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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaggattcttccctagattttctgctgtaaagcatttgatgtaattttcaacttttaatattacacacgttggtagtagctgactcttgcttcgcttggtgttcagGGAGCGAAAAATGTTCATGACTTAACACCTCCAAGTGCATCTGATATTTCTACTATCATGTATACCAGTGGCACAACTGGTGAGCCCAAGGGAGTGATCC

Basic information

species Physcomitrella patens
transcript PP1S218_19V6.1
intron # 9
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|162164429|gb|FC341048.1|FC341048
EST:     CTTCAGCTCAGGGTGCAGCACTTTACTCCTGGGATGAATTTGTGGATCTG                         GGAGCGAAAAATGTTCATGACTTAACACCTCCAAGTGCATCTGATATTTCT
genomic: CTTCAGCTCAGGGTGCAGCACTTTACTCCTGGGATGAATTTGTGGATCTGgtaggattct ... tggtgttcagGGAGCGAAAAATGTTCATGACTTAACACCTCCAAGTGCATCTGATATTTCT
EST: gi|162167702|gb|FC344016.1|FC344016
EST:     CTTCAGCTCAGGGTGCAGCACTTTACTCCTGGGATGAATTTGTGGATCTG                         GGAGCGAAAAATGTTCATGACTTAACACCTCCAAGTGCATCTGATATTTCT
genomic: CTTCAGCTCAGGGTGCAGCACTTTACTCCTGGGATGAATTTGTGGATCTGgtaggattct ... tggtgttcagGGAGCGAAAAATGTTCATGACTTAACACCTCCAAGTGCATCTGATATTTCT
EST: gi|162171311|gb|FC347236.1|FC347236
EST:     CTTCAGCTCAGGGTGCAGCACTTTACTCCTGGGATGAATTTGTGGATCTG                         GGAGCGAAAAATGTTCATGACTTAACACCTCCAAGTGCATCTGATATTTCT
genomic: CTTCAGCTCAGGGTGCAGCACTTTACTCCTGGGATGAATTTGTGGATCTGgtaggattct ... tggtgttcagGGAGCGAAAAATGTTCATGACTTAACACCTCCAAGTGCATCTGATATTTCT
EST: gi|162235485|gb|FC411308.1|FC411308
EST:     CTTCAGCTCAGGGTGCAGCACTTTACTCCTGGGATGAATTTGTGGATCTG                         GGAGCGAAAAATGTTCATGACTTAACACCTCCAAGTGCATCTGATATTTCT
genomic: CTTCAGCTCAGGGTGCAGCACTTTACTCCTGGGATGAATTTGTGGATCTGgtaggattct ... tggtgttcagGGAGCGAAAAATGTTCATGACTTAACACCTCCAAGTGCATCTGATATTTCT
EST: gi|162199213|gb|FC375049.1|FC375049
EST:     CTTCAGCTCAGGGTGCAGCACTTTACTCCTGGGATGAATTTGTGGATCTG                         GGAGCGAAAAATGTTCATGACTTAACACCTCCAAGTGCATCTGATATTTCT
genomic: CTTCAGCTCAGGGTGCAGCACTTTACTCCTGGGATGAATTTGTGGATCTGgtaggattct ... tggtgttcagGGAGCGAAAAATGTTCATGACTTAACACCTCCAAGTGCATCTGATATTTCT
EST: gi|162167280|gb|FC342845.1|FC342845
EST:     CTTCAGCTCAGGGTGCAGCACTTTACTCCTGGGATGAATTTGTGGATCTG                         GGAGCGAAAAATGTTCATGACTTAACACCTCCAAGTGCATCTGATATTTCT
genomic: CTTCAGCTCAGGGTGCAGCACTTTACTCCTGGGATGAATTTGTGGATCTGgtaggattct ... tggtgttcagGGAGCGAAAAATGTTCATGACTTAACACCTCCAAGTGCATCTGATATTTCT

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), 32 (downstream exon)
Score: 3

CCCTAGTGAGCTTTTCAACTTACACAGATGCACAGAAGACAGCAGCTTCAGCTCAGGGTGCAGCACTTTACTCCTGGGATGAATTTGTGGATCTGgtaggattct ... tggtgttcagGGAGCGAAAAATGTTCATGACTTAACACCTCCAAGTGCATCTGATATTTCTACTATCATGTATACCAGTGGCACAACTGGTGAGCCCAAGGGAGTGATCC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttttaatattacacacgttggtagtagctgactcttgcttcgcttggtgttcagGGAGCGAAAAATGTTCATGACTTAACACCTCCAAGTGCATCTGATATTTCTACTATCATGTATACCAGTGGCACAACTGGTGAGCCCAAGGGAGTGATCC
                          agctgac  putative branch site (score: 3)
                                ctcttgcttcgctt  CT-rich tract
     aatattaca  TA-rich tract