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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gacctctgatatgagtcaatcgaagctaacgtaactgagaggtctagtatgagttcggcgttttcaatatcattaacttaagttggttggtggtcattagATGTGTTTTAAGAGGATGTGTTCCTAAAAAGCTCCTGGTATACGGAGCCAACTTTCCACACGATTTTGAGAGCAGCCGAGGATTCGGGTGGTCATTCGAG

Basic information

species Physcomitrella patens
transcript PP1S13_127V6.2
intron # 3
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|100407241|gb|BY974073.1|BY974073
EST:     ATGCCATTCGCGCCCATCTCGTCCGATGAAGCTGGTGGTGTTGGGGGAAC                         ATGTGTTTTAAGAGGATGTGTTCCTAAAAAGCTCCTGGTATACGGAGCCAA
genomic: ATGCCATTCGCGCCCATCTCGTCCGATGAAGCTGGTGGTGTTGGGGGAACgtaagttgta ... tggtcattagATGTGTTTTAAGAGGATGTGTTCCTAAAAAGCTCCTGGTATACGGAGCCAA
EST: gi|162256497|gb|FC432528.1|FC432528
EST:     ATGCCATTCGCGCCCATCTCGTCCGATGAAGCTGGTGGTGTTGGGGGAAC                         ATGTGTTTTAAGAGGATGTGTTCCTAAAAAGCTCCTGGTATACGGAGCCAA
genomic: ATGCCATTCGCGCCCATCTCGTCCGATGAAGCTGGTGGTGTTGGGGGAACgtaagttgta ... tggtcattagATGTGTTTTAAGAGGATGTGTTCCTAAAAAGCTCCTGGTATACGGAGCCAA
EST: gi|18351331|gb|BJ183383.1|BJ183383
EST:     ATGCCATTCGCGCCCATCTCGTCCGATGAAGCTGGTGGTGTTGGGGGAAC                         ATGTGTTTTAAGAGG
genomic: ATGCCATTCGCGCCCATCTCGTCCGATGAAGCTGGTGGTGTTGGGGGAACgtaagttgta ... tggtcattagATGTGTTTTAAGAGG
EST: gi|100366004|gb|BY967247.1|BY967247
EST:     ATGCCATTCGCGCCCATCTCGTCCGATGAAGCTGGTGGTGTTGGGGGAAC                         ATGTGTTTTAAGAGGATGTGTTCCTAAAAAGCTCCTGGTATACGGAGCCAA
genomic: ATGCCATTCGCGCCCATCTCGTCCGATGAAGCTGGTGGTGTTGGGGGAACgtaagttgta ... tggtcattagATGTGTTTTAAGAGGATGTGTTCCTAAAAAGCTCCTGGTATACGGAGCCAA
EST: gi|162247058|gb|FC422232.1|FC422232
EST:     ATGCCATTCGCGCCCATCTCGTCCGATGAAGCTGGTGGTGTTGGGGGAAC                         ATGTGTTTTAAGAGGATGTGTTCCTAAAAAGCTCCTGGTATACGGAGCCAA
genomic: ATGCCATTCGCGCCCATCTCGTCCGATGAAGCTGGTGGTGTTGGGGGAACgtaagttgta ... tggtcattagATGTGTTTTAAGAGGATGTGTTCCTAAAAAGCTCCTGGTATACGGAGCCAA
EST: gi|18355834|gb|BJ187893.1|BJ187893
EST:     ATGCCATTCGCGCCCATCTCGTCCGATGAAGCTGGTGGTGTTGGGGGAAC                         ATGTGTTTTANGANGATGTGTTCCTAAAAAGCTCCTGGTATACGGAG
genomic: ATGCCATTCGCGCCCATCTCGTCCGATGAAGCTGGTGGTGTTGGGGGAACgtaagttgta ... tggtcattagATGTGTTTTAAGAGGATGTGTTCCTAAAAAGCTCCTGGTATACGGAG
EST: gi|18328557|gb|BJ160562.1|BJ160562
EST:     ATGCCATTCGCGCCCATCTCGTCCGATGAAGCTGGTGGTGTTGGGGGAAC                         ATGTGTTTTAAGAGGATGTGTTCCTAAAAAGCTCCTGGGTATACGGAGCCA
genomic: ATGCCATTCGCGCCCATCTCGTCCGATGAAGCTGGTGGTGTTGGGGGAACgtaagttgta ... tggtcattagATGTGTTTTAAGAGGATGTGTTCCTAAAAAGCTCCTGG-TATACGGAGCCA
EST: gi|208367054|gb|DC935910.1|DC935910
EST:     ATGCCATTCGCGCCCATCTCGTCCGATGAAGCTGGTGGTGTTGGGGGAAC                         ATGTGTTTTAAGAGGATGTGTTCCTAAAAAGCTCCTGGTATACGGAGCCAA
genomic: ATGCCATTCGCGCCCATCTCGTCCGATGAAGCTGGTGGTGTTGGGGGAACgtaagttgta ... tggtcattagATGTGTTTTAAGAGGATGTGTTCCTAAAAAGCTCCTGGTATACGGAGCCAA
EST: gi|67575873|gb|BJ948697.1|BJ948697
EST:     ATGCCATTCGCGCCCATCTCGTCCGATGAAGCTGGTGGTGTTGGGGGAAC                         ATGTGTTTTAAGAGGATGTGTTCCTAAAAAGCTCCTGGTATACGGAGCCAA
genomic: ATGCCATTCGCGCCCATCTCGTCCGATGAAGCTGGTGGTGTTGGGGGAACgtaagttgta ... tggtcattagATGTGTTTTAAGAGGATGTGTTCCTAAAAAGCTCCTGGTATACGGAGCCAA
EST: gi|208382201|gb|DC914834.1|DC914834
EST:     ATGCCATTCGCGCCCATCTCGTCCGATGAAGCTGGTGGTGTTGGGGGAAC                         ATGTGTTTTAAGAGGATGTGTTCCTAAAAAGCTCCTGGTATACGGAGCCAA
genomic: ATGCCATTCGCGCCCATCTCGTCCGATGAAGCTGGTGGTGTTGGGGGAACgtaagttgta ... tggtcattagATGTGTTTTAAGAGGATGTGTTCCTAAAAAGCTCCTGGTATACGGAGCCAA
EST: gi|67573975|gb|BJ946799.1|BJ946799
EST:     ATGCCATTCGCGCCCATCTCGTCCGATGAAGCTGGTGGTGTTGGGGGAAC                         ATGTGTTTTAAGAGGATGTGTTCCTAAAAAGCTCCTGGTATACGGAGCCAA
genomic: ATGCCATTCGCGCCCATCTCGTCCGATGAAGCTGGTGGTGTTGGGGGAACgtaagttgta ... tggtcattagATGTGTTTTAAGAGGATGTGTTCCTAAAAAGCTCCTGGTATACGGAGCCAA
EST: gi|18372687|gb|BJ204289.1|BJ204289
EST:     ATGCCATTCGCGCCCATCTCGTCCGATGAAGCTGGTGGTGTTGGGGGAAC                         ATGTGTTTTAAGAGGATGTGTTCCTAAAAAGCTCCTGGTATACGGAGCCA
genomic: ATGCCATTCGCGCCCATCTCGTCCGATGAAGCTGGTGGTGTTGGGGGAACgtaagttgta ... tggtcattagATGTGTTTTAAGAGGATGTGTTCCTAAAAAGCTCCTGGTATACGGAGCCA
EST: gi|18347787|gb|BJ179834.1|BJ179834
EST:     ATGCCATTCGCGCCCATCTCGTCCGATGAAGCTGGTGGTGTTGGGGGAAC                         ATGTGTTTTAAGAGGATGTGTTCCTAAAAAGCTCCTGGTATACGGAGCCAA
genomic: ATGCCATTCGCGCCCATCTCGTCCGATGAAGCTGGTGGTGTTGGGGGAACgtaagttgta ... tggtcattagATGTGTTTTAAGAGGATGTGTTCCTAAAAAGCTCCTGGTATACGGAGCCAA
EST: gi|100415484|gb|BY992866.1|BY992866
EST:     ATGCCATTCGCGCCCATCTCGTCCGATGAAGCTGGTGGTGTTGGGGGAAC                         ATGTGTTTTAAGAGGATGTGTTCCTAAAAAGCTCCTGGTATACGGAGCCAA
genomic: ATGCCATTCGCGCCCATCTCGTCCGATGAAGCTGGTGGTGTTGGGGGAACgtaagttgta ... tggtcattagATGTGTTTTAAGAGGATGTGTTCCTAAAAAGCTCCTGGTATACGGAGCCAA
EST: gi|18330436|gb|BJ162442.1|BJ162442
EST:     ATGCCATTCGCGCCCATCTCGTCCGATGAAGCTGGTGGTGTTGGGGGAAC                         ATGTGTTTTAAGAGGATGTGTTCCTAAAAAGCTCCTGGTATACGGAG
genomic: ATGCCATTCGCGCCCATCTCGTCCGATGAAGCTGGTGGTGTTGGGGGAACgtaagttgta ... tggtcattagATGTGTTTTAAGAGGATGTGTTCCTAAAAAGCTCCTGGTATACGGAG
EST: gi|18348525|gb|BJ180574.1|BJ180574
EST:     ATGCCATTCGCGCCCATCTCGTCCGATGAAGCTGGTGGTGTTGGGGGAAC                         ATGTGTTTTAAGAGGATGTGTTCCTAAAAAGCTCCTGGTATACGGAGCCAA
genomic: ATGCCATTCGCGCCCATCTCGTCCGATGAAGCTGGTGGTGTTGGGGGAACgtaagttgta ... tggtcattagATGTGTTTTAAGAGGATGTGTTCCTAAAAAGCTCCTGGTATACGGAGCCAA
EST: gi|100389613|gb|BY952419.1|BY952419
EST:     ATGCCATTCGCGCCCATCTCGTCCGATGAAGCTGGTGGTGTTGGGGGAAC                         ATGTGTTTTAAGAGGATGTGTTCCTAANAAGCTCCTGGTATACGGAGCCAA
genomic: ATGCCATTCGCGCCCATCTCGTCCGATGAAGCTGGTGGTGTTGGGGGAACgtaagttgta ... tggtcattagATGTGTTTTAAGAGGATGTGTTCCTAAAAAGCTCCTGGTATACGGAGCCAA
EST: gi|100443450|gb|BY981877.1|BY981877
EST:     ATGCCATTCGCGCCCATCTCGTCCGATGAAGCTGGTGGTGTTGGGGGAAC                         ATGTGTTTTAAGAGGATGTGTTCCTAAAAAGCTCCTGGGATACGGAGCCAA
genomic: ATGCCATTCGCGCCCATCTCGTCCGATGAAGCTGGTGGTGTTGGGGGAACgtaagttgta ... tggtcattagATGTGTTTTAAGAGGATGTGTTCCTAAAAAGCTCCTGGTATACGGAGCCAA
EST: gi|18373476|gb|BJ205054.1|BJ205054
EST:     ATGCCATTCGCGCCCATCTCGTCCGATGAAGCTGGTGGTGTTGGGGGAAC                         ATGTGTTTTAAGAGGATGTGTTCCTAAAAAGCTCCTGGTATACGGAGC
genomic: ATGCCATTCGCGCCCATCTCGTCCGATGAAGCTGGTGGTGTTGGGGGAACgtaagttgta ... tggtcattagATGTGTTTTAAGAGGATGTGTTCCTAAAAAGCTCCTGGTATACGGAGC

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: 27 (upstream exon), 28 (downstream exon)
Score: 21

GGGCAGCCCGGTTTGCATCTCAATTTGGGGCTAACGTTGCAGTTTGTGAAATGCCATTCGCGCCCATCTCGTCCGATGAAGCTGGTGGTGTTGGGGGAACgtaagttgta ... tggtcattagATGTGTTTTAAGAGGATGTGTTCCTAAAAAGCTCCTGGTATACGGAGCCAACTTTCCACACGATTTTGAGAGCAGCCGAGGATTCGGGTGGTCATTCGAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agtatgagttcggcgttttcaatatcattaacttaagttggttggtggtcattagATGTGTTTTAAGAGGATGTGTTCCTAAAAAGCTCCTGGTATACGGAGCCAACTTTCCACACGATTTTGAGAGCAGCCGAGGATTCGGGTGGTCATTCGAG
                         cattaac  putative branch site (score: 21)
               ttttcaatatcattaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gacctctgatatgagtcaatcgaagctaacgtaactgagaggtctagtatgagttcggcgttttcaatatcattaacttaagttggttggtggtcattagATGTGTTTTAAGAGGATGTGTTCCTAAAAAGCTCCTGGTATACGGAGCCAACTTTCCACACGATTTTGAGAGCAGCCGAGGATTCGGGTGGTCATTCGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAT