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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcactatctaaacccttctctttcttaatgagcatgtctaccactagaattaattgaaatggactatcaggttatgaatcatcacttgtgcacattgaaaatctccagaccttgagagtttttatgtgaatattgagtttaaccatccattgtgtaacgtagGGGTGTGGATTCATATGTGAATCGTTCATTTCATACTTTGAGATGTGTTTGAATGGATTGCACACGGGAAATGTAATCCTCCGACTTGTCGAAGCAGTTG

Basic information

species Physcomitrella patens
transcript PP1S6_194V6.1
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|162264350|gb|FC440516.1|FC440516
EST:     CTGCGATCGTTGGCTCGTTAGTAGGGTCCTTACTTTGCTTCGTCAAG                         GGGTGTGGATTCATATGTGAATCGTTCATTTCATACTTTGAGATGTGTTTG
genomic: CTGCGATCGTTGGCTCGTTAGTAGGGTCCTTACTTTGCTTCGTCAAGgtcactatct ... tgtaacgtagGGGTGTGGATTCATATGTGAATCGTTCATTTCATACTTTGAGATGTGTTTG
EST: gi|162192965|gb|FC371948.1|FC371948
EST:     TGACTGCGATCGTTGGCTCGTTAGTAGGGTCCTTACTTTGCTTCGTCAAG                         GGGTGTGGATTCATATGTGAATCGTTCATTTCATACTTTGAGATGTGTTTG
genomic: TGACTGCGATCGTTGGCTCGTTAGTAGGGTCCTTACTTTGCTTCGTCAAGgtcactatct ... tgtaacgtagGGGTGTGGATTCATATGTGAATCGTTCATTTCATACTTTGAGATGTGTTTG
EST: gi|162265400|gb|FC440726.1|FC440726
EST:     TGACTGCGATCGTTGGCTCGTTAGTAGGGTCCTTACTTTGCTTCGTCAAG                         GGGTGTGGATTCATATGTGAATCGTTCATTTCATACTNTGAGATGTGTTTG
genomic: TGACTGCGATCGTTGGCTCGTTAGTAGGGTCCTTACTTTGCTTCGTCAAGgtcactatct ... tgtaacgtagGGGTGTGGATTCATATGTGAATCGTTCATTTCATACTTTGAGATGTGTTTG
EST: gi|100403161|gb|BY991065.1|BY991065
EST:     TGACTGCGATCGTTGGCTCGTTAGTAGGGTCCTTACTTTGCTTCGTCAAA                         GGGTGTGGATTCATATGTGAATCGTTCATTTCATACTTTGAAAAGTGTTTG
genomic: TGACTGCGATCGTTGGCTCGTTAGTAGGGTCCTTACTTTGCTTCGTCAAGgtcactatct ... tgtaacgtagGGGTGTGGATTCATATGTGAATCGTTCATTTCATACTTTGAGATGTGTTTG
EST: gi|162211231|gb|FC386943.1|FC386943
EST:     TGACTGCGATCGTTGGCTCGTTAGTAGGGTCCTTACTTTGCTTCGTCAAG                         GGGTGTGGATTCATATGTGAATCGTTCATTTCATACTTTGAGATGTGTTTG
genomic: TGACTGCGATCGTTGGCTCGTTAGTAGGGTCCTTACTTTGCTTCGTCAAGgtcactatct ... tgtaacgtagGGGTGTGGATTCATATGTGAATCGTTCATTTCATACTTTGAGATGTGTTTG
EST: gi|162264351|gb|FC440517.1|FC440517
EST:     TGACTGCGATCGTTGGCTCGTTAGTAGGGTCCTTACTTTGCTTCGTCAAG                         GGGTGTGGATTCATATGTGAATCGTTCATTTCATACTTTGAGATGTGTTTG
genomic: TGACTGCGATCGTTGGCTCGTTAGTAGGGTCCTTACTTTGCTTCGTCAAGgtcactatct ... tgtaacgtagGGGTGTGGATTCATATGTGAATCGTTCATTTCATACTTTGAGATGTGTTTG
EST: gi|162254308|gb|FC430443.1|FC430443
EST:     TGACTGCGATCGTTGGCTCGTTAGTAGGGTCCTTACTTTGCTTCGTCAAG                         GGGTGTGGATTCATATGTGAATCGTTCATTTCATACTTTGAGATGTGTTTG
genomic: TGACTGCGATCGTTGGCTCGTTAGTAGGGTCCTTACTTTGCTTCGTCAAGgtcactatct ... tgtaacgtagGGGTGTGGATTCATATGTGAATCGTTCATTTCATACTTTGAGATGTGTTTG
EST: gi|162168288|gb|FC344602.1|FC344602
EST:     TGACTGCGATCGTTGGCTCGTTAGAAGGGTCCTTACTTTGCTTCGTCAAG                         GGGGGTGGATTCATATGTGAATCGTTCATTTCATACTTTGA
genomic: TGACTGCGATCGTTGGCTCGTTAGTAGGGTCCTTACTTTGCTTCGTCAAGgtcactatct ... tgtaacgtagGGGTGTGGATTCATATGTGAATCGTTCATTTCATACTTTGA
EST: gi|162228323|gb|FC404376.1|FC404376
EST:     TGACTGCGATCGTTGGCTCGTTAGTAGGGTCCTTACTTTGCTTCGTCAAG                         GGGTGTGGATTCATATGTGAATCGTTCATTTCATACTTTGAGATGTGTTTG
genomic: TGACTGCGATCGTTGGCTCGTTAGTAGGGTCCTTACTTTGCTTCGTCAAGgtcactatct ... tgtaacgtagGGGTGTGGATTCATATGTGAATCGTTCATTTCATACTTTGAGATGTGTTTG
EST: gi|162254307|gb|FC430442.1|FC430442
EST:     GCTCGTTAGTAGGGTCCTTACTTTGCTTCGTCAAG                         GGGTGTGGATTCATATGTGAATCGTTCATTTCATACTTTGAGATGTGTTTG
genomic: GCTCGTTAGTAGGGTCCTTACTTTGCTTCGTCAAGgtcactatct ... tgtaacgtagGGGTGTGGATTCATATGTGAATCGTTCATTTCATACTTTGAGATGTGTTTG
EST: gi|162184316|gb|FC359712.1|FC359712
EST:     TGACTGCGATCGTTGGCTCGTTAGTAGGGTCCTTACTTTGCTTCGTCAAG                         GGGTGTGGATTCATATGTGAATCGTTCATTTCATACTTTGAGATGTGTTTG
genomic: TGACTGCGATCGTTGGCTCGTTAGTAGGGTCCTTACTTTGCTTCGTCAAGgtcactatct ... tgtaacgtagGGGTGTGGATTCATATGTGAATCGTTCATTTCATACTTTGAGATGTGTTTG
EST: gi|162162785|gb|FC337839.1|FC337839
EST:     TGACTGCGATCGTTGGCTCGTTAGTAGGGTCCTTACTTTGCTTCGTCAAG                         GGGTGTGGATTCATATGTGAATCGTTCATTTCATACTTTGAGATGTGTTTG
genomic: TGACTGCGATCGTTGGCTCGTTAGTAGGGTCCTTACTTTGCTTCGTCAAGgtcactatct ... tgtaacgtagGGGTGTGGATTCATATGTGAATCGTTCATTTCATACTTTGAGATGTGTTTG
EST: gi|162152960|gb|FC329262.1|FC329262
EST:     TGACTGCGATCGTTGGCTCGTTAGTAGGGTCCTTACTTTGCTTCGTCAAG                         GGGTGTGGATTCATATGTGAATCGTTCATTTCATACTTTGAGATGTGTTTG
genomic: TGACTGCGATCGTTGGCTCGTTAGTAGGGTCCTTACTTTGCTTCGTCAAGgtcactatct ... tgtaacgtagGGGTGTGGATTCATATGTGAATCGTTCATTTCATACTTTGAGATGTGTTTG
EST: gi|162276264|gb|FC452098.1|FC452098
EST:     TGACTGCGATCGTTGGCTCGTTAGTAGGGTCCTTACTTTGCTTCGTCAAG                         GGGTGTGGATTCATATGTGAATCGTTCATTTCATAC
genomic: TGACTGCGATCGTTGGCTCGTTAGTAGGGTCCTTACTTTGCTTCGTCAAGgtcactatct ... tgtaacgtagGGGTGTGGATTCATATGTGAATCGTTCATTTCATAC
EST: gi|162198166|gb|FC373090.1|FC373090
EST:     TGACTGCGATCGTTGGCTCGTTAGTAGGGTCCTTACTTTGCTTCGTCAAG                         GGGTGTGGATTCATATGTGAA
genomic: TGACTGCGATCGTTGGCTCGTTAGTAGGGTCCTTACTTTGCTTCGTCAAGgtcactatct ... tgtaacgtagGGGTGTGGATTCATATGTGAA
EST: gi|162189668|gb|FC366306.1|FC366306
EST:     TGACTGCGATCGTTGGCTCGTTAGTAGGGTCCTTACTTTGCTTCGTCAAG                         GGGTGTGGATTCATATGTGAATCGTTCATTTCATACTNTGAGATGTGTTTG
genomic: TGACTGCGATCGTTGGCTCGTTAGTAGGGTCCTTACTTTGCTTCGTCAAGgtcactatct ... tgtaacgtagGGGTGTGGATTCATATGTGAATCGTTCATTTCATACTTTGAGATGTGTTTG
EST: gi|208397953|gb|DC916708.1|DC916708
EST:     TGACTGCGATCGTTGGCTCGTTAGTAGGGTCCTTACTTTGCTTCGTCAAG                         GGGTGTGGATTCATATGTGAATCGTTCATTTCATACTTTGAGATGTGTTTG
genomic: TGACTGCGATCGTTGGCTCGTTAGTAGGGTCCTTACTTTGCTTCGTCAAGgtcactatct ... tgtaacgtagGGGTGTGGATTCATATGTGAATCGTTCATTTCATACTTTGAGATGTGTTTG
EST: gi|208375595|gb|DC902812.1|DC902812
EST:     TGACTGCGATCGTTGGCTCGTTAGTAGGGTCCTTACTTTGCTTCGTCAAG                         GGGTGTGGATTCATATGTGAATCGTTCATTTCATACTTTGAGATGTGTTTG
genomic: TGACTGCGATCGTTGGCTCGTTAGTAGGGTCCTTACTTTGCTTCGTCAAGgtcactatct ... tgtaacgtagGGGTGTGGATTCATATGTGAATCGTTCATTTCATACTTTGAGATGTGTTTG
EST: gi|162179437|gb|FC355437.1|FC355437
EST:     TGACTGCGATCGTTGGCTCGTTAGTAGGGTCCTTACTTTGCTTCGTCAAG                         GGGTGTGGATTCATATGTGAATCGTTCATTTCATACTTTGAGATGTGTTTG
genomic: TGACTGCGATCGTTGGCTCGTTAGTAGGGTCCTTACTTTGCTTCGTCAAGgtcactatct ... tgtaacgtagGGGTGTGGATTCATATGTGAATCGTTCATTTCATACTTTGAGATGTGTTTG
EST: gi|100352991|gb|BY945552.1|BY945552
EST:     GACTGCGATCNGT-GGCTCGTTAGTAGGGTCCTTACTTTGCTTCGTCAAG                         GGGTGTGGATTCATATGTGAATCGTTCATTTCATACTTGGAGATGTGTTTG
genomic: GACTGCGATC-GTTGGCTCGTTAGTAGGGTCCTTACTTTGCTTCGTCAAGgtcactatct ... tgtaacgtagGGGTGTGGATTCATATGTGAATCGTTCATTTCATACTTTGAGATGTGTTTG
EST: gi|162179436|gb|FC355436.1|FC355436
EST:     GTAGGGTCCTTACTTTGCTTCGTCAAG                         GGGTGTGGATTCATATGTGAATCGTTCATTTCATACTNTGAGATGTGTTTG
genomic: GTAGGGTCCTTACTTTGCTTCGTCAAGgtcactatct ... tgtaacgtagGGGTGTGGATTCATATGTGAATCGTTCATTTCATACTTTGAGATGTGTTTG

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), 26 (downstream exon)
Score: 4

GCTATTTTTGATTTCCGGTTCCTTACCCTGACTGCGATCGTTGGCTCGTTAGTAGGGTCCTTACTTTGCTTCGTCAAGgtcactatct ... tgtaacgtagGGGTGTGGATTCATATGTGAATCGTTCATTTCATACTTTGAGATGTGTTTGAATGGATTGCACACGGGAAATGTAATCCTCCGACTTGTCGAAGCAGTTG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaccttgagagtttttatgtgaatattgagtttaaccatccattgtgtaacgtagGGGTGTGGATTCATATGTGAATCGTTCATTTCATACTTTGAGATGTGTTTGAATGGATTGCACACGGGAAATGTAATCCTCCGACTTGTCGAAGCAGTTG
                                            gtgtaac  putative branch site (score: 4)
           tttttatgtgaatatt  TA-rich tract