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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cccacgatgcctcgaatgcattgtagacatttgggggcagtcccattaccgcccttattgacttgtttgcaaacctaaagatcattcctttttttggcagGAGATATTTTTGAACATGCTGTCGTTCTGAGTGTGAAAATGGAGGATCAGGATGCATTCGAGCGTCATTTTCTTCAACTGAAGTCGTATTACACCGATAC

Basic information

species Physcomitrella patens
transcript PP1S48_71V6.1
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|18360944|gb|BJ193008.1|BJ193008
EST:     GCCTCTGTTCAAATCGTCTCCAACAGCTGTGCAAGAGCTCCTTCTCGCAA                         GAGATATTTTTGAACATGCTGTCGTTCTGAGTGTGAAAATGGAGGATCAGG
genomic: GCCTCTGTTCAAATCGTCTCCAACAGCTGTGCAAGAGCTCCTTCTCGCAAgtatgtatag ... tttttggcagGAGATATTTTTGAACATGCTGTCGTTCTGAGTGTGAAAATGGAGGATCAGG
EST: gi|37838835|gb|BJ596843.1|BJ596843
EST:     CTCCAACAGCTGTGCAAGAGCTCCTTCTCGCAA                         GAGATATTTTTGAACATGCTGTCGTTCTGAGTGTGAAAATGGAGGATCAGG
genomic: CTCCAACAGCTGTGCAAGAGCTCCTTCTCGCAAgtatgtatag ... tttttggcagGAGATATTTTTGAACATGCTGTCGTTCTGAGTGTGAAAATGGAGGATCAGG
EST: gi|37834588|gb|BJ592600.1|BJ592600
EST:     GTCTCCAACAGCTGTGCAAGAGCTCCTTCTCGCAA                         GAGATATTTTTGAACATGCTGTCGTTCTGAGTGTGAAAATGGAGGATCAGG
genomic: GTCTCCAACAGCTGTGCAAGAGCTCCTTCTCGCAAgtatgtatag ... tttttggcagGAGATATTTTTGAACATGCTGTCGTTCTGAGTGTGAAAATGGAGGATCAGG
EST: gi|18363518|gb|BJ195590.1|BJ195590
EST:     GCCTCTGTTCAAATCGNCTCCAACAGCTGTGCAAGAGCTCCTTCTCGCAA                         GAGATATTTTTGAACATGCTGTCGTTCTGAGTGTGAAAATGGAGGATCAGG
genomic: GCCTCTGTTCAAATCGTCTCCAACAGCTGTGCAAGAGCTCCTTCTCGCAAgtatgtatag ... tttttggcagGAGATATTTTTGAACATGCTGTCGTTCTGAGTGTGAAAATGGAGGATCAGG
EST: gi|18350863|gb|BJ182914.1|BJ182914
EST:     GCCTCTGTTCAAATCGTCTCCAACAGCTGTGCAAGAGCTCCTTCTCGCAA                         GAGATATTTTTGAACATGCTGTCGTTCTGAGTGTGAAAATGGAGGATCAGG
genomic: GCCTCTGTTCAAATCGTCTCCAACAGCTGTGCAAGAGCTCCTTCTCGCAAgtatgtatag ... tttttggcagGAGATATTTTTGAACATGCTGTCGTTCTGAGTGTGAAAATGGAGGATCAGG
EST: gi|162221494|gb|FC397303.1|FC397303
EST:     GCCTCTGTTCAAATCGTCTCCAACAGCTGTGCAAGAGCTCCTTCTCGCAA                         GAGATATTTTTGAACATGCTGTCGTTCTGAGTGTGAAAATGGAGGATCAGG
genomic: GCCTCTGTTCAAATCGTCTCCAACAGCTGTGCAAGAGCTCCTTCTCGCAAgtatgtatag ... tttttggcagGAGATATTTTTGAACATGCTGTCGTTCTGAGTGTGAAAATGGAGGATCAGG
EST: gi|37840652|gb|BJ598660.1|BJ598660
EST:     TGTGCAANGAGCTCCTTCTCGCAA                         G
genomic: TGTGCAA-GAGCTCCTTCTCGCAAgtatgtatag ... tttttggcag-
EST: gi|37840652|gb|BJ598660.1|BJ598660
EST:     TGTGCAANGAGCTCCTTCTCGCAA                         G
genomic: TGTGCAA-GAGCTCCTTCTCGCAAgtatgtatag ... tttttggcag-
EST: gi|18346080|gb|BJ178123.1|BJ178123
EST:     GCCTCTGTTCAAATCGTCTCCAACAGCTGTGCAAGAGCTCCTTCTCGCAA                         GAGATATTTTTGAACATGCTGTCGTTCTGAGTGTGAAAATGGAGGATCAGG
genomic: GCCTCTGTTCAAATCGTCTCCAACAGCTGTGCAAGAGCTCCTTCTCGCAAgtatgtatag ... tttttggcagGAGATATTTTTGAACATGCTGTCGTTCTGAGTGTGAAAATGGAGGATCAGG
EST: gi|18353130|gb|BJ185185.1|BJ185185
EST:     GCCTCTGTTCAAATCGTCTCCAACAGCTGTGCAAGAGCTCCTTCTCGCAA                         GAGATATTTTTGAACATGCTGTCGTTCTGAGTGTGAAAATGGAGGATCAGG
genomic: GCCTCTGTTCAAATCGTCTCCAACAGCTGTGCAAGAGCTCCTTCTCGCAAgtatgtatag ... tttttggcagGAGATATTTTTGAACATGCTGTCGTTCTGAGTGTGAAAATGGAGGATCAGG
EST: gi|208360510|gb|DC930265.1|DC930265
EST:     GCCTCTGTTCAAATCGTCTCCAACAGCTGTGCAAGAGCTCCTTCTCGCAA                         GAGATATTTTTGAACATGCTGTCGTTCTGAGTGTGAAAATGGAGGATCAGG
genomic: GCCTCTGTTCAAATCGTCTCCAACAGCTGTGCAAGAGCTCCTTCTCGCAAgtatgtatag ... tttttggcagGAGATATTTTTGAACATGCTGTCGTTCTGAGTGTGAAAATGGAGGATCAGG
EST: gi|208375002|gb|DC944797.1|DC944797
EST:     TCTCCAACAGCTGTGCAAGAGCTCCTTCTCGCAA                         GAGATATTTTTGAACATGCTGTCGTTCTGAGTGTGAAAATGGAGGATCAGG
genomic: TCTCCAACAGCTGTGCAAGAGCTCCTTCTCGCAAgtatgtatag ... tttttggcagGAGATATTTTTGAACATGCTGTCGTTCTGAGTGTGAAAATGGAGGATCAGG
EST: gi|37825192|gb|BJ583258.1|BJ583258
EST:     CAACAGCTGTGCAAGAGCTCNTTCTCGCAA                         GAGATATTTTTGAACATGCTGTCGTTCTGAGTGTGAAAATGGAGGATCAGG
genomic: CAACAGCTGTGCAAGAGCTCCTTCTCGCAAgtatgtatag ... tttttggcagGAGATATTTTTGAACATGCTGTCGTTCTGAGTGTGAAAATGGAGGATCAGG
EST: gi|37830197|gb|BJ588209.1|BJ588209
EST:     CCAACAGCTGTGCAAGGAGCTCCTTCTCGCAA                         GAGATATTTTTGAACATGCTGTCGTTCTGAGTGTGAAAATGGAGGATCAGG
genomic: CCAACAGCTGTGCAA-GAGCTCCTTCTCGCAAgtatgtatag ... tttttggcagGAGATATTTTTGAACATGCTGTCGTTCTGAGTGTGAAAATGGAGGATCAGG

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: 14 (upstream exon), 34 (downstream exon)
Score: 4

GTGAAGTTGACGGAGTTGCCTGGTCTTCCGCCTCTGTTCAAATCGTCTCCAACAGCTGTGCAAGAGCTCCTTCTCGCAAgtatgtatag ... tttttggcagGAGATATTTTTGAACATGCTGTCGTTCTGAGTGTGAAAATGGAGGATCAGGATGCATTCGAGCGTCATTTTCTTCAACTGAAGTCGTATTACACCGATAC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttaccgcccttattgacttgtttgcaaacctaaagatcattcctttttttggcagGAGATATTTTTGAACATGCTGTCGTTCTGAGTGTGAAAATGGAGGATCAGGATGCATTCGAGCGTCATTTTCTTCAACTGAAGTCGTATTACACCGATAC
                                    tcattccttttttt  CT-rich tract
                                           ttttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cccacgatgcctcgaatgcattgtagacatttgggggcagtcccattaccgcccttattgacttgtttgcaaacctaaagatcattcctttttttggcagGAGATATTTTTGAACATGCTGTCGTTCTGAGTGTGAAAATGGAGGATCAGGATGCATTCGAGCGTCATTTTCTTCAACTGAAGTCGTATTACACCGATAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG