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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgagatgtggtggccagtgaagtgtgatgtatggtgcatttctctggtacggagtttgtgtggtgtgttcgatgctgacgtttggtggacacggtggcagGTATGTGTTCTGTTGTTCTCACTCTCACAACGTGGCTCCGAAAGGCAAGTATATCGCGTTTGTTTCAGCGGAGGTGGAGACGGAGAACCCTGAGGCTGAG

Basic information

species Physcomitrella patens
transcript PP1S167_1V6.1
intron # 10
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|37836027|gb|BJ594035.1|BJ594035
EST:     TCAGTTCAGATTATTCTACCGCAAAAGCAACTTGGCCGCAGATCGGACAT                         GTATGTGTTCTGTTGTTCTCACTCTCACAACGTGGCTCCGAAAGGCAAGTA
genomic: TCAGTTCAGATTATTCTACCGCAAAAGCAACTTGGCCGCAGATCGGACATgtaagtggtg ... acggtggcagGTATGTGTTCTGTTGTTCTCACTCTCACAACGTGGCTCCGAAAGGCAAGTA
EST: gi|67727151|gb|BJ977410.1|BJ977410
EST:     TCAGTTCAGATTATTCTACCGCAAAAGCAACTTGGCCGCAGATCGGACAT                         GTATGTGTTCTGTTGTTCTCACTCTCACAACGTGGCTCCGAAAGGCAAGTA
genomic: TCAGTTCAGATTATTCTACCGCAAAAGCAACTTGGCCGCAGATCGGACATgtaagtggtg ... acggtggcagGTATGTGTTCTGTTGTTCTCACTCTCACAACGTGGCTCCGAAAGGCAAGTA
EST: gi|162182042|gb|FC356913.1|FC356913
EST:     TCAGTTCAGATTATTCTACCGCAAAAGCAACTTGGCCGCAGATCGGACAT                         GTATGTGTTCTGTTGTTCTCACTCTCACAACGTGGCTCCGAAAGGCAAGTA
genomic: TCAGTTCAGATTATTCTACCGCAAAAGCAACTTGGCCGCAGATCGGACATgtaagtggtg ... acggtggcagGTATGTGTTCTGTTGTTCTCACTCTCACAACGTGGCTCCGAAAGGCAAGTA
EST: gi|162260908|gb|FC437965.1|FC437965
EST:     TCAGTTCAGATTATTCTACCGCAAAAGCAACTTGGCCGCAGATCGGACAT                         GTATGTGTTCTGTTGTTCTCACTCTCACAACGTGGCTCCGAAAGGCAAGTA
genomic: TCAGTTCAGATTATTCTACCGCAAAAGCAACTTGGCCGCAGATCGGACATgtaagtggtg ... acggtggcagGTATGTGTTCTGTTGTTCTCACTCTCACAACGTGGCTCCGAAAGGCAAGTA
EST: gi|67695406|gb|BJ955639.1|BJ955639
EST:     TCAGTTCAGATTATTCTACCGCAAAAGCAACTTGGCCGCAGATCGGACAT                         GTATGTGTTCTGTTGTTCTCACTCTCACAACGTGGCTCCGAAAGGCAAGTA
genomic: TCAGTTCAGATTATTCTACCGCAAAAGCAACTTGGCCGCAGATCGGACATgtaagtggtg ... acggtggcagGTATGTGTTCTGTTGTTCTCACTCTCACAACGTGGCTCCGAAAGGCAAGTA
EST: gi|18338354|gb|BJ170378.1|BJ170378
EST:     TCAGTTCAGATTATTCTACCGCAAAAGCAACTTGGCCGCAGATCGGACAT                         GTATGTGTTCTGTTGTTCTCACTCTCACAACGTGGCTCCGAAAGGCAAGTA
genomic: TCAGTTCAGATTATTCTACCGCAAAAGCAACTTGGCCGCAGATCGGACATgtaagtggtg ... acggtggcagGTATGTGTTCTGTTGTTCTCACTCTCACAACGTGGCTCCGAAAGGCAAGTA
