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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaggtccttaaaaacctatttgccatgtcggtaagtggtttcaagtcttttgtcagaacttactgactcgcctgccactcatttgttacctccttttccatgcagACTGCTCAATTACGTTTGGAGAACGCCACTCTATCCCGTAGGTTAAAGATAGCCGAGCAGCTCGCCAAGAAACTCGAGCTCGAGAAGAATGAATTGGCTG

Basic information

species Physcomitrella patens
transcript PP1S48_101V6.2
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|208379608|gb|DC927105.1|DC927105
EST:     AACGGTCAAGACAAAGAAAGCAGGAGCGTCTGGACGAGCTCGAAATTTTG                         ACTGCTCAATTACGTTTGGAGAACGCCACTCTATCCCGTAGGTTAAAGATA
genomic: AACGGTCAAGACAAAGAAAGCAGGAGCGTCTGGACGAGCTCGAAATTTTGgtaaggtcct ... ttccatgcagACTGCTCAATTACGTTTGGAGAACGCCACTCTATCCCGTAGGTTAAAGATA
EST: gi|208345923|gb|DC921094.1|DC921094
EST:     ANC-GTCAAGACAACGAAAGCAGGAGCGTCTGGACGAGCTCGAAATTTTG                         ACTGCTCAATTACGTNTGGAGAACGCCACTCTATCCCGTAGGTTAAAGATA
genomic: AACGGTCAAGACAAAGAAAGCAGGAGCGTCTGGACGAGCTCGAAATTTTGgtaaggtcct ... ttccatgcagACTGCTCAATTACGTTTGGAGAACGCCACTCTATCCCGTAGGTTAAAGATA
EST: gi|208361173|gb|DC954279.1|DC954279
EST:     AACGGTCAAGACAAAGAAAGCAGGAGCGTCTGGACGAGCTCGAAATTTTG                         ACTGCTCAATTACGTTTGGAGAACGCCACTCTATCCCGTAGGTTAAAGATA
genomic: AACGGTCAAGACAAAGAAAGCAGGAGCGTCTGGACGAGCTCGAAATTTTGgtaaggtcct ... ttccatgcagACTGCTCAATTACGTTTGGAGAACGCCACTCTATCCCGTAGGTTAAAGATA
EST: gi|37851284|gb|BJ609292.1|BJ609292
EST:     ACGGTCAAGGACAAAGAAAGCAGGAGCGTCTGGACGAGCTCGAAATTTTG                         ACTGCTCAATTACGTTTGGAGAACGCCACTCTATCCCGTAGGTTAAAGATA
genomic: ACGGTCAA-GACAAAGAAAGCAGGAGCGTCTGGACGAGCTCGAAATTTTGgtaaggtcct ... ttccatgcagACTGCTCAATTACGTTTGGAGAACGCCACTCTATCCCGTAGGTTAAAGATA
EST: gi|162273040|gb|FC449171.1|FC449171
EST:     AACGGTCAAGACAAAGAAAGCAGGAGCGTCTGGACGAGCTCGAAATTTTG                         ACTGCTCAATTACGTTTGGAGAACGCCACTCTATCCCGTAGGTTAAAGATA
genomic: AACGGTCAAGACAAAGAAAGCAGGAGCGTCTGGACGAGCTCGAAATTTTGgtaaggtcct ... ttccatgcagACTGCTCAATTACGTTTGGAGAACGCCACTCTATCCCGTAGGTTAAAGATA
EST: gi|162273041|gb|FC449172.1|FC449172
EST:     AACGGTCAAGACAAAGAAAGCAGGAGCGTCTGGACGAGCTCGAAATTTTG                         ACTGCTCAATTACGTTTGGAGAACGCCACTCTATCCCGTAGGTTAAAGATA
genomic: AACGGTCAAGACAAAGAAAGCAGGAGCGTCTGGACGAGCTCGAAATTTTGgtaaggtcct ... ttccatgcagACTGCTCAATTACGTTTGGAGAACGCCACTCTATCCCGTAGGTTAAAGATA
EST: gi|162188134|gb|FC363900.1|FC363900
EST:     AACGGTCAAGACAAAGAAAGCAGGAGCGTCTGGACGAGCTCGAAATTTTG                         ACTGCTCAATTACGTTTGGAGAACGCCACTCTATCCCGTAGGTTAAAGATA
genomic: AACGGTCAAGACAAAGAAAGCAGGAGCGTCTGGACGAGCTCGAAATTTTGgtaaggtcct ... ttccatgcagACTGCTCAATTACGTTTGGAGAACGCCACTCTATCCCGTAGGTTAAAGATA
EST: gi|162182407|gb|FC358006.1|FC358006
EST:     CGGTCAAGACAAAGAAAGCAGGAGCGTCTGGACGAGCTCGAAATTTTG                         ACTGCTCAATTACGTTTGGAGAACGCCACTCTATCCCGTAGGTTAAAGATA
genomic: CGGTCAAGACAAAGAAAGCAGGAGCGTCTGGACGAGCTCGAAATTTTGgtaaggtcct ... ttccatgcagACTGCTCAATTACGTTTGGAGAACGCCACTCTATCCCGTAGGTTAAAGATA
EST: gi|208382944|gb|DC927694.1|DC927694
EST:     AACGGTCAAGACAAAGAAAGCAGGAGCGTCTGGACGAGCTCGAAATTTTG                         ACTGCTCAATTACGTTTGGAGAACGCCACTCTATCCCGTAGGTTAAAGATA
genomic: AACGGTCAAGACAAAGAAAGCAGGAGCGTCTGGACGAGCTCGAAATTTTGgtaaggtcct ... ttccatgcagACTGCTCAATTACGTTTGGAGAACGCCACTCTATCCCGTAGGTTAAAGATA
EST: gi|162177489|gb|FC353750.1|FC353750
EST:     AACGGTCAAGACAAAGAAAGCAGGAGCGTCTGGACGAGCTCGAAATTTTG                         ACTGCTCAATTACGTTTGGAGAACGCCACTCTATCCCGTAGGTTAAAGATA
genomic: AACGGTCAAGACAAAGAAAGCAGGAGCGTCTGGACGAGCTCGAAATTTTGgtaaggtcct ... ttccatgcagACTGCTCAATTACGTTTGGAGAACGCCACTCTATCCCGTAGGTTAAAGATA
EST: gi|37847539|gb|BJ605547.1|BJ605547
EST:     ANCGGTCAAGACAAAGAAAGCAGGAGCGTCTGGACGAGCTCGAAATTTTG                         ACTGCTCAATTACGTTTGGAGAACGCCACTCTATCCCGTAGGTTAAAGATA
genomic: AACGGTCAAGACAAAGAAAGCAGGAGCGTCTGGACGAGCTCGAAATTTTGgtaaggtcct ... ttccatgcagACTGCTCAATTACGTTTGGAGAACGCCACTCTATCCCGTAGGTTAAAGATA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtcagaacttactgactcgcctgccactcatttgttacctccttttccatgcagACTGCTCAATTACGTTTGGAGAACGCCACTCTATCCCGTAGGTTAAAGATAGCCGAGCAGCTCGCCAAGAAACTCGAGCTCGAGAAGAATGAATTGGCTG
          tactgac  putative branch site (score: 1)
                           ctcatttgttacctcc  putative PPT
                              atttgtta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaggtccttaaaaacctatttgccatgtcggtaagtggtttcaagtcttttgtcagaacttactgactcgcctgccactcatttgttacctccttttccatgcagACTGCTCAATTACGTTTGGAGAACGCCACTCTATCCCGTAGGTTAAAGATAGCCGAGCAGCTCGCCAAGAAACTCGAGCTCGAGAAGAATGAATTGGCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA