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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttttcagctattctgcaattgaacgactttttctttcactcaactcagttctaataattatctggagctgggtgttataatcttgtatctttgtgagcagTGGCTGGGTTTGAACAAGGATTTGAAGAGACTTGAAGTGCAGACAACCATGAACCAG

Basic information

species Physcomitrella patens
transcript PP1S174_60V6.1
intron # 3
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|162260962|gb|FC438019.1|FC438019
EST:     TTGCAAAGATGAATGCTGCGGGCGCTGGTGTGCAGGGATCCGGCTGGGTG                         TGGCTGGGTTTGAACAAGGATTTGAAGAGACTTGAAGTGCAGACAACCATG
genomic: TTGCAAAGATGAATGCTGCGGGCGCTGGTGTGCAGGGATCCGGCTGGGTGgtacgatcta ... ttgtgagcagTGGCTGGGTTTGAACAAGGATTTGAAGAGACTTGAAGTGCAGACAACCATG
EST: gi|208366209|gb|DC955308.1|DC955308
EST:     TTGCAAAGATGAATGCTGCGGGCGCTGGTGTGCAGGGATCCGGCTGGGTG                         TGGCTGGGTTTGAACAAGGATTTGAAGAGACTTGAAGTGCAGACAACCATG
genomic: TTGCAAAGATGAATGCTGCGGGCGCTGGTGTGCAGGGATCCGGCTGGGTGgtacgatcta ... ttgtgagcagTGGCTGGGTTTGAACAAGGATTTGAAGAGACTTGAAGTGCAGACAACCATG
EST: gi|162235362|gb|FC412329.1|FC412329
EST:     TTGCAAAGATGAATGCTGCGGGCGCTGGTGTGCAGGGATCCGGCTGGGTG                         TGGCTGGGTTTGAACAAGGATTTGAAGAGACTTGAAGTGCAGACAACCATG
genomic: TTGCAAAGATGAATGCTGCGGGCGCTGGTGTGCAGGGATCCGGCTGGGTGgtacgatcta ... ttgtgagcagTGGCTGGGTTTGAACAAGGATTTGAAGAGACTTGAAGTGCAGACAACCATG
EST: gi|208391751|gb|DC942313.1|DC942313
EST:     TTGCAAAGATGAATGCTGCGGGCGCTGGTGTGCAGGGATCCGGCTGGGTG                         TGGCTGGGTTTGAACAAGGATTTGAAGAGACTTGAAGTGCAGACAACCATG
genomic: TTGCAAAGATGAATGCTGCGGGCGCTGGTGTGCAGGGATCCGGCTGGGTGgtacgatcta ... ttgtgagcagTGGCTGGGTTTGAACAAGGATTTGAAGAGACTTGAAGTGCAGACAACCATG
EST: gi|208397933|gb|DC916688.1|DC916688
EST:     TTGCAAAGATGAATGCTGCGGGCGCTGGTGTGCAGGGATCCGGCTGGGTG                         TGGCTGGGTTTGAACAAGGATTTGAAGAGACTTGAAGTGCAGACAACCATG
genomic: TTGCAAAGATGAATGCTGCGGGCGCTGGTGTGCAGGGATCCGGCTGGGTGgtacgatcta ... ttgtgagcagTGGCTGGGTTTGAACAAGGATTTGAAGAGACTTGAAGTGCAGACAACCATG
EST: gi|208348700|gb|DC926375.1|DC926375
EST:     TTGCAAAGATGAATGCTGCGGGCGCTGGTGTGCAGGGATCCGGCTGGGTG                         TGGCTGGGTTTGAACAAGGATTTGAAGAGACTTGAAGTGCAGACAACCATG
genomic: TTGCAAAGATGAATGCTGCGGGCGCTGGTGTGCAGGGATCCGGCTGGGTGgtacgatcta ... ttgtgagcagTGGCTGGGTTTGAACAAGGATTTGAAGAGACTTGAAGTGCAGACAACCATG
EST: gi|208344646|gb|DC912592.1|DC912592
EST:     TTGCAAAGATGAATGCTGCGGGCGCTGGTGTGCAGGGATCCGGCTGGGTG                         TGGCTGGGTTTGAACAAGGATTTGAAGAGACTTGAAGTGCAGACAACCATG
genomic: TTGCAAAGATGAATGCTGCGGGCGCTGGTGTGCAGGGATCCGGCTGGGTGgtacgatcta ... ttgtgagcagTGGCTGGGTTTGAACAAGGATTTGAAGAGACTTGAAGTGCAGACAACCATG
EST: gi|19789071|gb|BQ041074.1|BQ041074
EST:     TTGCAAAGATGAATGCTGCGGGCGCTGGTGTGCAGGGATCCGGCTGGGTG                         TGGCTGGGTTTGAACAAGGATTTGAAGAGACTTGAAGTGCAGACAACCATG
genomic: TTGCAAAGATGAATGCTGCGGGCGCTGGTGTGCAGGGATCCGGCTGGGTGgtacgatcta ... ttgtgagcagTGGCTGGGTTTGAACAAGGATTTGAAGAGACTTGAAGTGCAGACAACCATG
EST: gi|37834392|gb|BJ592404.1|BJ592404
EST:     TTGCAAAGATGAATGCTGCGGGCGCTGGTGTGCAGGGATCCGGCTGGGTG                         TGGCTGGGTTTGAACAAGGATTTGAAGAGACTTGAAGTGCAGACAACCATG
genomic: TTGCAAAGATGAATGCTGCGGGCGCTGGTGTGCAGGGATCCGGCTGGGTGgtacgatcta ... ttgtgagcagTGGCTGGGTTTGAACAAGGATTTGAAGAGACTTGAAGTGCAGACAACCATG
EST: gi|67570006|gb|BJ942830.1|BJ942830
EST:     TTGCAAAGATGAATGCTGCGGGCGCTGGTGTGCAGGGATCCGGCTGGGTG                         TGGCTGGGTTTGAACAAGGATTTGAAGAGACTTGAAGTGCAGACAACCATG
genomic: TTGCAAAGATGAATGCTGCGGGCGCTGGTGTGCAGGGATCCGGCTGGGTGgtacgatcta ... ttgtgagcagTGGCTGGGTTTGAACAAGGATTTGAAGAGACTTGAAGTGCAGACAACCATG
EST: gi|37831305|gb|BJ589317.1|BJ589317
EST:     TTGCAAAGATGAATGCTGCGGGCGCTGGTGTGCAGGGATCCGGCTGGGTG                         TGGCTGGGTTTGAACAAGGATTTGAAGAGACTTGAAGTGCAGACAACCATG
genomic: TTGCAAAGATGAATGCTGCGGGCGCTGGTGTGCAGGGATCCGGCTGGGTGgtacgatcta ... ttgtgagcagTGGCTGGGTTTGAACAAGGATTTGAAGAGACTTGAAGTGCAGACAACCATG
EST: gi|67693275|gb|BJ953508.1|BJ953508
EST:     TTGCAAAGATGAATGCTGCGGGCGCTGGTGTGCAGGGATCCGGCTGGGTG                         TGGCTGGGTTTGAACAAGGATTTGAAGAGACTTGAAGTGCAGACAACCATG
genomic: TTGCAAAGATGAATGCTGCGGGCGCTGGTGTGCAGGGATCCGGCTGGGTGgtacgatcta ... ttgtgagcagTGGCTGGGTTTGAACAAGGATTTGAAGAGACTTGAAGTGCAGACAACCATG
EST: gi|100441642|gb|BY962733.1|BY962733
EST:     TTGCAAAGATGAATGCTGCGGGCGCTGGTGTGCAGGGATCCGGCTGGGTG                         TGGCTGGGTTTGAACAAGGATTTGAAGAGACTTGAAGTGCAGACAACCATG
genomic: TTGCAAAGATGAATGCTGCGGGCGCTGGTGTGCAGGGATCCGGCTGGGTGgtacgatcta ... ttgtgagcagTGGCTGGGTTTGAACAAGGATTTGAAGAGACTTGAAGTGCAGACAACCATG
EST: gi|208377497|gb|DC902792.1|DC902792
EST:     TTGCAAAGATGAATGCTGCGGGCGCTGGTGTGCAGGGATCCGGCTGGGTG                         TGGCTGGGTTTGAACAAGGATTTGAANANACTTGAANTGCANACAACCATG
genomic: TTGCAAAGATGAATGCTGCGGGCGCTGGTGTGCAGGGATCCGGCTGGGTGgtacgatcta ... ttgtgagcagTGGCTGGGTTTGAACAAGGATTTGAAGAGACTTGAAGTGCAGACAACCATG
EST: gi|162235361|gb|FC412328.1|FC412328
EST:     TTGCAAAGATGAATGCTGCGGGCGCTGGTGTGCAGGGATCCGGCTGGGTG                         TGGCTGGGTTTGAACAAGGATTTGAAGAGACTTGAAGTGCAGACAACCATG
genomic: TTGCAAAGATGAATGCTGCGGGCGCTGGTGTGCAGGGATCCGGCTGGGTGgtacgatcta ... ttgtgagcagTGGCTGGGTTTGAACAAGGATTTGAAGAGACTTGAAGTGCAGACAACCATG

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: 33 (upstream exon), 32 (downstream exon)
Score: 23

AAGCCTTTCTAAGGCCATTGATGCACAGTTTGGGGACCTGGACAAATTGATTGCAAAGATGAATGCTGCGGGCGCTGGTGTGCAGGGATCCGGCTGGGTGgtacgatcta ... ttgtgagcagTGGCTGGGTTTGAACAAGGATTTGAAGAGACTTGAAGTGCAGACAACCATGAACCAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cagttctaataattatctggagctgggtgttataatcttgtatctttgtgagcagTGGCTGGGTTTGAACAAGGATTTGAAGAGACTTGAAGTGCAGACAACCATGAACCAG
   ttctaat  putative branch site (score: 23)
                                        tatcttt  putative PPT
                             ttataatcttgtat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttttcagctattctgcaattgaacgactttttctttcactcaactcagttctaataattatctggagctgggtgttataatcttgtatctttgtgagcagTGGCTGGGTTTGAACAAGGATTTGAAGAGACTTGAAGTGCAGACAACCATGAACCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - ttctgca