EST: gi|162183902|gb|FC360208.1|FC360208
EST:     TCAGTTCAGATTATTCTACCGCAAAAGCAACTTGGCCGCAGATCGGACAT                         GTATGTGTTCTGTTGTTCTCACTCTCACAACGTGGCTCCGAAAGGCAAGTA
genomic: TCAGTTCAGATTATTCTACCGCAAAAGCAACTTGGCCGCAGATCGGACATgtaagtggtg ... acggtggcagGTATGTGTTCTGTTGTTCTCACTCTCACAACGTGGCTCCGAAAGGCAAGTA
EST: gi|162182856|gb|FC359772.1|FC359772
EST:     TCAGTTCAGATTATTCTACCGCAAAAGCAACTTGGCCGCAGATCGGACAT                         GTATGTGTTCTGTTGTTCTCACTCTCACAACGTGGCTCCGAAAGGCAAGTA
genomic: TCAGTTCAGATTATTCTACCGCAAAAGCAACTTGGCCGCAGATCGGACATgtaagtggtg ... acggtggcagGTATGTGTTCTGTTGTTCTCACTCTCACAACGTGGCTCCGAAAGGCAAGTA
EST: gi|67695866|gb|BJ956099.1|BJ956099
EST:     TCAGTTCAGATTATTCTACCGCAAAAGCAACTTGGCCGCAGATCGGACAT                         GTATGTGTTCTGTTGTTCTCACTCTCACAACGTGGCTCCGAAAGGCAAGTA
genomic: TCAGTTCAGATTATTCTACCGCAAAAGCAACTTGGCCGCAGATCGGACATgtaagtggtg ... acggtggcagGTATGTGTTCTGTTGTTCTCACTCTCACAACGTGGCTCCGAAAGGCAAGTA
EST: gi|162190903|gb|FC368101.1|FC368101
EST:     TCAGTTCAGATTATTCTACCGCAAAAGCAACTTGGCCGCAGATCGGACAT                         GTATGTGTTCTGTTGTTCTCACTCTCACAACGTGGCTCCGAAAGGCAAGTA
genomic: TCAGTTCAGATTATTCTACCGCAAAAGCAACTTGGCCGCAGATCGGACATgtaagtggtg ... acggtggcagGTATGTGTTCTGTTGTTCTCACTCTCACAACGTGGCTCCGAAAGGCAAGTA
EST: gi|162182855|gb|FC359771.1|FC359771
EST:     TCAGTTCAGATTATTCTACCGCAAAAGCAACTTGGCCGCAGATCGGACAT                         GTATGTGTTCTGTTGTTCTCACTCTCACAACGTGGCTCCGAAAGGCAAGTA
genomic: TCAGTTCAGATTATTCTACCGCAAAAGCAACTTGGCCGCAGATCGGACATgtaagtggtg ... acggtggcagGTATGTGTTCTGTTGTTCTCACTCTCACAACGTGGCTCCGAAAGGCAAGTA
EST: gi|162180550|gb|FC356192.1|FC356192
EST:     TCAGTTCAGATTATTCTACCGCAAAAGCAACTTGGCCGCAGATCGGACAT                         GTATGTGTTCTGTTGTTCTCACTCTCACAACGTGGCTCCGAAAGGCAAGTA
genomic: TCAGTTCAGATTATTCTACCGCAAAAGCAACTTGGCCGCAGATCGGACATgtaagtggtg ... acggtggcagGTATGTGTTCTGTTGTTCTCACTCTCACAACGTGGCTCCGAAAGGCAAGTA
EST: gi|162167540|gb|FC343711.1|FC343711
EST:     TCAGTTCAGATTATTCTACCGCAAAAGCAACTTGGCCGCAGATCGGACAT                         GTATGTGTTCTGTTGTTCTCACTCTCACAACGTGGCTCCGAAAGGCAAGTA
genomic: TCAGTTCAGATTATTCTACCGCAAAAGCAACTTGGCCGCAGATCGGACATgtaagtggtg ... acggtggcagGTATGTGTTCTGTTGTTCTCACTCTCACAACGTGGCTCCGAAAGGCAAGTA
EST: gi|208365337|gb|DC950780.1|DC950780
EST:     TCAGTTCAGATTATTCTACCGCAAAAGCAACTTGGCCGTAGATCGGACAT                         GTATGTGTTCTGTTGTTCTCACTCTCACAACGTGGCTCCGAAAGGCAAGTA
genomic: TCAGTTCAGATTATTCTACCGCAAAAGCAACTTGGCCGCAGATCGGACATgtaagtggtg ... acggtggcagGTATGTGTTCTGTTGTTCTCACTCTCACAACGTGGCTCCGAAAGGCAAGTA
EST: gi|67572493|gb|BJ945317.1|BJ945317
EST:     TCAGTTCAGATTATTCTACCGCAAAAGCAACTTGGCCGCAGATCGGACAT                         GTATGTGTTCTGTTGTTCTCACTCTCACAACGTGGCTCCGAAAGGCAAGTA
genomic: TCAGTTCAGATTATTCTACCGCAAAAGCAACTTGGCCGCAGATCGGACATgtaagtggtg ... acggtggcagGTATGTGTTCTGTTGTTCTCACTCTCACAACGTGGCTCCGAAAGGCAAGTA
EST: gi|37844266|gb|BJ602274.1|BJ602274
EST:     TCAGTTCAGATTATTCTACCGCAAAAGCAACTTGGCCGCAGATCGGACAT                         GTATGTGTTCTGTTGTTCTCACTCTCACAACGTGGCTCCGAAAGGCAAGTA
genomic: TCAGTTCAGATTATTCTACCGCAAAAGCAACTTGGCCGCAGATCGGACATgtaagtggtg ... acggtggcagGTATGTGTTCTGTTGTTCTCACTCTCACAACGTGGCTCCGAAAGGCAAGTA
EST: gi|162198833|gb|FC374316.1|FC374316
EST:     TCAGTTCAGATTATTCTACCGCAAAAGCAACTTGGCCGCAGATCGGACAT                         GTATGTGTTCTGTTGTTCTCACTCTCACAACGTGGCTCCGAAAGGCAAGTA
genomic: TCAGTTCAGATTATTCTACCGCAAAAGCAACTTGGCCGCAGATCGGACATgtaagtggtg ... acggtggcagGTATGTGTTCTGTTGTTCTCACTCTCACAACGTGGCTCCGAAAGGCAAGTA
EST: gi|37831207|gb|BJ589219.1|BJ589219
EST:     TCAGTTCAGATTATTCTACCGCAAAAGCAACTTGGCCGCAGATCGGACAT                         GTATGTGTTCTGTTGTTCTCACTCTCACAACGTGGCTCCGAAAGGCAAGTA
genomic: TCAGTTCAGATTATTCTACCGCAAAAGCAACTTGGCCGCAGATCGGACATgtaagtggtg ... acggtggcagGTATGTGTTCTGTTGTTCTCACTCTCACAACGTGGCTCCGAAAGGCAAGTA
EST: gi|162249711|gb|FC426825.1|FC426825
EST:     TCAGTTCAGATTATTCTACCGCACAAGCAACTTGGCCGCAGATCGGACAT                         GTATGTGTTCTGTTGTTCTCACTCTCACAACGTGGCTC
genomic: TCAGTTCAGATTATTCTACCGCAAAAGCAACTTGGCCGCAGATCGGACATgtaagtggtg ... acggtggcagGTATGTGTTCTGTTGTTCTCACTCTCACAACGTGGCTC
EST: gi|162180551|gb|FC356193.1|FC356193
EST:     TCAGTTCAGATTATTCTACCGCAAAAGCAACTTGGCCGCAGATCGGACAT                         GTATGTGTTCTGTTGTTCTCACTCTCACAACGTGGCTCCGAAAGGCAAGTA
genomic: TCAGTTCAGATTATTCTACCGCAAAAGCAACTTGGCCGCAGATCGGACATgtaagtggtg ... acggtggcagGTATGTGTTCTGTTGTTCTCACTCTCACAACGTGGCTCCGAAAGGCAAGTA
EST: gi|67726787|gb|BJ977046.1|BJ977046
EST:     TCAGTTCAGATTATTCTACCGCAAAAGCAACTTGGCCGCAGATCGGACAT                         GTATGTGTTCTGTTGTTCTCACTCTCACAACGTGGCTCCGAAAGGCAAGTA
genomic: TCAGTTCAGATTATTCTACCGCAAAAGCAACTTGGCCGCAGATCGGACATgtaagtggtg ... acggtggcagGTATGTGTTCTGTTGTTCTCACTCTCACAACGTGGCTCCGAAAGGCAAGTA
EST: gi|208399434|gb|DC924864.1|DC924864
EST:     TCAGTTCAGATTATTCTACCGCAAAAGCAACTTGGCCGCAGATCGGACAT                         GTATGTGTTCTGTTGTTCTCACTCTCACAACGTGGCTCCGAAAGGCAAGTA
genomic: TCAGTTCAGATTATTCTACCGCAAAAGCAACTTGGCCGCAGATCGGACATgtaagtggtg ... acggtggcagGTATGTGTTCTGTTGTTCTCACTCTCACAACGTGGCTCCGAAAGGCAAGTA
EST: gi|67724873|gb|BJ975132.1|BJ975132
EST:     TCAGTTCAGATTATTCTACCGCAAAAGCAACTTGGCCGCAGATCGGACAT                         GTATGTGTTCTGTTGTTCTCACTCTCACAACGTGGCTCCGAAAGGCAAGTA
genomic: TCAGTTCAGATTATTCTACCGCAAAAGCAACTTGGCCGCAGATCGGACATgtaagtggtg ... acggtggcagGTATGTGTTCTGTTGTTCTCACTCTCACAACGTGGCTCCGAAAGGCAAGTA
EST: gi|162182043|gb|FC356914.1|FC356914
EST:     TCAGTTCAGATTATTCTACCGCAAAAGCAACTTGGCCGCAGATCGGACAT                         GTATGTGTTCTGTTGTTCTCACTCTCACAACGTGGCTCCGAAAGGCAAGTA
genomic: TCAGTTCAGATTATTCTACCGCAAAAGCAACTTGGCCGCAGATCGGACATgtaagtggtg ... acggtggcagGTATGTGTTCTGTTGTTCTCACTCTCACAACGTGGCTCCGAAAGGCAAGTA
EST: gi|162194880|gb|FC368997.1|FC368997
EST:     TCAGTTCAGATTATTCTACCGCAAAAGCAACTTGGCCGCAGATCGGACAT                         GTATGTGTTCTGTTGTTCTCACTCTCACAACGTGGCTCCGAAAGGCAAGTA
genomic: TCAGTTCAGATTATTCTACCGCAAAAGCAACTTGGCCGCAGATCGGACATgtaagtggtg ... acggtggcagGTATGTGTTCTGTTGTTCTCACTCTCACAACGTGGCTCCGAAAGGCAAGTA
EST: gi|37852478|gb|BJ610486.1|BJ610486
EST:     TCAGTTCAGATTATTCTACCGCAAAAGCAACTTGGCCGCAGATCGGACAT                         GTATGTGTTCTGTTGTTCTCACTCTCACAACGTGGCTCCGAAAGGCAAGTA
genomic: TCAGTTCAGATTATTCTACCGCAAAAGCAACTTGGCCGCAGATCGGACATgtaagtggtg ... acggtggcagGTATGTGTTCTGTTGTTCTCACTCTCACAACGTGGCTCCGAAAGGCAAGTA
EST: gi|208364369|gb|DC950670.1|DC950670
EST:     TCAGTTCAGATTATTCTACCGCAAAAGCAACTTGGCCGCAGATCGGACAT                         GTATGTGTTCTGTTGTTCTCACTCTCACAACGTGGCTCCGAAAGGCAAGTA
genomic: TCAGTTCAGATTATTCTACCGCAAAAGCAACTTGGCCGCAGATCGGACATgtaagtggtg ... acggtggcagGTATGTGTTCTGTTGTTCTCACTCTCACAACGTGGCTCCGAAAGGCAAGTA
EST: gi|162239318|gb|FC415404.1|FC415404
EST:     TCAGTTCAGATTATTCTACCGCAAAAGCAACTTGGCCGCAGATCGGACAT                         GTATGTGTTCTGTTGTTCTCACTCTCACAACGTGGCTCCGAAAGGCAAGTA
genomic: TCAGTTCAGATTATTCTACCGCAAAAGCAACTTGGCCGCAGATCGGACATgtaagtggtg ... acggtggcagGTATGTGTTCTGTTGTTCTCACTCTCACAACGTGGCTCCGAAAGGCAAGTA
EST: gi|162202239|gb|FC378095.1|FC378095
EST:     TCAGTTCAGATTATTCTACCGCAAAAGCAACTTGGCCGCAGATCGGACAT                         GTATGTGTTCTGTTGTTCTCACTCTCACAACGTGGCTCCGAAAGGCAAGTA
genomic: TCAGTTCAGATTATTCTACCGCAAAAGCAACTTGGCCGCAGATCGGACATgtaagtggtg ... acggtggcagGTATGTGTTCTGTTGTTCTCACTCTCACAACGTGGCTCCGAAAGGCAAGTA
EST: gi|67700068|gb|BJ960301.1|BJ960301
EST:     TCAGTTCAGATTATTCTACCGCAAAAGCAACTTGGCCGCAGATCGGACAT                         GTATGTGTTCTGTTGTTCTCACTCTCACAACGTGGCTCCGAAAGGCAAGTA
genomic: TCAGTTCAGATTATTCTACCGCAAAAGCAACTTGGCCGCAGATCGGACATgtaagtggtg ... acggtggcagGTATGTGTTCTGTTGTTCTCACTCTCACAACGTGGCTCCGAAAGGCAAGTA
EST: gi|208370153|gb|DC951752.1|DC951752
EST:     TCAGTTCAGATTATTCTACCGCAAAAGCAACTTGGCCGCAGATCGGACAT                         GTATGTGTTCTGTTGTTCTCACTCTCACAACGTGGCTCCGAAAGGCAAGTA
genomic: TCAGTTCAGATTATTCTACCGCAAAAGCAACTTGGCCGCAGATCGGACATgtaagtggtg ... acggtggcagGTATGTGTTCTGTTGTTCTCACTCTCACAACGTGGCTCCGAAAGGCAAGTA
EST: gi|162183901|gb|FC360207.1|FC360207
EST:     TCAGTTCAGATTATTCTACCGCAAAAGCAACTTGGCCGCAGATCGGACAT                         GTATGTGTTCTGTTGTTCTCACTCTCACAACGTGGCTCCGAAAGGCAAGTA
genomic: TCAGTTCAGATTATTCTACCGCAAAAGCAACTTGGCCGCAGATCGGACATgtaagtggtg ... acggtggcagGTATGTGTTCTGTTGTTCTCACTCTCACAACGTGGCTCCGAAAGGCAAGTA

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: 35 (upstream exon), 30 (downstream exon)
Score: 18

GTGCTATCTGCTTTATGAGCCATCCGATTCCGAACACCGGGGACTCCGATTCAGTTCAGATTATTCTACCGCAAAAGCAACTTGGCCGCAGATCGGACATgtaagtggtg ... acggtggcagGTATGTGTTCTGTTGTTCTCACTCTCACAACGTGGCTCCGAAAGGCAAGTATATCGCGTTTGTTTCAGCGGAGGTGGAGACGGAGAACCCTGAGGCTGAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggtacggagtttgtgtggtgtgttcgatgctgacgtttggtggacacggtggcagGTATGTGTTCTGTTGTTCTCACTCTCACAACGTGGCTCCGAAAGGCAAGTATATCGCGTTTGTTTCAGCGGAGGTGGAGACGGAGAACCCTGAGGCTGAG
                           tgctgac  putative branch site (score: 18)
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgagatgtggtggccagtgaagtgtgatgtatggtgcatttctctggtacggagtttgtgtggtgtgttcgatgctgacgtttggtggacacggtggcagGTATGTGTTCTGTTGTTCTCACTCTCACAACGTGGCTCCGAAAGGCAAGTATATCGCGTTTGTTTCAGCGGAGGTGGAGACGGAGAACCCTGAGGCTGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA
- - - - - - - - - - - - - - - -tggtgca