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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatttcttagaacccatcttagactcctattttcgtttttctagcgattaggttttatttttctttgttaggtacgattttagggcagtagccatgtaaagtttgcgtatacattaataactaattacggtcatgccaattgcacatctttactctttgcagGGTAACATAGCTGTTTGGCGGAAGAAAGAGGGAGATGAAGTTGTCGCGGGAGATGTTCTGTGTGAAATTGAGACG

Basic information

species Physcomitrella patens
transcript PP1S78_56V6.1
intron # 4
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|100446669|gb|CJ970968.1|CJ970968
EST:     ACTCTGTCATGGAAATTGGGATGCCATCACTTTCACCGACCATGACCCAG                         GGTAACATAGCTGTTTGGCGGAAGAAAGAGGGAGATGAAGTTGTCGCGGGA
genomic: ACTCTGTCATGGAAATTGGGATGCCATCACTTTCACCGACCATGACCCAGgtatttctta ... ctctttgcagGGTAACATAGCTGTTTGGCGGAAGAAAGAGGGAGATGAAGTTGTCGCGGGA
EST: gi|67573356|gb|BJ946180.1|BJ946180
EST:     ACTCTGTCATGGAAATTGGGATGCCATCACTTTCACCGACCATGACCCAG                         GGTAACATAGCTGTTTGGCGGAAGAAAGAGGGAGATGAAGTTGTCGCGGGA
genomic: ACTCTGTCATGGAAATTGGGATGCCATCACTTTCACCGACCATGACCCAGgtatttctta ... ctctttgcagGGTAACATAGCTGTTTGGCGGAAGAAAGAGGGAGATGAAGTTGTCGCGGGA
EST: gi|208371650|gb|DC932479.1|DC932479
EST:     ACTCTGTCATGGAAATTGGGATGCCATCACTTTCACCGACCATGACCCAG                         GGTAACATAGCTGTTTGGCGGAAGAAAGAGGGAGATGAAGTTGTCGCGGGA
genomic: ACTCTGTCATGGAAATTGGGATGCCATCACTTTCACCGACCATGACCCAGgtatttctta ... ctctttgcagGGTAACATAGCTGTTTGGCGGAAGAAAGAGGGAGATGAAGTTGTCGCGGGA
EST: gi|208360125|gb|DC939164.1|DC939164
EST:     ACTCTGTCATGGAAATTGGGATGCCATCACTTTCACCGACCATGACCCAG                         GGTAACATAGCTGTTTGGCGGAAGAAAGAGGGAGATGAAGTTGTCGCGGGA
genomic: ACTCTGTCATGGAAATTGGGATGCCATCACTTTCACCGACCATGACCCAGgtatttctta ... ctctttgcagGGTAACATAGCTGTTTGGCGGAAGAAAGAGGGAGATGAAGTTGTCGCGGGA
EST: gi|100451962|gb|CJ975030.1|CJ975030
EST:     ACTCTGTCATGGAAATTGGGATGCCATCACTTTCACCGACCATGACCCAG                         GGTAACATAGCTGTTTGGCGGAAGAAAGAGGGAGATGAAGTTGTCGCGGGA
genomic: ACTCTGTCATGGAAATTGGGATGCCATCACTTTCACCGACCATGACCCAGgtatttctta ... ctctttgcagGGTAACATAGCTGTTTGGCGGAAGAAAGAGGGAGATGAAGTTGTCGCGGGA
EST: gi|208354823|gb|DC934355.1|DC934355
EST:     ACTCTGTCATGGAAATTGGGATGCCATCACTTTCACCGACCATGACCCAG                         GGTAACATAGCTGTTTGGCGGAAGAAAGAGGGAGATGAAGTTGTCGCGGGA
genomic: ACTCTGTCATGGAAATTGGGATGCCATCACTTTCACCGACCATGACCCAGgtatttctta ... ctctttgcagGGTAACATAGCTGTTTGGCGGAAGAAAGAGGGAGATGAAGTTGTCGCGGGA
EST: gi|67569974|gb|BJ942798.1|BJ942798
EST:     ACTCTGTCATGGAAATTGGGATGCCATCACTTTCACCGACCATGACCCAG                         GGTAACATAGCTGTTTGGCGGAAGAAAGAGGGAG
genomic: ACTCTGTCATGGAAATTGGGATGCCATCACTTTCACCGACCATGACCCAGgtatttctta ... ctctttgcagGGTAACATAGCTGTTTGGCGGAAGAAAGAGGGAG
EST: gi|100363847|gb|BY966200.1|BY966200
EST:     ACTCTGTCATGGAAATTGGGATGCCATCACTTTCACCGACCATGACCCAG                         GGTAACATAGCTGTTTGGCGGAAGAAAGAGGGAGATGAAGTTGTCGCGGGA
genomic: ACTCTGTCATGGAAATTGGGATGCCATCACTTTCACCGACCATGACCCAGgtatttctta ... ctctttgcagGGTAACATAGCTGTTTGGCGGAAGAAAGAGGGAGATGAAGTTGTCGCGGGA
EST: gi|67574997|gb|BJ947821.1|BJ947821
EST:     ACTCTGTCATGGAAATTGGGATGCCATCACTTTCACCGACCATGACCCAG                         GGTAACATAGCTGTTTGGCGGAAGAAAGAGGGAGATGAAGTTGTCGCGGGA
genomic: ACTCTGTCATGGAAATTGGGATGCCATCACTTTCACCGACCATGACCCAGgtatttctta ... ctctttgcagGGTAACATAGCTGTTTGGCGGAAGAAAGAGGGAGATGAAGTTGTCGCGGGA

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), 34 (downstream exon)
Score: 20

TTAACTCTGTCATGGAAATTGGGATGCCATCACTTTCACCGACCATGACCCAGgtatttctta ... ctctttgcagGGTAACATAGCTGTTTGGCGGAAGAAAGAGGGAGATGAAGTTGTCGCGGGAGATGTTCTGTGTGAAATTGAGACG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatacattaataactaattacggtcatgccaattgcacatctttactctttgcagGGTAACATAGCTGTTTGGCGGAAGAAAGAGGGAGATGAAGTTGTCGCGGGAGATGTTCTGTGTGAAATTGAGACG
                                     catctttactcttt  CT-rich tract
     attaataactaatta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatttcttagaacccatcttagactcctattttcgtttttctagcgattaggttttatttttctttgttaggtacgattttagggcagtagccatgtaaagtttgcgtatacattaataactaattacggtcatgccaattgcacatctttactctttgcagGGTAACATAGCTGTTTGGCGGAAGAAAGAGGGAGATGAAGTTGTCGCGGGAGATGTTCTGTGTGAAATTGAGACG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG