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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGTTTGTGGATCGAATCAAGTTCACTGTTTTACCTTGAACCCAATTCTTAGAATCCCCCTTTCGTTACTTGTTCACgtaagcatcagcaatcattcctgagttcccctgatcgagcgttgcctttgggttgcgtagggttcaggtttattgcttggaattgagtgagtttggttgg...

Basic information

species Physcomitrella patens
transcript PP1S9_37V6.5
intron # 1
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|67570162|gb|BJ942986.1|BJ942986
EST:     GTTTTACCTTGAACCCAATTCTTAGAATCCCCCTTTCGTTACTTGTTCAC                         ATCATTGGATTAAGAGGAAGGCTTGAAGATGTTGCGCAGTATATCAAAGGT
genomic: GTTTTACCTTGAACCCAATTCTTAGAATCCCCCTTTCGTTACTTGTTCACgtaagcatca ... ttggtcgcagATCATTGGATTAAGAGGAAGGCTTGAAGATGTTGCGCAGTATATCAAAGGT
EST: gi|162196408|gb|FC373554.1|FC373554
EST:     CTTGAACCCAATTCTTAGAATCCCCCTTTCGTTACTTGTTCAC                         ATCATTGGATTAAGAGGAAGGCTTGAAGATGTTGCGCAGTATATCAAAGGT
genomic: CTTGAACCCAATTCTTAGAATCCCCCTTTCGTTACTTGTTCACgtaagcatca ... ttggtcgcagATCATTGGATTAAGAGGAAGGCTTGAAGATGTTGCGCAGTATATCAAAGGT
EST: gi|100452754|gb|CJ975427.1|CJ975427
EST:     CTTTTACCTTGAACCCAATTCTTAGAATCCCCCTTTCGTTACTTGTTCAC                         ATCATTGGATTAAGAGGAAGGCTTGAAGATGTTGCGCAGTATATCAAAGGT
genomic: -TTTTACCTTGAACCCAATTCTTAGAATCCCCCTTTCGTTACTTGTTCACgtaagcatca ... ttggtcgcagATCATTGGATTAAGAGGAAGGCTTGAAGATGTTGCGCAGTATATCAAAGGT
EST: gi|208356450|gb|DC914312.1|DC914312
EST:     AATTCTTAGAATCCCCCTTTCGTTACTTGTTCAC                         ATCATTGGATTAAGAGGAAGGCTTGAAGATGTTGCGCAGTATATCAAAGGT
genomic: AATTCTTAGAATCCCCCTTTCGTTACTTGTTCACgtaagcatca ... ttggtcgcagATCATTGGATTAAGAGGAAGGCTTGAAGATGTTGCGCAGTATATCAAAGGT
EST: gi|208398405|gb|DC912334.1|DC912334
EST:     GTTTTACCTTGAACCCAATTCTTAGAATCCCCCTTTCGTTACTTGTTCAC                         ATCATTGGATTAAGAGGAAGGCTTGAAGATGTTGCGCAGTATATCAAAGGT
genomic: GTTTTACCTTGAACCCAATTCTTAGAATCCCCCTTTCGTTACTTGTTCACgtaagcatca ... ttggtcgcagATCATTGGATTAAGAGGAAGGCTTGAAGATGTTGCGCAGTATATCAAAGGT
EST: gi|100404598|gb|BY973658.1|BY973658
EST:     CTTAGAATCCCCCTTTCGTTACTTGTTCAC                         ATCATTGGATTAAGAGGAAGGCTTGAAGATGTTGCGCAGTATATCAAAGGT
genomic: CTTAGAATCCCCCTTTCGTTACTTGTTCACgtaagcatca ... ttggtcgcagATCATTGGATTAAGAGGAAGGCTTGAAGATGTTGCGCAGTATATCAAAGGT

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: 9 (upstream exon), 27 (downstream exon)
Score: 1

TGTTTGTGGATCGAATCAAGTTCACTGTTTTACCTTGAACCCAATTCTTAGAATCCCCCTTTCGTTACTTGTTCACgtaagcatca ... ttggtcgcagATCATTGGATTAAGAGGAAGGCTTGAAGATGTTGCGCAGTATATCAAAGGTCGCAG




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