATTCGCTgtaagttcgc ... ctgtatgcagAACTCGTCCTCTATATCGAGTGCTGCCTATTTTGACCGTGAAGAAGTTGGC

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: 31 (upstream exon), 10 (downstream exon)
Score: 6

GAAATTTGCCAATGCCAAATCCATCTCTTCTGCACAGTTTTTTGGTGATCAATATAAAAACAATGATCAGGGAAATTCTGGGCGTCTAGAGAAATTCGCTgtaagttcgc ... ctgtatgcagAACTCGTCCTCTATATCGAGTGCTGCCTATTTTGACCGTGAAGAAGTTGGCTCTCCCGGCAGTTCTTCTATTGACGTTACGGCGAGTGAGCTCATGTCTA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttatagtggatgaggcgaacatgatgtgaacttggtgattattactgtatgcagAACTCGTCCTCTATATCGAGTGCTGCCTATTTTGACCGTGAAGAAGTTGGCTCTCCCGGCAGTTCTTCTATTGACGTTACGGCGAGTGAGCTCATGTCTA
                                    tgattatta  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagttcgcaacgttggtgtgcttgctgtctgtaatggctgttattagtgcactattgaggcaatgatctctgatcaatatgtgcatctcgttatagtggatgaggcgaacatgatgtgaacttggtgattattactgtatgcagAACTCGTCCTCTATATCGAGTGCTGCCTATTTTGACCGTGAAGAAGTTGGCTCTCCCGGCAGTTCTTCTATTGACGTTACGGCGAGTGAGCTCATGTCTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA