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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttgtccttatttcatcaccatcatcatatgaagaattcaattctatttcgctatagttgccgcaatacatgtgcctaacaatttcgtttgtcagttcagACTGAAAGTGAATTCGCAAAGGCTTACGAAGGCGGATTGCACAAGAGCAA

Basic information

species Physcomitrella patens
transcript PP1S37_33V6.2
intron # 8
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|162194038|gb|FC370213.1|FC370213
EST:     AGACTGCACATCCCATGACCCAGTTAACGACAGGCATCATGGCCCTTCAG                         ACTGAAAGTGAATTCGCAAAGGCTTACGAAGGCGGATTGCACAAGAGCAA
genomic: AGACTGCACATCCCATGACCCAGTTAACGACAGGCATCATGGCCCTTCAGgtgtatttta ... gtcagttcagACTGAAAGTGAATTCGCAAAGGCTTACGAAGGCGGATTGCACAAGAGCAA
EST: gi|162202113|gb|FC378034.1|FC378034
EST:     AGACTGCACATCCCATGACCCAGTTAACGACAGGCATCATGGCCCTTCAG                         ACTGAAAGTGAATTCGCANAGGCTTACGAAGGCGGATTGCACAAGAGCAA
genomic: AGACTGCACATCCCATGACCCAGTTAACGACAGGCATCATGGCCCTTCAGgtgtatttta ... gtcagttcagACTGAAAGTGAATTCGCAAAGGCTTACGAAGGCGGATTGCACAAGAGCAA
EST: gi|162165709|gb|FC340890.1|FC340890
EST:     AGACTGCACATCCCATGACCCAGTTAACGACAGGCATCATGGCCCTTCAG                         ACTGAAAGTGAATTCGCAAAGGCTTACGAAGGCGGATTGCACAAGAGCAA
genomic: AGACTGCACATCCCATGACCCAGTTAACGACAGGCATCATGGCCCTTCAGgtgtatttta ... gtcagttcagACTGAAAGTGAATTCGCAAAGGCTTACGAAGGCGGATTGCACAAGAGCAA
EST: gi|67574071|gb|BJ946895.1|BJ946895
EST:     AGACTGCACATCCCATGACCCAGTTAACGACAGGCATCATGGCCCTTCAG                         ACTGAAAGTGAATTCGCAAAGGCTTACGAAGGCGGATTGCACAAGAGCAA
genomic: AGACTGCACATCCCATGACCCAGTTAACGACAGGCATCATGGCCCTTCAGgtgtatttta ... gtcagttcagACTGAAAGTGAATTCGCAAAGGCTTACGAAGGCGGATTGCACAAGAGCAA
EST: gi|208373915|gb|DC940426.1|DC940426
EST:     AGACTGCACATCCCATGACCCAGTTAACGACAGGCATCATGGCCCTTCAG                         ACTGAAAGTGAATTCGCAAAGGCTTACGAAGGCGGATTGCACAAGAGCAA
genomic: AGACTGCACATCCCATGACCCAGTTAACGACAGGCATCATGGCCCTTCAGgtgtatttta ... gtcagttcagACTGAAAGTGAATTCGCAAAGGCTTACGAAGGCGGATTGCACAAGAGCAA
EST: gi|208363044|gb|DC957985.1|DC957985
EST:     ATGACCCAGTTAACGACAGGCATCATGGCCCTTCAG                         ACTGAAAGTGAATTCGCAAAGGCTTACGAAGGCGGATTGCACAAGAGCAA
genomic: ATGACCCAGTTAACGACAGGCATCATGGCCCTTCAGgtgtatttta ... gtcagttcagACTGAAAGTGAATTCGCAAAGGCTTACGAAGGCGGATTGCACAAGAGCAA
EST: gi|208398177|gb|DC908406.1|DC908406
EST:     AGACTGCACATCCCATGACCCAGTTANCGACAGGCATCATGGCCCTTCAG                         ACTGAAAGTGAATNCGCAA
genomic: AGACTGCACATCCCATGACCCAGTTAACGACAGGCATCATGGCCCTTCAGgtgtatttta ... gtcagttcagACTGAAAGTGAATTCGCAA
EST: gi|100427449|gb|BY977503.1|BY977503
EST:     ACTGCACATCCCATGACCCAGGTAACGAACGGG-ATCATGGGCCTTTCAA                         ACTGAAAGGGAATTCGCAAAGGCTT
genomic: ACTGCACATCCCATGACCCAGTTAACGA-CAGGCATCATGGCCCTT-CAGgtgtatttta ... gtcagttcagACTGAAAGTGAATTCGCAAAGGCTT
EST: gi|162176173|gb|FC351915.1|FC351915
EST:     AGACTGCACATCCCATGACCCAGTTAACGACAGGCATCATGGCCCTTCAG                         ACTGAAAGTGAATTCGCAAAGGCTTACGAAGGCGGATTGCACAAGAGCAA
genomic: AGACTGCACATCCCATGACCCAGTTAACGACAGGCATCATGGCCCTTCAGgtgtatttta ... gtcagttcagACTGAAAGTGAATTCGCAAAGGCTTACGAAGGCGGATTGCACAAGAGCAA
EST: gi|162233299|gb|FC409849.1|FC409849
EST:     AGACTGCACATCCCATGACCCAGTTAACGACAGGCATCATGGCCCTTCAG                         ACTGAAAGTGAATTCGCAAAGGCTTACGAAGGCGGATTGCACAAGAGCAA
genomic: AGACTGCACATCCCATGACCCAGTTAACGACAGGCATCATGGCCCTTCAGgtgtatttta ... gtcagttcagACTGAAAGTGAATTCGCAAAGGCTTACGAAGGCGGATTGCACAAGAGCAA
EST: gi|208362586|gb|DC939510.1|DC939510
EST:     AGACTGCACATCCCATGACCCAGTTAACGACAGGCATCATGGCCCTTCAG                         ACTGAAAGTGAATTCGCAAAGGCTTACGAAGGCGGATTGCACAAGAGCA-
genomic: AGACTGCACATCCCATGACCCAGTTAACGACAGGCATCATGGCCCTTCAGgtgtatttta ... gtcagttcagACTGAAAGTGAATTCGCAAAGGCTTACGAAGGCGGATTGCACAAGAGCAA
EST: gi|162152562|gb|FC328840.1|FC328840
EST:     AGACTGCACATCCCATGACCCAGTTAACGACAGGCATCATGGCCCTTCAG                         ACTGAAAGTGAATTCGCAAAGGCTTACGAAGGCGGATTGCACAAG
genomic: AGACTGCACATCCCATGACCCAGTTAACGACAGGCATCATGGCCCTTCAGgtgtatttta ... gtcagttcagACTGAAAGTGAATTCGCAAAGGCTTACGAAGGCGGATTGCACAAG
EST: gi|100352729|gb|BY945419.1|BY945419
EST:     AGACTGCACATCCCATGACCCAGTTAACGACAGGCATCATGGCCCTTCAG                         ACTGAAAGTGAATTCGCAAAGGCTTACGAAGGCGGATTGCACAAGAGCAA
genomic: AGACTGCACATCCCATGACCCAGTTAACGACAGGCATCATGGCCCTTCAGgtgtatttta ... gtcagttcagACTGAAAGTGAATTCGCAAAGGCTTACGAAGGCGGATTGCACAAGAGCAA
EST: gi|162173170|gb|FC349237.1|FC349237
EST:     AGACTGCACATCCCATGACCCAGTTAACGACAGGCATCATGGCCCTTCAG                         ACTGAAAGTGAATTCGCAAAGGCTTACGAAGGCGGATTGCACAAGAGCAAG
genomic: AGACTGCACATCCCATGACCCAGTTAACGACAGGCATCATGGCCCTTCAGgtgtatttta ... gtcagttcagACTGAAAGTGAATTCGCAAAGGCTTACGAAGGCGGATTGCACAAGAGCAAG
EST: gi|19783472|gb|BQ040017.1|BQ040017
EST:     AGACTGCACATCCCATGACCCAGTTAACGACAGGCATCATGGCCCTTCAG                         ACTGAAAGTGAATTCGCAAAGGCTTACGAAGGCGGATTGCACAAGAGCAA
genomic: AGACTGCACATCCCATGACCCAGTTAACGACAGGCATCATGGCCCTTCAGgtgtatttta ... gtcagttcagACTGAAAGTGAATTCGCAAAGGCTTACGAAGGCGGATTGCACAAGAGCAA
EST: gi|162258522|gb|FC434737.1|FC434737
EST:     AGACTGCACATCCCATGACCCAGTTAACGACAGGCATCATGGCCCTTCAG                         ACTGAAAGTGAATTCGCAAAGGCTTACGAAGGCGGATTGCACAAGAGCAA
genomic: AGACTGCACATCCCATGACCCAGTTAACGACAGGCATCATGGCCCTTCAGgtgtatttta ... gtcagttcagACTGAAAGTGAATTCGCAAAGGCTTACGAAGGCGGATTGCACAAGAGCAA

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: 33 (upstream exon), 35 (downstream exon)
Score: 17

GTCACGTGTTTGATGTCATCAACGCACTCCCAAAGACTGCACATCCCATGACCCAGTTAACGACAGGCATCATGGCCCTTCAGgtgtatttta ... gtcagttcagACTGAAAGTGAATTCGCAAAGGCTTACGAAGGCGGATTGCACAAGAGCAA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atttcgctatagttgccgcaatacatgtgcctaacaatttcgtttgtcagttcagACTGAAAGTGAATTCGCAAAGGCTTACGAAGGCGGATTGCACAAGAGCAA
                            gcctaac  putative branch site (score: 17)
                               taacaattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttgtccttatttcatcaccatcatcatatgaagaattcaattctatttcgctatagttgccgcaatacatgtgcctaacaatttcgtttgtcagttcagACTGAAAGTGAATTCGCAAAGGCTTACGAAGGCGGATTGCACAAGAGCAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCA