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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatcatgagtcatacctcgtcgaatctttttcctgcaccttgtaaatttcttactagcttgcgtggattccaattcggagaactcgttcaattttccacatgcagATGCTTCATGTGCCGCACGTCAACGTCCTGGGGCCGATCACCGACGCATTGCAATCCCACTTAGGAGTGACCCCATCAGGCATCCCACGAGGTGCCCCGG

Basic information

species Physcomitrella patens
transcript PP1S123_99V6.1
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|208356171|gb|DC918411.1|DC918411
EST:     ATACGCTCGCCGACCCACAAATGGCAGAGGCTGCTCAGAGAGCTTGCGAG                         ATGCTTCATGTGCCGCACGTCAACGTCCTGGGGCCGATCACCGACGCATTG
genomic: ATACGCTCGCCGACCCACAAATGGCAGAGGCTGCTCAGAAAGCTTGCGAGgtatcatgag ... ccacatgcagATGCTTCATGTGCCGCACGTCAACGTCCTGGGGCCGATCACCGACGCATTG
EST: gi|100389507|gb|BY988985.1|BY988985
EST:     TACGCTCGCCGAAACCACAA-TGGCAGAAGCTGCTCAGAAAGCTTGCGAG                         ATGCTTCATGTGCCGCA
genomic: TACGCTCGCCGAC-CCACAAATGGCAGAGGCTGCTCAGAAAGCTTGCGAGgtatcatgag ... ccacatgcagATGCTTCATGTGCCGCA
EST: gi|208399111|gb|DC904520.1|DC904520
EST:     ATACGCTCGCCGACCCACAAATGGCAGAGGCTGCTCAGAGAGCTTGCGAG                         ATGCTTCATGTGCCGCACGTCAACGTCCTGGGGCCGATCACCGACGCATTG
genomic: ATACGCTCGCCGACCCACAAATGGCAGAGGCTGCTCAGAAAGCTTGCGAGgtatcatgag ... ccacatgcagATGCTTCATGTGCCGCACGTCAACGTCCTGGGGCCGATCACCGACGCATTG
EST: gi|208361876|gb|DC953926.1|DC953926
EST:     ATACGCTCGCCGACCCACAAATGGCAGAGGCTGCTCAGAAAGCTTGCGAG                         ATGCTTCATGTGCCGCACGTCAACGTCCTGGGGCCGATCACCGACGCATTG
genomic: ATACGCTCGCCGACCCACAAATGGCAGAGGCTGCTCAGAAAGCTTGCGAGgtatcatgag ... ccacatgcagATGCTTCATGTGCCGCACGTCAACGTCCTGGGGCCGATCACCGACGCATTG
EST: gi|208368590|gb|DC936029.1|DC936029
EST:     ATACGCTCGCCGACCCACAAATGGCAGAGGCTGCTCAGAAAGCTTGCGAG                         ATGCTTCATGTGCCGCACGTCAACGTCCTGGGGCCGATCACCGACGCATTG
genomic: ATACGCTCGCCGACCCACAAATGGCAGAGGCTGCTCAGAAAGCTTGCGAGgtatcatgag ... ccacatgcagATGCTTCATGTGCCGCACGTCAACGTCCTGGGGCCGATCACCGACGCATTG

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: 16

GCTGATGGAGATTATCCGGCAAGGAGCGCAGGAGGAGGCATTGGTTCTCTATACGCTCGCCGACCCACAAATGGCAGAGGCTGCTCAGAAAGCTTGCGAGgtatcatgag ... ccacatgcagATGCTTCATGTGCCGCACGTCAACGTCCTGGGGCCGATCACCGACGCATTGCAATCCCACTTAGGAGTGACCCCATCAGGCATCCCACGAGGTGCCCCGG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttactagcttgcgtggattccaattcggagaactcgttcaattttccacatgcagATGCTTCATGTGCCGCACGTCAACGTCCTGGGGCCGATCACCGACGCATTGCAATCCCACTTAGGAGTGACCCCATCAGGCATCCCACGAGGTGCCCCGG
 ttcttac  putative branch site (score: 16)
 ttttccac  putative PPT
 ttcaatttt  TA-rich tract