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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCTGGGAAGTACATTTGGTTTAATTACCAGCAAGTATATGAAACAGTGGTCCAAATCGGTTCTGCTATTCGTCACATTGGCGTACAGCCGgtttgttccgtttaccttttgccaatgtgttcgtagtaaaaatgctcgacgatacaggacatttctttgaagtcagtgaggacatcaagaaaattactca...

Basic information

species Physcomitrella patens
transcript PP1S218_19V6.1
intron # 4
splice site 5'
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|162164429|gb|FC341048.1|FC341048
EST:     AAACAGTGGTCCAAATCGGTTCTGCTATTCGTCACATTGGCGTACAGCCG                         AAAAGCAAAATTGGAGTTTATGGCATAAATTGCCCGCAGTGGTTCATGGCC
genomic: AAACAGTGGTCCAAATCGGTTCTGCTATTCGTCACATTGGCGTACAGCCGgtttgttccg ... ttccgtccagAAAAGCAAAATTGGAGTTTATGGCATAAATTGCCCGCAGTGGTTCATGGCC
EST: gi|162167702|gb|FC344016.1|FC344016
EST:     AAACAGTGGTCCAAATCGGTTCTGCTATTCGTCACATTGGCGTACAGCCG                         AAAAGCAAAATTGGAGTTTATGGCATAAATTGCCCGCAGTGGTTCATGGCC
genomic: AAACAGTGGTCCAAATCGGTTCTGCTATTCGTCACATTGGCGTACAGCCGgtttgttccg ... ttccgtccagAAAAGCAAAATTGGAGTTTATGGCATAAATTGCCCGCAGTGGTTCATGGCC
EST: gi|18371694|gb|BJ203296.1|BJ203296
EST:     AAACAGTGGTCCAAATCGGTTCTGCTATTCGTCACATTGGCGTACAGCCG                         AAAAGCAAAATTGGAGTTTATGGCATAAATTGCCCGCAGTG
genomic: AAACAGTGGTCCAAATCGGTTCTGCTATTCGTCACATTGGCGTACAGCCGgtttgttccg ... ttccgtccagAAAAGCAAAATTGGAGTTTATGGCATAAATTGCCCGCAGTG
EST: gi|18355808|gb|BJ187867.1|BJ187867
EST:     AAACAGTGGTCCAAATCGGTTCTGCTATTCGTCACATTGGCGTACAGCCG                         AAAAGCAAAATTGGAGTTTATGGCATAAATTG
genomic: AAACAGTGGTCCAAATCGGTTCTGCTATTCGTCACATTGGCGTACAGCCGgtttgttccg ... ttccgtccagAAAAGCAAAATTGGAGTTTATGGCATAAATTG
EST: gi|162171311|gb|FC347236.1|FC347236
EST:     AAACAGTGGTCCAAATCGGTTCTGCTATTCGTCACATTGGCGTACAGCCG                         AAAAGCAAAATTGGAGTTTATGGCATAAATTGCCCGCAGTGGTTCATGGCC
genomic: AAACAGTGGTCCAAATCGGTTCTGCTATTCGTCACATTGGCGTACAGCCGgtttgttccg ... ttccgtccagAAAAGCAAAATTGGAGTTTATGGCATAAATTGCCCGCAGTGGTTCATGGCC
EST: gi|18361267|gb|BJ193332.1|BJ193332
EST:     AACAGTGGTCCAAAATCGGTTCTGCTATTCGTCACATTGGCGTACAGCCG                         AAAAGCAAAATTGGAGTTTATGGCATAAATTGCCCGCAGTGGTT
genomic: AACAGTGGTCCAAA-TCGGTTCTGCTATTCGTCACATTGGCGTACAGCCGgtttgttccg ... ttccgtccagAAAAGCAAAATTGGAGTTTATGGCATAAATTGCCCGCAGTGGTT
EST: gi|18355950|gb|BJ188009.1|BJ188009
EST:     AAACAGTGGTCCAAATCGGTTCTGCTATTCGTCACATTGGCGTACAGCCG                         AAAAGCAAAATTGGAGTTTATGGCATAAATTGCCCGCAG
genomic: AAACAGTGGTCCAAATCGGTTCTGCTATTCGTCACATTGGCGTACAGCCGgtttgttccg ... ttccgtccagAAAAGCAAAATTGGAGTTTATGGCATAAATTGCCCGCAG
EST: gi|18346122|gb|BJ178165.1|BJ178165
EST:     AAACAGTGGTCCAAATCGGTTCTGCTATTCGTCACATTGGCGTACAGCCG                         AAAAGCAAAATTGGAGTTTATGGCATAAATTGCCCGCAGTGGTTCATGGCC
genomic: AAACAGTGGTCCAAATCGGTTCTGCTATTCGTCACATTGGCGTACAGCCGgtttgttccg ... ttccgtccagAAAAGCAAAATTGGAGTTTATGGCATAAATTGCCCGCAGTGGTTCATGGCC
