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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATTCACGGCAGACATAAATAACGGCCGTTGGGATGCCGTTTTGCCACAAGTGGCTCAGCTCAAACTTCCCCGCAAGAAATTGGAGGACTTGTACGAGCAGgtgctcccgtcatggcctctttcaaccccgcatcatttggagtaactacattggatttggtgatccacttgtgcgcatcttgtgtactttcttgactgatcacatgtgatctacgactttctcatgtgaatgttcaactgggtgacgactatgcaaagattaatcataggtaggcttgtggcag

Basic information

species Physcomitrella patens
transcript PP1S31_68V6.1
intron # 2
splice site 5'
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|208378663|gb|DC903694.1|DC903694
EST:     TGGCTCAGCTCAAACTTCCCCGCAAGAAATTGGAGGACTTGTACGAGCAG                         ATTGTCCTGGAAATGATAGAGCTTCGTGAGTTGGATACTGCCAGGGCCATT
genomic: TGGCTCAGCTCAAACTTCCCCGCAAGAAATTGGAGGACTTGTACGAGCAGgtgctcccgt ... cttgtggcagATTGTCCTGGAAATGATAGAGCTTCGTGAGTTGGATACTGCCAGGGCCATT
EST: gi|18362895|gb|BJ194967.1|BJ194967
EST:     TGGCTCAGCTCAAACTTCCCCGCAAGAAATTGGAGGACTTGTACGAGCAG                         ATTGTCCTGGAAATGATAGAGCTTCGTGAGTTGGATACTGCCAGGGCCATT
genomic: TGGCTCAGCTCAAACTTCCCCGCAAGAAATTGGAGGACTTGTACGAGCAGgtgctcccgt ... cttgtggcagATTGTCCTGGAAATGATAGAGCTTCGTGAGTTGGATACTGCCAGGGCCATT
EST: gi|67717592|gb|BJ967851.1|BJ967851
EST:     TGGCTCAGCTCAAACTTCCCCGCAAGAAATTGGAGGACTTGTACGAGCAG                         ATTGTCCTGGAAATGATAGAGCTTCGTGAGTTGGATACTGCCAGGGCCATT
genomic: TGGCTCAGCTCAAACTTCCCCGCAAGAAATTGGAGGACTTGTACGAGCAGgtgctcccgt ... cttgtggcagATTGTCCTGGAAATGATAGAGCTTCGTGAGTTGGATACTGCCAGGGCCATT
EST: gi|208379508|gb|DC911119.1|DC911119
EST:     TGGCTCAGCTCAAACTTCCCCGCAAGAAATTGGAGGACTTGTACGAGCAG                         ATTGTCCTGGAAATGATAGAGCTTCNTGAGTTGGATACTGCCAGGGCCATT
genomic: TGGCTCAGCTCAAACTTCCCCGCAAGAAATTGGAGGACTTGTACGAGCAGgtgctcccgt ... cttgtggcagATTGTCCTGGAAATGATAGAGCTTCGTGAGTTGGATACTGCCAGGGCCATT
EST: gi|162182459|gb|FC358058.1|FC358058
EST:     TGGCTCAGCTCAAACTTCCCCGCAAGAAATTGGAGGACTTGTACGAGCAG                         ATTGTCCTGGAAATGATAGAGCTTCGTGAGTTGGATACTGCCAGGGCCATT
genomic: TGGCTCAGCTCAAACTTCCCCGCAAGAAATTGGAGGACTTGTACGAGCAGgtgctcccgt ... cttgtggcagATTGTCCTGGAAATGATAGAGCTTCGTGAGTTGGATACTGCCAGGGCCATT
EST: gi|18352925|gb|BJ184980.1|BJ184980
EST:     TGGCTCAGCTCAAACTTCCCCGCAAGAAATTGGAGGACTTGTACGAGCAN                         ATTGTCCTGGAAATGATAGAGCTTCGTGAGTTGGATACTGCCAGGGCCATT
genomic: TGGCTCAGCTCAAACTTCCCCGCAAGAAATTGGAGGACTTGTACGAGCAGgtgctcccgt ... cttgtggcagATTGTCCTGGAAATGATAGAGCTTCGTGAGTTGGATACTGCCAGGGCCATT
EST: gi|67573598|gb|BJ946422.1|BJ946422
EST:     TGGCTCAGCTCAAACTTCCCCGCAAGAAATTGGAGGACTTGTACGAGCAG                         ATTGTCCTGGAAATGATAGAGCTTCGTGAGTTGGATACTGCCAGGGCCATT
genomic: TGGCTCAGCTCAAACTTCCCCGCAAGAAATTGGAGGACTTGTACGAGCAGgtgctcccgt ... cttgtggcagATTGTCCTGGAAATGATAGAGCTTCGTGAGTTGGATACTGCCAGGGCCATT
EST: gi|18356245|gb|BJ188304.1|BJ188304
EST:     TGGCTCAGCTCAAACTTCCCCGCAAGAAATTGGAGGACTTGTACGAGCAG                         ATTGTCCTGGAAATGATAGAGCTTCGTGAGTTGGATACTGCCAGGGCCATT
genomic: TGGCTCAGCTCAAACTTCCCCGCAAGAAATTGGAGGACTTGTACGAGCAGgtgctcccgt ... cttgtggcagATTGTCCTGGAAATGATAGAGCTTCGTGAGTTGGATACTGCCAGGGCCATT
EST: gi|100450837|gb|CJ974464.1|CJ974464
EST:     TGGCTCAGCTCAAACTTCCCCGCAAGAAATTGGAGGACTTGTACGAGCAG                         ATTGTCCTGGAAATGATAGAGCTTCGTGAGTTGGATACTGCCAGGGCCATT
genomic: TGGCTCAGCTCAAACTTCCCCGCAAGAAATTGGAGGACTTGTACGAGCAGgtgctcccgt ... cttgtggcagATTGTCCTGGAAATGATAGAGCTTCGTGAGTTGGATACTGCCAGGGCCATT
EST: gi|100431243|gb|BY960099.1|BY960099
EST:     TGGCTCAGCTCAAACTTCCCCGCAAGAAATTGGAGGACTTGTACGAGCAG                         ATTGTCCTGGAAATGATAGAGCTTCGTGAGTTGGATACTGCCAGGGCCATT
genomic: TGGCTCAGCTCAAACTTCCCCGCAAGAAATTGGAGGACTTGTACGAGCAGgtgctcccgt ... cttgtggcagATTGTCCTGGAAATGATAGAGCTTCGTGAGTTGGATACTGCCAGGGCCATT
EST: gi|208377120|gb|DC940820.1|DC940820
EST:     AATTGGAGGACTTGTACGAGCAG                         ATTGTCCTGGAAATGATAGAGCTTCGTGAGTTGGATACTGCCAGGGCCATT
genomic: AATTGGAGGACTTGTACGAGCAGgtgctcccgt ... cttgtggcagATTGTCCTGGAAATGATAGAGCTTCGTGAGTTGGATACTGCCAGGGCCATT
EST: gi|18350111|gb|BJ182162.1|BJ182162
EST:     TGGCTCAGCTCAAACTTCCCCGCAAGAAATTGGAGGACTTGTACGAGCAG                         ATTGTCCTGGAAATGATAGAGCTTCGTGAGTTGGATACTGCCAGGGCCATT
genomic: TGGCTCAGCTCAAACTTCCCCGCAAGAAATTGGAGGACTTGTACGAGCAGgtgctcccgt ... cttgtggcagATTGTCCTGGAAATGATAGAGCTTCGTGAGTTGGATACTGCCAGGGCCATT
EST: gi|100407287|gb|BY974097.1|BY974097
EST:     TGGCTCAGCTCAAACTTCCCCGCAAGAAATTGGAGGACTTGTACGAGCAG                         ATTTGTCCTGGAAAAGATAGAG
genomic: TGGCTCAGCTCAAACTTCCCCGCAAGAAATTGGAGGACTTGTACGAGCAGgtgctcccgt ... cttgtggcagATT-GTCCTGGAAATGATAGAG

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: 26 (upstream exon), 10 (downstream exon)
Score: 1

ATTCACGGCAGACATAAATAACGGCCGTTGGGATGCCGTTTTGCCACAAGTGGCTCAGCTCAAACTTCCCCGCAAGAAATTGGAGGACTTGTACGAGCAGgtgctcccgt ... cttgtggcagATTGTCCTGGAAATGATAGAGCTTCGTGAGTTGGATACTGCCAGGGCCATTTTGAGGCAAACGCAAGCTATGGGATTCATGAAACAGGAACAGCCTGAGC




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATTCACGGCAGACATAAATAACGGCCGTTGGGATGCCGTTTTGCCACAAGTGGCTCAGCTCAAACTTCCCCGCAAGAAATTGGAGGACTTGTACGAGCAGgtgctcccgtcatggcctctttcaaccccgcatcatttggagtaactacattggatttggtgatccacttgtgcgcatcttgtgtactttcttgactgatcacatgtgatctacgactttctcatgtgaatgttcaactgggtgacgactatgcaaagattaatcataggtaggcttgtggcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG