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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagttgatttctgggtagaatgtatgcagtgactgtgaattgtggttatgcggtttggagtgtggcaaaatgctacctctgcgactttccttctcgtgtggcaattggcaggaaaactgatgattgctttgtttgtccacgaagATACAAGGACGACGTTTTGAACCCGAAGAGGAAGGATACTAGCTTAGAGAAGCTCCCTAGAAACGT

Basic information

species Physcomitrella patens
transcript PP1S153_101V6.1
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|208359401|gb|DC939140.1|DC939140
EST:     CGGAAGTTCGCTCAAGTGAAGCGTATGCTCGCGCCGAAAGCAATTAAACA                         ATACAAGGACGACGTTTTGAACCCGAAGAGGAAGGATACTAGCTTAGAGAA
genomic: CGGAAGTTCGCTCAAGTGAAGCGTATGCTCGCGCCGAAAGCAATTAAACAgtgagttgat ... gtccacgaagATACAAGGACGACGTTTTGAACCCGAAGAGGAAGGATACTAGCTTAGAGAA
EST: gi|100365650|gb|BY948205.1|BY948205
EST:     CGGAAGTTCGCTCAAGTGAAGCGTATGCTCGCGCCGAAAGCAATTAAACA                         ATACAAGGACGACGTTTTGAACCCGAAGAGGAAGGATACTAGCTTAGAGAA
genomic: CGGAAGTTCGCTCAAGTGAAGCGTATGCTCGCGCCGAAAGCAATTAAACAgtgagttgat ... gtccacgaagATACAAGGACGACGTTTTGAACCCGAAGAGGAAGGATACTAGCTTAGAGAA
EST: gi|208383700|gb|DC928031.1|DC928031
EST:     CGGAAGTTCGCTCAAGTGAAGCGTATGCTCGCGCCGAAAGCAATTAAACA                         ATACAAGGACGACGTTTTGAACCCGAAGAGGAAGGATACTAGCTTAGAGAA
genomic: CGGAAGTTCGCTCAAGTGAAGCGTATGCTCGCGCCGAAAGCAATTAAACAgtgagttgat ... gtccacgaagATACAAGGACGACGTTTTGAACCCGAAGAGGAAGGATACTAGCTTAGAGAA
EST: gi|18348287|gb|BJ180334.1|BJ180334
EST:     CGGAAGTTCGCTCAAGTGAAGCGTATGCTCGCGCCGAAAGCAATTAAACA                         ATACAAGGACGACGTTTTGAACCCGAAGAGGAAGGATACTAGCTTAGAGAA
genomic: CGGAAGTTCGCTCAAGTGAAGCGTATGCTCGCGCCGAAAGCAATTAAACAgtgagttgat ... gtccacgaagATACAAGGACGACGTTTTGAACCCGAAGAGGAAGGATACTAGCTTAGAGAA
EST: gi|18344506|gb|BJ176547.1|BJ176547
EST:     CGGAAGTTCGCTCAAGTGAAGCGTATGCTCGCGCCGAAAGCAATTAAACA                         ATACAAGGACGACGTTTTGAACCCGAAGAGGAAGGATACTAGCTTAGAGAA
genomic: CGGAAGTTCGCTCAAGTGAAGCGTATGCTCGCGCCGAAAGCAATTAAACAgtgagttgat ... gtccacgaagATACAAGGACGACGTTTTGAACCCGAAGAGGAAGGATACTAGCTTAGAGAA
EST: gi|208356397|gb|DC914287.1|DC914287
EST:     CGGAAGTTCGCTCAAGTGAAGCGTATGCTCGCGCCGAAAGCAATTAAACA                         ATACAAGGACGACGTTTTGAACCCGAAGAGGAAGGATACTAGCTTAGAGAA
genomic: CGGAAGTTCGCTCAAGTGAAGCGTATGCTCGCGCCGAAAGCAATTAAACAgtgagttgat ... gtccacgaagATACAAGGACGACGTTTTGAACCCGAAGAGGAAGGATACTAGCTTAGAGAA
EST: gi|18355693|gb|BJ187752.1|BJ187752
EST:     CGGAAGTTCGCTCAAGTGAAGCGTATGCTCGCGCCGAAAGCAATTAAACA                         ATACAAGGACGACGTTTTGAACCCGAAGAGGAAGGATACTAGCTTAGAGAA
genomic: CGGAAGTTCGCTCAAGTGAAGCGTATGCTCGCGCCGAAAGCAATTAAACAgtgagttgat ... gtccacgaagATACAAGGACGACGTTTTGAACCCGAAGAGGAAGGATACTAGCTTAGAGAA
EST: gi|208400155|gb|DC904803.1|DC904803
EST:     CGGAAGTTCGCTCAAGTGAAGCGTATGCTCGCGCCGAAAGCAATTAAACA                         ATACAAGGACGACGTTTTGAACCCGAAGAGGAAGGATACTAGCTTAGAGAA
genomic: CGGAAGTTCGCTCAAGTGAAGCGTATGCTCGCGCCGAAAGCAATTAAACAgtgagttgat ... gtccacgaagATACAAGGACGACGTTTTGAACCCGAAGAGGAAGGATACTAGCTTAGAGAA
EST: gi|208370447|gb|DC952150.1|DC952150
EST:     TCGCGCCGAAAGCANTT-AACA                         ATNCAAGGACGACG-TTTGNACCCGAAGAGGGAGGATACTAGCTTAGAGAA
genomic: TCGCGCCGAAAGCAATTAAACAgtgagttgat ... gtccacgaagATACAAGGACGACGTTTTGAACCCGAAGAGGAAGGATACTAGCTTAGAGAA
EST: gi|100416555|gb|BY975445.1|BY975445
EST:     CGGAAGTTCGCTCAAGTGAAGCGTATGCTCGCGCCGAAAGCAATTAAACA                         ATACAAGGACGACGTTTTGAACCCGAAGAGGAAGGATACTAGCTTAGAGAC
genomic: CGGAAGTTCGCTCAAGTGAAGCGTATGCTCGCGCCGAAAGCAATTAAACAgtgagttgat ... gtccacgaagATACAAGGACGACGTTTTGAACCCGAAGAGGAAGGATACTAGCTTAGAGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttctcgtgtggcaattggcaggaaaactgatgattgctttgtttgtccacgaagATACAAGGACGACGTTTTGAACCCGAAGAGGAAGGATACTAGCTTAGAGAAGCTCCCTAGAAACGT
                         aactgat  putative branch site (score: 3)
                                          tttgtcc  putative PPT
                                      tttgttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagttgatttctgggtagaatgtatgcagtgactgtgaattgtggttatgcggtttggagtgtggcaaaatgctacctctgcgactttccttctcgtgtggcaattggcaggaaaactgatgattgctttgtttgtccacgaagATACAAGGACGACGTTTTGAACCCGAAGAGGAAGGATACTAGCTTAGAGAAGCTCCCTAGAAACGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC