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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatacctctcttcacaaataggaactccttcatccagttgccgcagtgagggacgtgttttttctttattttatagttttgttgaagtgaatgctgcaaaggtgtcatctcaattgtcttgaagccaataaacactgagttgaaattgttgtttgtgatgcagGGACCTGCGACAATAAAGGAGGAATATCGTTTTCGTAGAGTGGCATGCGAGTCAAATGCGGCTGACGGCCGGCACCAGCGTCTGTCAAGGAGGTCTAAAC

Basic information

species Physcomitrella patens
transcript PP1S69_234V6.1
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|162210828|gb|FC387238.1|FC387238
EST:     TGAGGTCGTCGTGAACAGCAAGTTCGGTGCTGACAGTGACTGCCTGGACG                         GGACCTGCGACAATAAAGGAGGAATATCGTTTTCGTAGAGTGGCATGCGAG
genomic: TGAGGTCGTCGTGAACAGCAAGTTCGGTGCTGACAGTGACTGCCTGGACGgtatacctct ... tgtgatgcagGGACCTGCGACAATAAAGGAGGAATATCGTTTTCGTAGAGTGGCATGCGAG
EST: gi|208375174|gb|DC945324.1|DC945324
EST:     TGAGGTCGTCGTGAACAGCAAGTTCGGTGCTGACAGTGACTGCCTGGACG                         GGACCTGCGACAATAAAGGAGGAATATCGTTTTCGTAGAGTGGCATGCGAG
genomic: TGAGGTCGTCGTGAACAGCAAGTTCGGTGCTGACAGTGACTGCCTGGACGgtatacctct ... tgtgatgcagGGACCTGCGACAATAAAGGAGGAATATCGTTTTCGTAGAGTGGCATGCGAG
EST: gi|208369164|gb|DC956039.1|DC956039
EST:     TGAGGTCGTCGTGAACAGCAAGTTCGGTGCTGACAGTGACTGCCTGGACG                         GGACCTGCGACAATAAAGGAGGAATATCGTTTTCGTAGAGTGGCATGCGAG
genomic: TGAGGTCGTCGTGAACAGCAAGTTCGGTGCTGACAGTGACTGCCTGGACGgtatacctct ... tgtgatgcagGGACCTGCGACAATAAAGGAGGAATATCGTTTTCGTAGAGTGGCATGCGAG
EST: gi|162222853|gb|FC399315.1|FC399315
EST:     TGAGGTCGTCGTGAACAGCAAGTTCGGTGCTGACAGTGACTGCCTGGACG                         GGACCTGCGACAATAAAGGAGGAATATCGTTTTCGTAGAGTGGCATGCGAG
genomic: TGAGGTCGTCGTGAACAGCAAGTTCGGTGCTGACAGTGACTGCCTGGACGgtatacctct ... tgtgatgcagGGACCTGCGACAATAAAGGAGGAATATCGTTTTCGTAGAGTGGCATGCGAG
EST: gi|208387415|gb|DC949200.1|DC949200
EST:     TGAGGTCGTCGTGAACAGCAAGTTCGGTGCTGACAGTGACTGCCTGGACG                         GGACCTGCGACAATAAAGGAGGAATATCGTTTTCGTAGAGTGGCATGCGAG
genomic: TGAGGTCGTCGTGAACAGCAAGTTCGGTGCTGACAGTGACTGCCTGGACGgtatacctct ... tgtgatgcagGGACCTGCGACAATAAAGGAGGAATATCGTTTTCGTAGAGTGGCATGCGAG
EST: gi|162241075|gb|FC417733.1|FC417733
EST:     TGAGGTCGTCGTGAACAGCAAGTTCGGTGCTGACAGTGACTGCCTGGACG                         GGACCTGCGACAATAAAGGAGGAATATCGTTTTCGTAGAGTGGCATGCGAG
genomic: TGAGGTCGTCGTGAACAGCAAGTTCGGTGCTGACAGTGACTGCCTGGACGgtatacctct ... tgtgatgcagGGACCTGCGACAATAAAGGAGGAATATCGTTTTCGTAGAGTGGCATGCGAG
EST: gi|67697171|gb|BJ957404.1|BJ957404
EST:     TGAGGTCGTCGTGAACAGCAAGTTCGGTGCTGACAGTGACTGCCTGGACG                         GGACCTGCGACAATAAAGGAGGAATATCGTTTTCGTAGAGTGGCATGCGAG
genomic: TGAGGTCGTCGTGAACAGCAAGTTCGGTGCTGACAGTGACTGCCTGGACGgtatacctct ... tgtgatgcagGGACCTGCGACAATAAAGGAGGAATATCGTTTTCGTAGAGTGGCATGCGAG
EST: gi|208388297|gb|DC949297.1|DC949297
EST:     TGAGGTCGTCGTGAACAGCAAGTTCGGTGCTGACAGTGACTGCCTGGACG                         GGACCTGCGACAATAAAGGAGGAATATCGTTTTCGTAGAGTGGCATGCGAG
genomic: TGAGGTCGTCGTGAACAGCAAGTTCGGTGCTGACAGTGACTGCCTGGACGgtatacctct ... tgtgatgcagGGACCTGCGACAATAAAGGAGGAATATCGTTTTCGTAGAGTGGCATGCGAG
EST: gi|208363965|gb|DC947209.1|DC947209
EST:     TGAGGTCGTCGTGAACAGCAAGTTCGGTGCTGACAGTGACTGCCTGGACG                         GGACCTGCGACAATAAAGGAGGAATATCGTTTTCGTAGAGTGGCATGCGAG
genomic: TGAGGTCGTCGTGAACAGCAAGTTCGGTGCTGACAGTGACTGCCTGGACGgtatacctct ... tgtgatgcagGGACCTGCGACAATAAAGGAGGAATATCGTTTTCGTAGAGTGGCATGCGAG
EST: gi|208352536|gb|DC918245.1|DC918245
EST:     TGAGGTCGTCGTGAACAGCAAGTTCGGTGCTGACAGTGACTGCCTGGACG                         GGACCTGCGACAATAAAGGAGGAATATCGTTTTCGTAGAGTGGCATGCGAG
genomic: TGAGGTCGTCGTGAACAGCAAGTTCGGTGCTGACAGTGACTGCCTGGACGgtatacctct ... tgtgatgcagGGACCTGCGACAATAAAGGAGGAATATCGTTTTCGTAGAGTGGCATGCGAG
EST: gi|208368487|gb|DC947888.1|DC947888
EST:     TGAGGTCGTCGTGAACAGCAAGTTCGGTGCTGACAGTGACTGCCTGGACG                         GGACCTGCGACAATAAAGGAGGAATATCGTTTTCGTAGAGTGGCATGCGAG
genomic: TGAGGTCGTCGTGAACAGCAAGTTCGGTGCTGACAGTGACTGCCTGGACGgtatacctct ... tgtgatgcagGGACCTGCGACAATAAAGGAGGAATATCGTTTTCGTAGAGTGGCATGCGAG
EST: gi|162220044|gb|FC396521.1|FC396521
EST:     TGAGGTCGTCGTGAACAGCAAGTTCGGTGCTGACAGTGACTGCCTGGACG                         GGACCTGCGACAATAAAGGAGGAATATCGTTTTCGTAGAGTGGCATGCGAG
genomic: TGAGGTCGTCGTGAACAGCAAGTTCGGTGCTGACAGTGACTGCCTGGACGgtatacctct ... tgtgatgcagGGACCTGCGACAATAAAGGAGGAATATCGTTTTCGTAGAGTGGCATGCGAG
EST: gi|162216049|gb|FC393506.1|FC393506
EST:     TGAGGTCGTCGTGAACAGCAAGTTCGGTGCTGACAGTGACTGCCTGGACG                         GGACCTGCGACAATAAAGGAGGAATATCGTTTTCGTAGAGTGGCATGCGAG
genomic: TGAGGTCGTCGTGAACAGCAAGTTCGGTGCTGACAGTGACTGCCTGGACGgtatacctct ... tgtgatgcagGGACCTGCGACAATAAAGGAGGAATATCGTTTTCGTAGAGTGGCATGCGAG
EST: gi|162179728|gb|FC356319.1|FC356319
EST:     TGAGGTCGTCGTGAACAGCAAGTTCGGTGCTGACAGTGACTGCCTGGACG                         GGACCTGCGACAATAAAGGAGGAATATCGTTTTCGTAGAGTGGCATGCGAG
genomic: TGAGGTCGTCGTGAACAGCAAGTTCGGTGCTGACAGTGACTGCCTGGACGgtatacctct ... tgtgatgcagGGACCTGCGACAATAAAGGAGGAATATCGTTTTCGTAGAGTGGCATGCGAG
EST: gi|162226950|gb|FC403333.1|FC403333
EST:     TGAGGTCGTCGTGAACAGCAAGTTCGGTGCTGACAGTGACTGCCTGGACG                         GGACCTGCGACAATAAAGGAGGAATATCGTTTTCGTAGAGTGGCATGCGAG
genomic: TGAGGTCGTCGTGAACAGCAAGTTCGGTGCTGACAGTGACTGCCTGGACGgtatacctct ... tgtgatgcagGGACCTGCGACAATAAAGGAGGAATATCGTTTTCGTAGAGTGGCATGCGAG
EST: gi|162204327|gb|FC380515.1|FC380515
EST:     TGAGGTCGTCGTGAACAGCAAGTTCGGTGCTGACAGTGACTGCCTGGACG                         GGACCTGCGACAATAAAGGAGGAATATCGTTTTCGTAGAGTGGCATGCGAG
genomic: TGAGGTCGTCGTGAACAGCAAGTTCGGTGCTGACAGTGACTGCCTGGACGgtatacctct ... tgtgatgcagGGACCTGCGACAATAAAGGAGGAATATCGTTTTCGTAGAGTGGCATGCGAG
EST: gi|37840597|gb|BJ598605.1|BJ598605
EST:     TGAGGTCGTCGTGAACAGCAAGTTCGGTGCTGACAGTGACTGCCTGGACG                         GGACCTGCGACAATAAAGGAGGAATATCGTTTTCGTAGAGTGGCATGCGAG
genomic: TGAGGTCGTCGTGAACAGCAAGTTCGGTGCTGACAGTGACTGCCTGGACGgtatacctct ... tgtgatgcagGGACCTGCGACAATAAAGGAGGAATATCGTTTTCGTAGAGTGGCATGCGAG
EST: gi|162226951|gb|FC403334.1|FC403334
EST:     TGAGGTCGTCGTGAACAGCAAGTTCGGTGCTGACAGTGACTGCCTGGACG                         GGACCTGCGACAATAAAGGAGGAATATCGTTTTCGTAGAGTGGCATGCGAG
genomic: TGAGGTCGTCGTGAACAGCAAGTTCGGTGCTGACAGTGACTGCCTGGACGgtatacctct ... tgtgatgcagGGACCTGCGACAATAAAGGAGGAATATCGTTTTCGTAGAGTGGCATGCGAG

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), 35 (downstream exon)
Score: 15

TGGTCCTTTGGAACCTGCGGTGATGATGATTCAAGCGAATGCTATTTCTCTGAGGTCGTCGTGAACAGCAAGTTCGGTGCTGACAGTGACTGCCTGGACGgtatacctct ... tgtgatgcagGGACCTGCGACAATAAAGGAGGAATATCGTTTTCGTAGAGTGGCATGCGAGTCAAATGCGGCTGACGGCCGGCACCAGCGTCTGTCAAGGAGGTCTAAAC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctcaattgtcttgaagccaataaacactgagttgaaattgttgtttgtgatgcagGGACCTGCGACAATAAAGGAGGAATATCGTTTTCGTAGAGTGGCATGCGAGTCAAATGCGGCTGACGGCCGGCACCAGCGTCTGTCAAGGAGGTCTAAAC
                  aataaaca  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatacctctcttcacaaataggaactccttcatccagttgccgcagtgagggacgtgttttttctttattttatagttttgttgaagtgaatgctgcaaaggtgtcatctcaattgtcttgaagccaataaacactgagttgaaattgttgtttgtgatgcagGGACCTGCGACAATAAAGGAGGAATATCGTTTTCGTAGAGTGGCATGCGAGTCAAATGCGGCTGACGGCCGGCACCAGCGTCTGTCAAGGAGGTCTAAAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG