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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cttggagggacctgtagtgcagtttgcctggctttgatgtgactgaggcttttgtcaaacaatgaatgtgaatttgatcatcatttccttcactgcgcagAGAGAAAATGCCTTCTGTGTATATGGAGCAGGAGCCAATCTTGGCTGAAAATCCGGGTCGATTCTGCATGTTTCCCATTAAATACCCACAAGTATGGGAG

Basic information

species Physcomitrella patens
transcript PP1S215_91V6.1
intron # 3
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|18347727|gb|BJ179774.1|BJ179774
EST:     ATTCCTGGTTCTGCCACAAGCGAGTTATCCGAGCAGCTTCAAGGCACTAG                         AGAGAAAATGCCTTCTGTGTATATGGAGCAGGAGCCAATCTTGGCTGAAAA
genomic: ATTCCTGGTTCTGCCACAAGCGAGTTATCCGAGCAGCTTCAAGGCACTAGgtgccgccaa ... cactgcgcagAGAGAAAATGCCTTCTGTGTATATGGAGCAGGAGCCAATCTTGGCTGAAAA
EST: gi|208358338|gb|DC943197.1|DC943197
EST:     ATTCCTGGTTCTGCCACAAGCGAGTTATCCGAGCAGCTTCAAGGCACTAG                         AGAGAAAATGCCTTCTGTGTATATGGAGCAGGAGCCAATCTTGGCTGAAAA
genomic: ATTCCTGGTTCTGCCACAAGCGAGTTATCCGAGCAGCTTCAAGGCACTAGgtgccgccaa ... cactgcgcagAGAGAAAATGCCTTCTGTGTATATGGAGCAGGAGCCAATCTTGGCTGAAAA
EST: gi|100427993|gb|BY959229.1|BY959229
EST:     ATTCCTGGTTCTGCCACAAGCGAGTTATCCGAGCAGCTTCAAGGCACTAG                         AGAGAAAATGCCTTCTGTGTATATGGAGCAGGAGCCAATCTTGGCTGANAA
genomic: ATTCCTGGTTCTGCCACAAGCGAGTTATCCGAGCAGCTTCAAGGCACTAGgtgccgccaa ... cactgcgcagAGAGAAAATGCCTTCTGTGTATATGGAGCAGGAGCCAATCTTGGCTGAAAA
EST: gi|100395351|gb|BY953694.1|BY953694
EST:     ATTCCTGGTTCTGCCACAAGCGAGTTATCCGAGCAGCTTCAAGGCACTAG                         AGAGAAAATGCCTTCTGTGTATGTGGAGCAGGAGCCAATCTTGGCTGAAAA
genomic: ATTCCTGGTTCTGCCACAAGCGAGTTATCCGAGCAGCTTCAAGGCACTAGgtgccgccaa ... cactgcgcagAGAGAAAATGCCTTCTGTGTATATGGAGCAGGAGCCAATCTTGGCTGAAAA
EST: gi|18369564|gb|BJ201652.1|BJ201652
EST:     ATTCCTGGTTCTGCCACAAGCGAGTTATCCGAGCAGCTTCAAGGCACTAG                         AGAGAAAATGCCTTCTGTGTATATGGAGCAGGAGCCAATCTTGGCTGAAAA
genomic: ATTCCTGGTTCTGCCACAAGCGAGTTATCCGAGCAGCTTCAAGGCACTAGgtgccgccaa ... cactgcgcagAGAGAAAATGCCTTCTGTGTATATGGAGCAGGAGCCAATCTTGGCTGAAAA
EST: gi|18372330|gb|BJ203932.1|BJ203932
EST:     ATTCCTGGTTCTGCCACAAGCGAGTTATCCGAGCAGCTTCAAGGCACTAG                         AGAGAAAATGCCTTCTGTGTATATGGAGCAGGAGCCAATCTTGGCTGAAAA
genomic: ATTCCTGGTTCTGCCACAAGCGAGTTATCCGAGCAGCTTCAAGGCACTAGgtgccgccaa ... cactgcgcagAGAGAAAATGCCTTCTGTGTATATGGAGCAGGAGCCAATCTTGGCTGAAAA
EST: gi|162262142|gb|FC437911.1|FC437911
EST:     ATTCCTGGTTCTGCCACAAGCGAGTTATCCGAGCAGCTTCAAGGCACTAG                         AGAGAAAATGCCTTCTGTGTATATGGAGCAGGAGCCAATCTTGGCTGAAAA
genomic: ATTCCTGGTTCTGCCACAAGCGAGTTATCCGAGCAGCTTCAAGGCACTAGgtgccgccaa ... cactgcgcagAGAGAAAATGCCTTCTGTGTATATGGAGCAGGAGCCAATCTTGGCTGAAAA

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: 18 (upstream exon), 18 (downstream exon)
Score: 1

GTATTTTGTCATGGCTCCATGCATTCCTGGTTCTGCCACAAGCGAGTTATCCGAGCAGCTTCAAGGCACTAGgtgccgccaa ... cactgcgcagAGAGAAAATGCCTTCTGTGTATATGGAGCAGGAGCCAATCTTGGCTGAAAATCCGGGTCGATTCTGCATGTTTCCCATTAAATACCCACAAGTATGGGAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aggcttttgtcaaacaatgaatgtgaatttgatcatcatttccttcactgcgcagAGAGAAAATGCCTTCTGTGTATATGGAGCAGGAGCCAATCTTGGCTGAAAATCCGGGTCGATTCTGCATGTTTCCCATTAAATACCCACAAGTATGGGAG
                          atttgat  putative branch site (score: 1)
                                tcatcatttccttc  CT-rich tract
                         aatttgat  TA-rich tract