EST: gi|18331390|gb|BJ163401.1|BJ163401
EST:     AAACAGTGGTCCAAATCGGTTCTGCTATTCGTCACATTGGCGTACAGCCG                         AAAAGCAAAATTGGAGTTTATGGCATAAA
genomic: AAACAGTGGTCCAAATCGGTTCTGCTATTCGTCACATTGGCGTACAGCCGgtttgttccg ... ttccgtccagAAAAGCAAAATTGGAGTTTATGGCATAAA
EST: gi|162235485|gb|FC411308.1|FC411308
EST:     AAACAGTGGTCCAAATCGGTTCTGCTATTCGTCACATTGGCGTACAGCCG                         AAAAGCAAAATTGGAGTTTATGGCATAAATTGCCCGCAGTGGTTCATGGCC
genomic: AAACAGTGGTCCAAATCGGTTCTGCTATTCGTCACATTGGCGTACAGCCGgtttgttccg ... ttccgtccagAAAAGCAAAATTGGAGTTTATGGCATAAATTGCCCGCAGTGGTTCATGGCC
EST: gi|18346188|gb|BJ178231.1|BJ178231
EST:     AAACAGTGGTCCAAATCGGTTCTGCTATTCGTCACATTGGCGTACAGCCG                         AAAAGCAAAATTGGAGTTTATGGCATAAATTGCCCGCAGTGGTTCATGGC
genomic: AAACAGTGGTCCAAATCGGTTCTGCTATTCGTCACATTGGCGTACAGCCGgtttgttccg ... ttccgtccagAAAAGCAAAATTGGAGTTTATGGCATAAATTGCCCGCAGTGGTTCATGGC
EST: gi|18350093|gb|BJ182144.1|BJ182144
EST:     AAACAGTGGTCCAAATCGGTTCTGCTATTCGTCACATTGGCGTACAGCCG                         AAAAGCAAAATTGGAGTTTATGGCATAAATTGCC
genomic: AAACAGTGGTCCAAATCGGTTCTGCTATTCGTCACATTGGCGTACAGCCGgtttgttccg ... ttccgtccagAAAAGCAAAATTGGAGTTTATGGCATAAATTGCC
EST: gi|18367433|gb|BJ199516.1|BJ199516
EST:     AAACAGTGGTCCAAATCGGTTCTGCTATTCGTCACATTGGCGTACAGCCG                         AAAAGCAAAATTGGAGTTTATGGCATAAATTGCCCGCAGTGGTT
genomic: AAACAGTGGTCCAAATCGGTTCTGCTATTCGTCACATTGGCGTACAGCCGgtttgttccg ... ttccgtccagAAAAGCAAAATTGGAGTTTATGGCATAAATTGCCCGCAGTGGTT
EST: gi|162199213|gb|FC375049.1|FC375049
EST:     AAACAGTGGTCCAAATCGGTTCTGCTATTCGTCACATTGGCGTACAGCCG                         AAAAGCAAAATTGGAGTTTATGGCATAAATTGCCCGCAGTGGTTCATGGCC
genomic: AAACAGTGGTCCAAATCGGTTCTGCTATTCGTCACATTGGCGTACAGCCGgtttgttccg ... ttccgtccagAAAAGCAAAATTGGAGTTTATGGCATAAATTGCCCGCAGTGGTTCATGGCC
EST: gi|162167280|gb|FC342845.1|FC342845
EST:     AAACAGTGGTCCAAATCGGTTCTGCTATTCGTCACATTGGCGTACAGCCG                         AAAAGCAAAATTGGAGTTTATGGCATAAATTGCCCGCAGTGGTTCATGGCC
genomic: AAACAGTGGTCCAAATCGGTTCTGCTATTCGTCACATTGGCGTACAGCCGgtttgttccg ... ttccgtccagAAAAGCAAAATTGGAGTTTATGGCATAAATTGCCCGCAGTGGTTCATGGCC

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: 10 (upstream exon), 26 (downstream exon)
Score: 1

GCTGGGAAGTACATTTGGTTTAATTACCAGCAAGTATATGAAACAGTGGTCCAAATCGGTTCTGCTATTCGTCACATTGGCGTACAGCCGgtttgttccg ... ttccgtccagAAAAGCAAAATTGGAGTTTATGGCATAAATTGCCCGCAGTGGTTCATGGCCATGGAG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCTGGGAAGTACATTTGGTTTAATTACCAGCAAGTATATGAAACAGTGGTCCAAATCGGTTCTGCTATTCGTCACATTGGCGTACAGCCGgtttgttccgtttaccttttgccaatgtgttcgtagtaaaaatgctcgacgatacaggacatttctttgaagtcagtgaggacatcaagaaaattactca

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- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -caagaaaa