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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aggtagttcgtgtaggttgaatttgtttttttggaaatggacacaattaggaacaattgtcttcgtcttccttaagccacatgaattactgaaactgcagGTTGTAGATCATTACGACAACCCTCGCAATGTTGGATCTTTCGACAAGAACGATCCTAATGTTGGGACTGGCTTGGTTGGTGCCCCAGCATGTGGAGATG

Basic information

species Physcomitrella patens
transcript PP1S39_352V6.2
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|18330965|gb|BJ162971.1|BJ162971
EST:     GTGAGGAGTTATCATGAGAAG                         GTTGTAGATCATTACGACAACCCTCGCAATGTTGGATCTTTCGACAAGAAC
genomic: GTGAGGAGTTATCATGAGAAGgtgtgtattg ... gaaactgcagGTTGTAGATCATTACGACAACCCTCGCAATGTTGGATCTTTCGACAAGAAC
EST: gi|162269290|gb|FC445821.1|FC445821
EST:     ACGCTGCTCGGGGAGCTCTTGTGCCTGGAGTGAGGAGTTATCATGAGAAG                         GTTGTAGATCATTACGACAACCCTCGCAATGTTGGATCTTTCGACAAGAAC
genomic: ACGCTGCTCGGGGAGCTCTTGTGCCTGGAGTGAGGAGTTATCATGAGAAGgtgtgtattg ... gaaactgcagGTTGTAGATCATTACGACAACCCTCGCAATGTTGGATCTTTCGACAAGAAC
EST: gi|162272889|gb|FC448838.1|FC448838
EST:     ACGCTGCTCGGGGAGCTCTTGTGCCTGGAGTGAGGAGTTATCATGAGAAG                         GTTGTAGATCATTACGACAACCCTCGCAATGTTGGATCTTTCGACAAGAAC
genomic: ACGCTGCTCGGGGAGCTCTTGTGCCTGGAGTGAGGAGTTATCATGAGAAGgtgtgtattg ... gaaactgcagGTTGTAGATCATTACGACAACCCTCGCAATGTTGGATCTTTCGACAAGAAC
EST: gi|162240736|gb|FC417459.1|FC417459
EST:     ACGCTGCTCGGGGAGCTCTTGTGCCTGGAGTGAGGAGTTATCATGAGAAG                         GTTGTAGATCATTACGACAACCCTCGCAATGTTGGATCTTTCGACAAGAAC
genomic: ACGCTGCTCGGGGAGCTCTTGTGCCTGGAGTGAGGAGTTATCATGAGAAGgtgtgtattg ... gaaactgcagGTTGTAGATCATTACGACAACCCTCGCAATGTTGGATCTTTCGACAAGAAC
EST: gi|100445500|gb|CJ975649.1|CJ975649
EST:     ACGCTGCTCGGGGAGCTCTTGTGCCTGGAGTGAGGAGTTATCATGAGAAG                         GTTGTAGATCATTACGACAACCCTCGCAATGTTGGATCTTTCGACAAGAAC
genomic: ACGCTGCTCGGGGAGCTCTTGTGCCTGGAGTGAGGAGTTATCATGAGAAGgtgtgtattg ... gaaactgcagGTTGTAGATCATTACGACAACCCTCGCAATGTTGGATCTTTCGACAAGAAC
EST: gi|162232570|gb|FC408913.1|FC408913
EST:     ACGCTGCTCGGGGAGCTCTTGTGCCTGGAGTGAGGAGTTATCATGAGAAG                         GTTGTAGATCATTACGACAACCCTCGCAATGTTGGATCTTTCGACAAGAAC
genomic: ACGCTGCTCGGGGAGCTCTTGTGCCTGGAGTGAGGAGTTATCATGAGAAGgtgtgtattg ... gaaactgcagGTTGTAGATCATTACGACAACCCTCGCAATGTTGGATCTTTCGACAAGAAC
EST: gi|18358237|gb|BJ190296.1|BJ190296
EST:     ACGCTGCTCGGGGAGCTCTTGTGCCTGGAGTGAGGAGTTATCATGAGAAG                         GTTGTAGATCATTACGACAACCCTCGCAATGTTGGATCTTTCGACAAGAAC
genomic: ACGCTGCTCGGGGAGCTCTTGTGCCTGGAGTGAGGAGTTATCATGAGAAGgtgtgtattg ... gaaactgcagGTTGTAGATCATTACGACAACCCTCGCAATGTTGGATCTTTCGACAAGAAC
EST: gi|67573048|gb|BJ945872.1|BJ945872
EST:     ACGCTGCTCGGGGAGCTCTTGTGCCTGGAGTGAGGAGTTATCATGAGAAG                         GTTGTAGATCATTACGACAACCCTCGCAATGTTGGATCTTTCGACAAGAAC
genomic: ACGCTGCTCGGGGAGCTCTTGTGCCTGGAGTGAGGAGTTATCATGAGAAGgtgtgtattg ... gaaactgcagGTTGTAGATCATTACGACAACCCTCGCAATGTTGGATCTTTCGACAAGAAC
EST: gi|100446443|gb|CJ970742.1|CJ970742
EST:     ACGCTGCTCGGGGAGCTCTTGTGCCTGGAGTGAGGAGTTATCATGAGAAG                         GTTGTAGATCATTACGACAACCCTCGCAATGTTGGATCTTTCGACAAGAAC
genomic: ACGCTGCTCGGGGAGCTCTTGTGCCTGGAGTGAGGAGTTATCATGAGAAGgtgtgtattg ... gaaactgcagGTTGTAGATCATTACGACAACCCTCGCAATGTTGGATCTTTCGACAAGAAC

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: 35 (upstream exon), 35 (downstream exon)
Score: 58

TCATTTCGCCAAGGGAATTGCCAGGGCGGCGGGTTCCGCCGGTGCCCCGCACGCTGCTCGGGGAGCTCTTGTGCCTGGAGTGAGGAGTTATCATGAGAAGgtgtgtattg ... gaaactgcagGTTGTAGATCATTACGACAACCCTCGCAATGTTGGATCTTTCGACAAGAACGATCCTAATGTTGGGACTGGCTTGGTTGGTGCCCCAGCATGTGGAGATG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attaggaacaattgtcttcgtcttccttaagccacatgaattactgaaactgcagGTTGTAGATCATTACGACAACCCTCGCAATGTTGGATCTTTCGACAAGAACGATCCTAATGTTGGGACTGGCTTGGTTGGTGCCCCAGCATGTGGAGATG
                                   atgaatta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aggtagttcgtgtaggttgaatttgtttttttggaaatggacacaattaggaacaattgtcttcgtcttccttaagccacatgaattactgaaactgcagGTTGTAGATCATTACGACAACCCTCGCAATGTTGGATCTTTCGACAAGAACGATCCTAATGTTGGGACTGGCTTGGTTGGTGCCCCAGCATGTGGAGATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cacatga