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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtgtccatggggttggtggatgttccgtttgtgtattgaaggaggggctgcatgctagtagcacgaacgggatagatgtttgattaggaggatgggtttgagttatggtcggggttgggagattccttttagggagacgttatgaaaggaactgacaggtaactgtaacgtggttgatttgtgatgcagTCGGAGACTTAAACCATTTGATTTCTGCGACAATGAGTGGTATTACTTGCTGCTTGCGTTTCCCGGGACAGCTGAACTCCGATCTGCGCAAGTTGGCGGT

Basic information

species Physcomitrella patens
transcript PP1S93_136V6.1
intron # 2
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|162248838|gb|FC422039.1|FC422039
EST:     GGCTCTATACGATATCTGCTTTAGGACGTTGAAGCTCATTACTCCGTCGT                         TCGGAGACTTAAACCATTTGATTTCTGCGACAATGAGTGGTATTACTTGCT
genomic: GGCTCTATACGATATCTGCTTTAGGACGTTGAAGCTCATTACTCCGTCGTgtaagtgtcc ... tgtgatgcagTCGGAGACTTAAACCATTTGATTTCTGCGACAATGAGTGGTATTACTTGCT
EST: gi|208397135|gb|DC908149.1|DC908149
EST:     GGCTCTATACGATATCTGCTTTANGACGTTGAANCTCATTACTCCGTCGT                         TCGGAGACTTAAACCATTTGATTTCTGCGACAATGANTGGTATTACTTGCT
genomic: GGCTCTATACGATATCTGCTTTAGGACGTTGAAGCTCATTACTCCGTCGTgtaagtgtcc ... tgtgatgcagTCGGAGACTTAAACCATTTGATTTCTGCGACAATGAGTGGTATTACTTGCT
EST: gi|208390437|gb|DC933694.1|DC933694
EST:     GGCTCTATACGATATCTGCTTTANGACGTTGAA-CTCATTACTCCGTCGT                         TCGAA-ACTTAA-CCATTTGATT-CTGCG
genomic: GGCTCTATACGATATCTGCTTTAGGACGTTGAAGCTCATTACTCCGTCGTgtaagtgtcc ... tgtgatgcagTCGGAGACTTAAACCATTTGATTTCTGCG
EST: gi|67726903|gb|BJ977162.1|BJ977162
EST:     GCTTTAGGGACG-TGAAGCTCATTACTCCGTCGT                         TCGGAGACTTAAACCATTTGATTTCTGCGACAATGAGTGGTATTACTTGCT
genomic: GCTTTA-GGACGTTGAAGCTCATTACTCCGTCGTgtaagtgtcc ... tgtgatgcagTCGGAGACTTAAACCATTTGATTTCTGCGACAATGAGTGGTATTACTTGCT
EST: gi|100421755|gb|BY993628.1|BY993628
EST:     GGCTCTATACGATATCTGCTTTAGGACGTTGAAGCTCATTACTCCGTCGT                         TCGGAGACTTAAACCATTTGATTTCTGCGACAATGAGTGGTATTACTTGCT
genomic: GGCTCTATACGATATCTGCTTTAGGACGTTGAAGCTCATTACTCCGTCGTgtaagtgtcc ... tgtgatgcagTCGGAGACTTAAACCATTTGATTTCTGCGACAATGAGTGGTATTACTTGCT
EST: gi|100387767|gb|BY951767.1|BY951767
EST:     CTCTATACGATATCTGCTTTAGGAACGT-GAAGCTCATTACTCCGTCGGT                         TCGAA-ACTTAAACCATTTGATTT
genomic: CTCTATACGATATCTGCTTTAGGA-CGTTGAAGCTCATTACTCCGTCG-Tgtaagtgtcc ... tgtgatgcagTCGGAGACTTAAACCATTTGATTT
EST: gi|162189889|gb|FC366099.1|FC366099
EST:     GGCTCTATACGATATCTGCTTTAGGACGTTGAAGCTCATTACTCCGTCGT                         TCGGAGACTTAAACCATTTGATT
genomic: GGCTCTATACGATATCTGCTTTAGGACGTTGAAGCTCATTACTCCGTCGTgtaagtgtcc ... tgtgatgcagTCGGAGACTTAAACCATTTGATT
EST: gi|67716816|gb|BJ967075.1|BJ967075
EST:     GGCTCTATACGATATCTGCTTTAGGACGTTGAAGCTCATTACTCCGTCGT                         TCGGAGACTTAAGCCATTTGATTTCTGCGACAATGAGTGGTATTACTTGCT
genomic: GGCTCTATACGATATCTGCTTTAGGACGTTGAAGCTCATTACTCCGTCGTgtaagtgtcc ... tgtgatgcagTCGGAGACTTAAACCATTTGATTTCTGCGACAATGAGTGGTATTACTTGCT
EST: gi|208375316|gb|DC940454.1|DC940454
EST:     GNCTCTATACGATATCTGCTTTANGACGTNNAN-CTCATNACTCCGTCGT                         TCGAA-ACTTAA-CCATTTGATT-CTGC
genomic: GGCTCTATACGATATCTGCTTTAGGACGTTGAAGCTCATTACTCCGTCGTgtaagtgtcc ... tgtgatgcagTCGGAGACTTAAACCATTTGATTTCTGC

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: 26

GTGCATCAGTTGGTGGAGAATGCAGACGAGTGTATGGTGTTGGATAACGAGGCTCTATACGATATCTGCTTTAGGACGTTGAAGCTCATTACTCCGTCGTgtaagtgtcc ... tgtgatgcagTCGGAGACTTAAACCATTTGATTTCTGCGACAATGAGTGGTATTACTTGCTGCTTGCGTTTCCCGGGACAGCTGAACTCCGATCTGCGCAAGTTGGCGGT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agacgttatgaaaggaactgacaggtaactgtaacgtggttgatttgtgatgcagTCGGAGACTTAAACCATTTGATTTCTGCGACAATGAGTGGTATTACTTGCTGCTTGCGTTTCCCGGGACAGCTGAACTCCGATCTGCGCAAGTTGGCGGT
     ttatgaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtgtccatggggttggtggatgttccgtttgtgtattgaaggaggggctgcatgctagtagcacgaacgggatagatgtttgattaggaggatgggtttgagttatggtcggggttgggagattccttttagggagacgttatgaaaggaactgacaggtaactgtaacgtggttgatttgtgatgcagTCGGAGACTTAAACCATTTGATTTCTGCGACAATGAGTGGTATTACTTGCTGCTTGCGTTTCCCGGGACAGCTGAACTCCGATCTGCGCAAGTTGGCGGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA