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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cggctaaatgcaattacgatgctgttaagttcagcagacgcgctctttttccttcatgacttccgaggcctcacttgcccgcatgggtgtggctatgcagGTAATACTTCACTGACGTGTTGTGGTTAAGTATCGGAAGCACGAAATGGTGCGATCAAGGTTGTCAGCGTCTGTTGAGGATCCTTCCCTTAACGTCATTG

Basic information

species Physcomitrella patens
transcript PP1S424_22V6.3
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|18327010|gb|BJ159011.1|BJ159011
EST:     GCTTCTACTTGTCCTTCACTGTGCAGATTTTCTCACCCACTCCGCTGAAG                         GTAATACTTCACTGACGTGTTGTGGTTAAGTATCGGAAGCACGAAATGGTG
genomic: GCTTCTACTTGTCCTTCACTGTGCAGATTTTCTCACCCACTCCGCTGAAGgtgaagctcg ... ggctatgcagGTAATACTTCACTGACGTGTTGTGGTTAAGTATCGGAAGCACGAAATGGTG
EST: gi|162273977|gb|FC450116.1|FC450116
EST:     CTCACCCACTCCGCTGAAG                         GTAATACTTCACTGACGTGTTGTGGTTAAGTATCGGAAGCACGAAATGGTG
genomic: CTCACCCACTCCGCTGAAGgtgaagctcg ... ggctatgcagGTAATACTTCACTGACGTGTTGTGGTTAAGTATCGGAAGCACGAAATGGTG
EST: gi|19788276|gb|BQ040746.1|BQ040746
EST:     GCTTCTACTTGTCCTTCACTGTGCAGATTTTCTCACCCACTCCGCTGAAG                         GTAATACTTCACTGACGTGTTGTGGTTAAGTATCGGAAGCACGAAATGGTG
genomic: GCTTCTACTTGTCCTTCACTGTGCAGATTTTCTCACCCACTCCGCTGAAGgtgaagctcg ... ggctatgcagGTAATACTTCACTGACGTGTTGTGGTTAAGTATCGGAAGCACGAAATGGTG
EST: gi|208382870|gb|DC928295.1|DC928295
EST:     GCTTCTACTTGTCCTTCACTGTGCAGATTTTCTCACCCACTCCGCTGAAG                         GTAATACTTCACTGACGTGTTGTGGTTAAGTATCGGAAGCACGAAATGGTG
genomic: GCTTCTACTTGTCCTTCACTGTGCAGATTTTCTCACCCACTCCGCTGAAGgtgaagctcg ... ggctatgcagGTAATACTTCACTGACGTGTTGTGGTTAAGTATCGGAAGCACGAAATGGTG
EST: gi|162278876|gb|FC454927.1|FC454927
EST:     CCTTCACTGTGCAGATTTTCTCACCCACTCCGCTGAAG                         GTAATACTTCACTGACGTGTTGTGGTTAAGTATCGGAAGCACGAAATGGTG
genomic: CCTTCACTGTGCAGATTTTCTCACCCACTCCGCTGAAGgtgaagctcg ... ggctatgcagGTAATACTTCACTGACGTGTTGTGGTTAAGTATCGGAAGCACGAAATGGTG
EST: gi|162263104|gb|FC440082.1|FC440082
EST:     CTTGTCCTTCACTGTGCAGATTTTCTCACCCACTCCGCTGAAG                         GTAATACTTCACTGACGTGTTGTGGTTAAGTATCGGAAGCACGAAATGGTG
genomic: CTTGTCCTTCACTGTGCAGATTTTCTCACCCACTCCGCTGAAGgtgaagctcg ... ggctatgcagGTAATACTTCACTGACGTGTTGTGGTTAAGTATCGGAAGCACGAAATGGTG
EST: gi|162270768|gb|FC446381.1|FC446381
EST:     CTCACCCACTCCGCTGAAG                         GTAATACTTCACTGACGTGTTGTGGTTAAGTATCGGAAGCACGAAATGGTG
genomic: CTCACCCACTCCGCTGAAGgtgaagctcg ... ggctatgcagGTAATACTTCACTGACGTGTTGTGGTTAAGTATCGGAAGCACGAAATGGTG
EST: gi|100411270|gb|BY974553.1|BY974553
EST:     GCTTCTACTTGTCCTTCACTGTGCAGATTTTCTCACCCACTCCGCTGAAG                         GTAATACTTCACTGACGTGTTGTGGTTAAGTATCGGAAGCACGAAATGGTG
genomic: GCTTCTACTTGTCCTTCACTGTGCAGATTTTCTCACCCACTCCGCTGAAGgtgaagctcg ... ggctatgcagGTAATACTTCACTGACGTGTTGTGGTTAAGTATCGGAAGCACGAAATGGTG
EST: gi|162270220|gb|FC447232.1|FC447232
EST:     GCTTCTACTTGTCCTTCACTGTGCAGATTTTCTCACCCACTCCGCTGAAG                         GTAATACTTCACTGACGTGTTGTGGTTAAGTATCGGAAGCACGAAATGGTG
genomic: GCTTCTACTTGTCCTTCACTGTGCAGATTTTCTCACCCACTCCGCTGAAGgtgaagctcg ... ggctatgcagGTAATACTTCACTGACGTGTTGTGGTTAAGTATCGGAAGCACGAAATGGTG
EST: gi|162273757|gb|FC449480.1|FC449480
EST:     CTCACCCACTCCGCTGAAG                         GTAATACTTCACTGACGTGTTGTGGTTAAGTATCGGAAGCACGAAATGGTG
genomic: CTCACCCACTCCGCTGAAGgtgaagctcg ... ggctatgcagGTAATACTTCACTGACGTGTTGTGGTTAAGTATCGGAAGCACGAAATGGTG
EST: gi|18325347|gb|BJ157343.1|BJ157343
EST:     GCTTCTACTTGTCCTTCACTGTGCAGATTTTCTCACCCACTCCGCTGAAG                         GTAATACTTCACTGACGTGTTGTGGTTAAGTATCGGAAGCACGAAATGGTG
genomic: GCTTCTACTTGTCCTTCACTGTGCAGATTTTCTCACCCACTCCGCTGAAGgtgaagctcg ... ggctatgcagGTAATACTTCACTGACGTGTTGTGGTTAAGTATCGGAAGCACGAAATGGTG
EST: gi|67568787|gb|BJ941611.1|BJ941611
EST:     GCAGATTTTCTCACCCACTCCGCTGAAG                         GTAATACTTCACTGACGTGTTGTGGTTAAGTATCGGAAGCACGAAATGGTG
genomic: GCAGATTTTCTCACCCACTCCGCTGAAGgtgaagctcg ... ggctatgcagGTAATACTTCACTGACGTGTTGTGGTTAAGTATCGGAAGCACGAAATGGTG
EST: gi|162265463|gb|FC440789.1|FC440789
EST:     CTCACCCACTCCGCTGAAG                         GTAATACTTCACTGACGTGTTGTGGTTAAGTATCGGAAGCACGAAATGGTG
genomic: CTCACCCACTCCGCTGAAGgtgaagctcg ... ggctatgcagGTAATACTTCACTGACGTGTTGTGGTTAAGTATCGGAAGCACGAAATGGTG
EST: gi|100362718|gb|BY947493.1|BY947493
EST:     GCTTCTACTTGTCCTTCACTGTGCAGATTTTCTCACCCACTCCGCTGAAG                         GTAATACTTCACTGACGTGTTGTGGTTAAGTATCGGAAGCACGAAATGGTG
genomic: GCTTCTACTTGTCCTTCACTGTGCAGATTTTCTCACCCACTCCGCTGAAGgtgaagctcg ... ggctatgcagGTAATACTTCACTGACGTGTTGTGGTTAAGTATCGGAAGCACGAAATGGTG
EST: gi|162272168|gb|FC448677.1|FC448677
EST:     CTCACCCACTCCGCTGAAG                         GTAATACTTCACTGACGTGTTGTGGTTAAGTATCGGAAGCACGAAATGGTG
genomic: CTCACCCACTCCGCTGAAGgtgaagctcg ... ggctatgcagGTAATACTTCACTGACGTGTTGTGGTTAAGTATCGGAAGCACGAAATGGTG
EST: gi|162265762|gb|FC443168.1|FC443168
EST:     CTTGTCCTTCACTGTGCAGATTTTCTCACCCACTCCGCTGAAG                         GTAATACTTCACTGACGTGTTGTGGTTAAGTATCGGAAGCACGAAATGGTG
genomic: CTTGTCCTTCACTGTGCAGATTTTCTCACCCACTCCGCTGAAGgtgaagctcg ... ggctatgcagGTAATACTTCACTGACGTGTTGTGGTTAAGTATCGGAAGCACGAAATGGTG
EST: gi|162273702|gb|FC449425.1|FC449425
EST:     CTTGTCCTTCACTGTGCAGATTTTCTCACCCACTCCGCTGAAG                         GTAATACTTCACTGACGTGTTGTGGTTAAGTATCGGAAGCACGAAATGGTG
genomic: CTTGTCCTTCACTGTGCAGATTTTCTCACCCACTCCGCTGAAGgtgaagctcg ... ggctatgcagGTAATACTTCACTGACGTGTTGTGGTTAAGTATCGGAAGCACGAAATGGTG
EST: gi|208397629|gb|DC912247.1|DC912247
EST:     GCTTCTACTTGTCCTTCACTGTGCAGATTTTCTCACCCACTCCGCTGAAG                         GTAATACTTCACTGACGTGTTGTGGTTAAGTATCGGAAGCACGAAATGGTG
genomic: GCTTCTACTTGTCCTTCACTGTGCAGATTTTCTCACCCACTCCGCTGAAGgtgaagctcg ... ggctatgcagGTAATACTTCACTGACGTGTTGTGGTTAAGTATCGGAAGCACGAAATGGTG

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: 28 (upstream exon), 35 (downstream exon)
Score: 36

GTGTATGTGTGTGTATATATACGCCCAGTCTGTCTAGATCTTATCTTCGTGCTTCTACTTGTCCTTCACTGTGCAGATTTTCTCACCCACTCCGCTGAAGgtgaagctcg ... ggctatgcagGTAATACTTCACTGACGTGTTGTGGTTAAGTATCGGAAGCACGAAATGGTGCGATCAAGGTTGTCAGCGTCTGTTGAGGATCCTTCCCTTAACGTCATTG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttttccttcatgacttccgaggcctcacttgcccgcatgggtgtggctatgcagGTAATACTTCACTGACGTGTTGTGGTTAAGTATCGGAAGCACGAAATGGTGCGATCAAGGTTGTCAGCGTCTGTTGAGGATCCTTCCCTTAACGTCATTG
                      gcctcac  putative branch site (score: 36)
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cggctaaatgcaattacgatgctgttaagttcagcagacgcgctctttttccttcatgacttccgaggcctcacttgcccgcatgggtgtggctatgcagGTAATACTTCACTGACGTGTTGTGGTTAAGTATCGGAAGCACGAAATGGTGCGATCAAGGTTGTCAGCGTCTGTTGAGGATCCTTCCCTTAACGTCATTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAT