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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aataatggttgtaatgaatgtcatatggctaggtattatgatatttactttctcattgattttacttgtggaccattttcttaataaagtgcgactacagACGGATTGGATTGGAAAGGAGTTTCAATACACCGATTTCCAG

Basic information

species Physcomitrella patens
transcript PP1S6_51V6.1
intron # 3
splice site 3'
intron type U12 (go to U12 genes for details)

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|162266780|gb|FC442296.1|FC442296
EST:     CGCGCTCGGAGTGCTACATGCTGGACGTGGATAATCATTTTTATGACTTT                         ACGGATTGGATTGGAAAGGAGTTTCAATACACCGATTTCCAG
genomic: CGCGCTCGGAGTGCTACATGCTGGACGTGGATAATCATTTTTATGACTTTgtatcctccc ... gcgactacagACGGATTGGATTGGAAAGGAGTTTCAATACACCGATTTCCAG
EST: gi|7148019|gb|AW509941.1|AW509941
EST:     CGCGCTCGGAGTGATACATGCTGGACGTGGATAATCATTTTTATGACTCT                         ACGCATTGGATTGGAAAGGAGTTTCAATACACCGATTTCCAG
genomic: CGCGCTCGGAGTGCTACATGCTGGACGTGGATAATCATTTTTATGACTTTgtatcctccc ... gcgactacagACGGATTGGATTGGAAAGGAGTTTCAATACACCGATTTCCAG
EST: gi|162275966|gb|FC452034.1|FC452034
EST:     CGCGCTCGGAGTGCTACATGCTGGACGTGGATAATCATTTTTATGACTTT                         ACGGATTGGATTGGAAAGGAGTTTCAATACACCGATTTCCAG
genomic: CGCGCTCGGAGTGCTACATGCTGGACGTGGATAATCATTTTTATGACTTTgtatcctccc ... gcgactacagACGGATTGGATTGGAAAGGAGTTTCAATACACCGATTTCCAG

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: 32 (upstream exon), 22 (downstream exon)
Score: 10

TGCTTGTATTTTCATTTGCCTGTCATGCGACGTTATCTCTAAGCCCGCGCTCGGAGTGCTACATGCTGGACGTGGATAATCATTTTTATGACTTTgtatcctccc ... gcgactacagACGGATTGGATTGGAAAGGAGTTTCAATACACCGATTTCCAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tactttctcattgattttacttgtggaccattttcttaataaagtgcgactacagACGGATTGGATTGGAAAGGAGTTTCAATACACCGATTTCCAG
                               tttcttaat  putative branch site 
                             attttcttaataaagt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aataatggttgtaatgaatgtcatatggctaggtattatgatatttactttctcattgattttacttgtggaccattttcttaataaagtgcgactacagACGGATTGGATTGGAAAGGAGTTTCAATACACCGATTTCCAG

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