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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cgttttcgtggtttcttttttttttatttaatttcaaaacccatggattaaacagaactgctacgacgagattgttgatagcagttttacatgaatgcagGCATCGCTGAAACGCTTGGACATGAGTTATGTGGATCTGCTGTACTGCCATCGGCCAGATCCCTCGACTCCAATTGAAGAGACTGTACGAGCTATGAACT

Basic information

species Physcomitrella patens
transcript PP1S83_53V6.1
intron # 1
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|37842032|gb|BJ600040.1|BJ600040
EST:     TCGCAAGCACATCATCGAAGGCGTTAAG                         GCATCGCTGAAACGCTTGGACATGAGTTATGTGGATCTGCTGTACTGCCAT
genomic: TCGCAAGCACATCATCGAAGGCGTTAAGgtgagtcacg ... atgaatgcagGCATCGCTGAAACGCTTGGACATGAGTTATGTGGATCTGCTGTACTGCCAT
EST: gi|208380713|gb|DC919429.1|DC919429
EST:     CGATAAAGGT-TTTNTCGCAAGCACATCATCGAAGGCGTTAAG                         GCATCGCTGAAACGCTTGGACATGAGTTATGTGGATNTGCTGTACTGCCAT
genomic: CGATAAAGGTCTCTCTCGCAAGCACATCATCGAAGGCGTTAAGgtgagtcacg ... atgaatgcagGCATCGCTGAAACGCTTGGACATGAGTTATGTGGATCTGCTGTACTGCCAT
EST: gi|162236006|gb|FC412165.1|FC412165
EST:     GCCCTAACGATAAAGGTCTCTCTCGCAAGCACATCATCGAAGGCGTTAAG                         GCATCGCTGAAACGCTTGGACATGAGTTATGTGGATCTGCTGTACTGCCAT
genomic: GCCCTAACGATAAAGGTCTCTCTCGCAAGCACATCATCGAAGGCGTTAAGgtgagtcacg ... atgaatgcagGCATCGCTGAAACGCTTGGACATGAGTTATGTGGATCTGCTGTACTGCCAT
EST: gi|208391694|gb|DC942284.1|DC942284
EST:     GCCCTAACGATAAAGGTCTCTCTCGCAAGCACATCATCGAAGGCGTTAAG                         GCATCGCTGAAACGCTTGGACATGAGTTATGTGGATCTGCTGTACTGCCAT
genomic: GCCCTAACGATAAAGGTCTCTCTCGCAAGCACATCATCGAAGGCGTTAAGgtgagtcacg ... atgaatgcagGCATCGCTGAAACGCTTGGACATGAGTTATGTGGATCTGCTGTACTGCCAT
EST: gi|22492212|gb|BU052135.1|BU052135
EST:     GCCCTAACGATAAAGGTCTCTCTCGCAAGCACATCATCGAAGGCGTTAAG                         GCATCGCTGAAACGCTTGGACATGAGTTATGTGGATCTGCTGTACTGCCAT
genomic: GCCCTAACGATAAAGGTCTCTCTCGCAAGCACATCATCGAAGGCGTTAAGgtgagtcacg ... atgaatgcagGCATCGCTGAAACGCTTGGACATGAGTTATGTGGATCTGCTGTACTGCCAT
EST: gi|162207556|gb|FC384009.1|FC384009
EST:     GCCCTAACGATAAAGGTCTCTCTCGCAAGCACATCATCGAAGGCGTTAAG                         GCATCGCTGAAACGCTTGGACATGAGTTATGTGGATCTGCTGTACTGCCAT
genomic: GCCCTAACGATAAAGGTCTCTCTCGCAAGCACATCATCGAAGGCGTTAAGgtgagtcacg ... atgaatgcagGCATCGCTGAAACGCTTGGACATGAGTTATGTGGATCTGCTGTACTGCCAT
EST: gi|208371173|gb|DC955979.1|DC955979
EST:     CTCTCGCAAGCACATCATCGAAGGCGTTAAG                         GCATCGCTGAAACGC-TNGACATGAGTTATGTGGATCTGCTGTACTGCCAT
genomic: CTCTCGCAAGCACATCATCGAAGGCGTTAAGgtgagtcacg ... atgaatgcagGCATCGCTGAAACGCTTGGACATGAGTTATGTGGATCTGCTGTACTGCCAT
EST: gi|208346033|gb|DC921278.1|DC921278
EST:     TCTCGCNAGCACATCATNGAAGGCGTTTAG                         GCATCGNTGAAACGCTTGGACATGAGTTATGTGGATCTGCTGTACTGCCAT
genomic: TCTCGCAAGCACATCATCGAAGGCGTTAAGgtgagtcacg ... atgaatgcagGCATCGCTGAAACGCTTGGACATGAGTTATGTGGATCTGCTGTACTGCCAT
EST: gi|208366178|gb|DC955279.1|DC955279
EST:     TCTCTCGCAAGCACATCATCGAAGGCGTTAAG                         GCATCGCTGAAACGCTTGGACATGAGTTATGTGGATCTGCTGTACTGCCAT
genomic: TCTCTCGCAAGCACATCATCGAAGGCGTTAAGgtgagtcacg ... atgaatgcagGCATCGCTGAAACGCTTGGACATGAGTTATGTGGATCTGCTGTACTGCCAT
EST: gi|208370555|gb|DC951591.1|DC951591
EST:     GCCCTAACGATAAAGGTCTCTCTCGCAAGCACATCATCGAAGGCGTTAAG                         GCATCGCTGAAACGCTTGGACATGAGTTATGTGGATCTGCTGTACTGCCAT
genomic: GCCCTAACGATAAAGGTCTCTCTCGCAAGCACATCATCGAAGGCGTTAAGgtgagtcacg ... atgaatgcagGCATCGCTGAAACGCTTGGACATGAGTTATGTGGATCTGCTGTACTGCCAT
EST: gi|162236005|gb|FC412164.1|FC412164
EST:     CGCAAGCACATCATCGAAGGCGTTAAG                         GCATCGCTGAAACGCTGGGACATGAGTTATGTGGATCTGCTGTACTGCCAT
genomic: CGCAAGCACATCATCGAAGGCGTTAAGgtgagtcacg ... atgaatgcagGCATCGCTGAAACGCTTGGACATGAGTTATGTGGATCTGCTGTACTGCCAT
EST: gi|208355973|gb|DC946189.1|DC946189
EST:     GCCCTNACGAT-AANGTCTCTCTNGCNAGCACATCATCGAAGGCGNTAAG                         GCATCGCTGAAACGCTTGGACATGAGTTATGTGGATTTGCTGTACTGCCAT
genomic: GCCCTAACGATAAAGGTCTCTCTCGCAAGCACATCATCGAAGGCGTTAAGgtgagtcacg ... atgaatgcagGCATCGCTGAAACGCTTGGACATGAGTTATGTGGATCTGCTGTACTGCCAT

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), 29 (downstream exon)
Score: 8

GAAGCGGTCGGACCTTGTGATCTCCACCAAGCTTTTCTGGGGTGGGAATGGCCCTAACGATAAAGGTCTCTCTCGCAAGCACATCATCGAAGGCGTTAAGgtgagtcacg ... atgaatgcagGCATCGCTGAAACGCTTGGACATGAGTTATGTGGATCTGCTGTACTGCCATCGGCCAGATCCCTCGACTCCAATTGAAGAGACTGTACGAGCTATGAACT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gattaaacagaactgctacgacgagattgttgatagcagttttacatgaatgcagGCATCGCTGAAACGCTTGGACATGAGTTATGTGGATCTGCTGTACTGCCATCGGCCAGATCCCTCGACTCCAATTGAAGAGACTGTACGAGCTATGAACT
                           tgttgat  putative branch site (score: 8)
                                       ttttacat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cgttttcgtggtttcttttttttttatttaatttcaaaacccatggattaaacagaactgctacgacgagattgttgatagcagttttacatgaatgcagGCATCGCTGAAACGCTTGGACATGAGTTATGTGGATCTGCTGTACTGCCATCGGCCAGATCCCTCGACTCCAATTGAAGAGACTGTACGAGCTATGAACT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA