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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgcacacatggttgctttcaccaacttttctctgatatattcgcttctttgatttaaagcttttgggaaaagaggattcctaaaaaaattatgaaggaaggcaagccctaattttatttttcttcaatgtgcttttgttagGTGGGAGCGGCAAATTTCGATAGGCAGTCAGTTGCTGACCACGCCAACAACCTGGCCACTAAAATTCGAGGAAATCTCACCAACTCTATGAAGGCACTTG

Basic information

species Physcomitrella patens
transcript PP1S35_94V6.1
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|162167619|gb|FC343751.1|FC343751
EST:     GGATGCGCGAACTCCGAGATGAGCACCATCTCAAGGCCCTCGGAATCCAG                         GTGGGAGCGGCAAATTTCGATAGGCAGTCAGTTGCTGACCACGCCAACAAC
genomic: GGATGCGCGAACTCCGAGATGAGCACCATCTCAAGGCCCTCGGAATCCAGgtttgcacac ... cttttgttagGTGGGAGCGGCAAATTTCGATAGGCAGTCAGTTGCTGACCACGCCAACAAC
EST: gi|162166909|gb|FC343294.1|FC343294
EST:     GGATGCGCGAACTCCGAGATGAGCACCATCTCAAGGCCCTCGGAATCCAG                         GTGGGAGCGGCAAATTTCGATAGGCAGTCAGTTGCTGACCACGCCAACAAC
genomic: GGATGCGCGAACTCCGAGATGAGCACCATCTCAAGGCCCTCGGAATCCAGgtttgcacac ... cttttgttagGTGGGAGCGGCAAATTTCGATAGGCAGTCAGTTGCTGACCACGCCAACAAC
EST: gi|100420741|gb|BY993485.1|BY993485
EST:     GGATGCGCGAACTCCGAGATGAGCACCATCTCAAGGCCCTCGGAATCCAG                         GTGGGAGCGGCAAATTTCGATAGGCAGTCAGTTGCTGACCACGCCAACAAC
genomic: GGATGCGCGAACTCCGAGATGAGCACCATCTCAAGGCCCTCGGAATCCAGgtttgcacac ... cttttgttagGTGGGAGCGGCAAATTTCGATAGGCAGTCAGTTGCTGACCACGCCAACAAC
EST: gi|162154175|gb|FC330618.1|FC330618
EST:     GGATGCGCGAACTCCGAGATGAGCACCATCTCAAGGCCCTCGGAATCCAG                         GTGGGAGCGGCAAATTTCGATAGGCAGTCAGTTGCTGACCACGCCAACAAC
genomic: GGATGCGCGAACTCCGAGATGAGCACCATCTCAAGGCCCTCGGAATCCAGgtttgcacac ... cttttgttagGTGGGAGCGGCAAATTTCGATAGGCAGTCAGTTGCTGACCACGCCAACAAC
EST: gi|162170369|gb|FC346774.1|FC346774
EST:     GGATGCGCGAACTCCGAGATGAGCACCATCTCAAGGCCCTCGGAATCCAG                         GTGGGAGCGGCAAATTTCGATAGGCAGTCAGTTGCTGACCACGCCAACAAC
genomic: GGATGCGCGAACTCCGAGATGAGCACCATCTCAAGGCCCTCGGAATCCAGgtttgcacac ... cttttgttagGTGGGAGCGGCAAATTTCGATAGGCAGTCAGTTGCTGACCACGCCAACAAC
EST: gi|162189578|gb|FC365800.1|FC365800
EST:     GGATGCGCGAACTCCGAGATGAGCACCATCTCAAGGCCCTCGGAATCCAG                         GTGGGAGCGGCAAATTTCGATAGGCAGTCAGTTGCTGACCACGCCAACAAC
genomic: GGATGCGCGAACTCCGAGATGAGCACCATCTCAAGGCCCTCGGAATCCAGgtttgcacac ... cttttgttagGTGGGAGCGGCAAATTTCGATAGGCAGTCAGTTGCTGACCACGCCAACAAC

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: 23 (upstream exon), 35 (downstream exon)
Score: 8

CGTGAACCGAGGGTGTGTACCTTCGAAAGCTCTCTTGGCTGTGAGTGGACGGATGCGCGAACTCCGAGATGAGCACCATCTCAAGGCCCTCGGAATCCAGgtttgcacac ... cttttgttagGTGGGAGCGGCAAATTTCGATAGGCAGTCAGTTGCTGACCACGCCAACAACCTGGCCACTAAAATTCGAGGAAATCTCACCAACTCTATGAAGGCACTTG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aattatgaaggaaggcaagccctaattttatttttcttcaatgtgcttttgttagGTGGGAGCGGCAAATTTCGATAGGCAGTCAGTTGCTGACCACGCCAACAACCTGGCCACTAAAATTCGAGGAAATCTCACCAACTCTATGAAGGCACTTG
                   ccctaat  putative branch site (score: 8)
                                             cttttgtt  putative PPT
                      taattttatttttctt  TA-rich tract