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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGCTTCGAAAGATAGAGATGGTAAAAAAGAAATGTTGGGGTATCGTGAAATCACTGACGGTGTGgtaagtctctagacttattcctttcatcctgctgggtaggtagctgctgaagtcttttcagtgttgaagtttaatgtgtgctgactatgaaatcgcgcag

Basic information

species Physcomitrella patens
transcript PP1S218_19V6.1
intron # 3
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|162167702|gb|FC344016.1|FC344016
EST:     GAGATGGTAAAAAAGAAATGTTGGGGTATCGTGAAATCACTGACGGTGTG                         GCTGGGAAGTACATTTGGTTTAATTACCAGCAAGTATATGAAACAGTGGTC
genomic: GAGATGGTAAAAAAGAAATGTTGGGGTATCGTGAAATCACTGACGGTGTGgtaagtctct ... aatcgcgcagGCTGGGAAGTACATTTGGTTTAATTACCAGCAAGTATATGAAACAGTGGTC
EST: gi|18371694|gb|BJ203296.1|BJ203296
EST:     GAGATGGTAAAAAAGAAATGTTGGGGTATCGTGAAATCACTGACGGTGTG                         GCTGGGAAGTACATTTGGTTTAATTACCAGCAAGTATATGAAACAGTGGTC
genomic: GAGATGGTAAAAAAGAAATGTTGGGGTATCGTGAAATCACTGACGGTGTGgtaagtctct ... aatcgcgcagGCTGGGAAGTACATTTGGTTTAATTACCAGCAAGTATATGAAACAGTGGTC
EST: gi|18355808|gb|BJ187867.1|BJ187867
EST:     GAGATGGTAAAAAAGAAATGTTGGGGTATCGTGAAATCACTGACGGTGTG                         GCTGGGAAGTACATTTGGTTTAATTACCAGCAAGTATATGAAACAGTGGTC
genomic: GAGATGGTAAAAAAGAAATGTTGGGGTATCGTGAAATCACTGACGGTGTGgtaagtctct ... aatcgcgcagGCTGGGAAGTACATTTGGTTTAATTACCAGCAAGTATATGAAACAGTGGTC
EST: gi|162171311|gb|FC347236.1|FC347236
EST:     GAGATGGTAAAAAAGAAATGTTGGGGTATCGTGAAATCACTGACGGTGTG                         GCTGGGAAGTACATTTGGTTTAATTACCAGCAAGTATATGAAACAGTGGTC
genomic: GAGATGGTAAAAAAGAAATGTTGGGGTATCGTGAAATCACTGACGGTGTGgtaagtctct ... aatcgcgcagGCTGGGAAGTACATTTGGTTTAATTACCAGCAAGTATATGAAACAGTGGTC
EST: gi|18361267|gb|BJ193332.1|BJ193332
EST:     GAGATGGTAAAAAAGAAATGTTGGGGTATCGTGAAATCACTGACGGTGTG                         GCTGGGAAGTACATTTGGTTTAATTACCAGCAAGTATATGAAACAGTGGTC
genomic: GAGATGGTAAAAAAGAAATGTTGGGGTATCGTGAAATCACTGACGGTGTGgtaagtctct ... aatcgcgcagGCTGGGAAGTACATTTGGTTTAATTACCAGCAAGTATATGAAACAGTGGTC
EST: gi|18355950|gb|BJ188009.1|BJ188009
EST:     GAGATGGTAAAAAAGAAATGTTGGGGTATCGTGAAATCACTGACGGTGTG                         GCTGGGAAGTACATTTGGTTTAATTAACAGCAAGTATATGAAACAGTGGTC
genomic: GAGATGGTAAAAAAGAAATGTTGGGGTATCGTGAAATCACTGACGGTGTGgtaagtctct ... aatcgcgcagGCTGGGAAGTACATTTGGTTTAATTACCAGCAAGTATATGAAACAGTGGTC
EST: gi|18346122|gb|BJ178165.1|BJ178165
EST:     GAGATGGTAAAAAAGAAATGTTGGGGTATCGTGAAATCACTGACGGTGTG                         GCTGGGAAGTACATTTGGTTTAATTACCAGCAAGTATATGAAACAGTGGTC
genomic: GAGATGGTAAAAAAGAAATGTTGGGGTATCGTGAAATCACTGACGGTGTGgtaagtctct ... aatcgcgcagGCTGGGAAGTACATTTGGTTTAATTACCAGCAAGTATATGAAACAGTGGTC
EST: gi|18331390|gb|BJ163401.1|BJ163401
EST:     GAGATGGTAAAAAAGAAATGTTGGGGTATCGTGAAATCACTGACGGTGTG                         GCTGGGAAGTACATTTGGTTTAATTACCAGCAAGTATATGAAACAGTGGTC
genomic: GAGATGGTAAAAAAGAAATGTTGGGGTATCGTGAAATCACTGACGGTGTGgtaagtctct ... aatcgcgcagGCTGGGAAGTACATTTGGTTTAATTACCAGCAAGTATATGAAACAGTGGTC
EST: gi|18346188|gb|BJ178231.1|BJ178231
EST:     GAGATGGTAAAAAAGAAATGTTGGGGTATCGTGAAATCACTGACGGTGTG                         GCTGGGAAGTACATTTGGTTTAATTACCAGCAAGTATATGAAACAGTGGTC
genomic: GAGATGGTAAAAAAGAAATGTTGGGGTATCGTGAAATCACTGACGGTGTGgtaagtctct ... aatcgcgcagGCTGGGAAGTACATTTGGTTTAATTACCAGCAAGTATATGAAACAGTGGTC
EST: gi|18343706|gb|BJ175744.1|BJ175744
EST:     GAGATGGTAAAAAAGAAATGTTGGGGTATCGTGAAATCACTGACGGTGTG                         GCTGGGAAGTACATTTGGTTTAATTACCAGCAAGTATATGAAACAGTGGTC
genomic: GAGATGGTAAAAAAGAAATGTTGGGGTATCGTGAAATCACTGACGGTGTGgtaagtctct ... aatcgcgcagGCTGGGAAGTACATTTGGTTTAATTACCAGCAAGTATATGAAACAGTGGTC
EST: gi|18350093|gb|BJ182144.1|BJ182144
EST:     GAGATGGTAAAAAAGAAATGTTGGGGTATCGTGAAATCACTGACGGTGTG                         GCTGGGAAGTACATTTGGTTTAATTACCAGCAAGTATATGAAACAGTGGTC
genomic: GAGATGGTAAAAAAGAAATGTTGGGGTATCGTGAAATCACTGACGGTGTGgtaagtctct ... aatcgcgcagGCTGGGAAGTACATTTGGTTTAATTACCAGCAAGTATATGAAACAGTGGTC
EST: gi|18367433|gb|BJ199516.1|BJ199516
EST:     GAGATGGTAAAAAAGAAATGTTGGGGTATCGTGAAATCACTGACGGTGTG                         GCTGGGAAGTACATTTGGTTTAATTACCAGCAAGTATATGAAACAGTGGTC
genomic: GAGATGGTAAAAAAGAAATGTTGGGGTATCGTGAAATCACTGACGGTGTGgtaagtctct ... aatcgcgcagGCTGGGAAGTACATTTGGTTTAATTACCAGCAAGTATATGAAACAGTGGTC
EST: gi|162199213|gb|FC375049.1|FC375049
EST:     CACTGACGGTGTG                         GCTGGGAAGTACATTTGGTTTAATTACCAGCAAGTATATGAAACAGTGGTC
genomic: CACTGACGGTGTGgtaagtctct ... aatcgcgcagGCTGGGAAGTACATTTGGTTTAATTACCAGCAAGTATATGAAACAGTGGTC

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), 9 (downstream exon)
Score: 1

AGCTTCGAAAGATAGAGATGGTAAAAAAGAAATGTTGGGGTATCGTGAAATCACTGACGGTGTGgtaagtctct ... aatcgcgcagGCTGGGAAGTACATTTGGTTTAATTACCAGCAAGTATATGAAACAGTGGTCCAAATCGGTTCTGCTATTCGTCACATTGGCGTACAGCCG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGCTTCGAAAGATAGAGATGGTAAAAAAGAAATGTTGGGGTATCGTGAAATCACTGACGGTGTGgtaagtctctagacttattcctttcatcctgctgggtaggtagctgctgaagtcttttcagtgttgaagtttaatgtgtgctgactatgaaatcgcgcag

- - - - - - - GAGATG
- - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - AAGAAA