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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...acgctggatggcgtcatagcaacttgtgatgtcctgtcttttccatgaagctgtgcaaatagggttattctcagtgaaactgaattaatgtccaatgcagATTTCGAAGGGGGATATTGTGCCTCCAGTCGGACTCAAAGATGAGGAAGGCAAATTGGTGAATCTAGACAAGTTCAGGGGCAAGCCCCTGGTGCTGTACT

Basic information

species Physcomitrella patens
transcript PP1S95_45V6.1
intron # 1
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|67569415|gb|BJ942239.1|BJ942239
EST:     CCTCGTTCCATGTCAAGTCCCGCCACACCTCACCCCTCACCATCTGCAAG                         ATTTCGAAGGGGGATATTGTGCCTCCAGTCGGACTCAAAGATGAGGAAGGC
genomic: CCTCGTTCCATGTCAAGTCCCGCCACACCTCACCCCTCACCATCTGCAAGgtatgtattg ... tccaatgcagATTTCGAAGGGGGATATTGTGCCTCCAGTCGGACTCAAAGATGAGGAAGGC
EST: gi|208397835|gb|DC912030.1|DC912030
EST:     CCTCGTTCCATGTCAAGTCCCGCCACACCTCACCCCTCACCATCTGCAAG                         ATTTCGAAGGGGGATATTGTGCCTCCAGTCGGACTCAAAGATGAGGAAGGC
genomic: CCTCGTTCCATGTCAAGTCCCGCCACACCTCACCCCTCACCATCTGCAAGgtatgtattg ... tccaatgcagATTTCGAAGGGGGATATTGTGCCTCCAGTCGGACTCAAAGATGAGGAAGGC
EST: gi|162269655|gb|FC445588.1|FC445588
EST:     CCTCGTTCCATGTCAAGTCCCGCCACACCTCACCCCTCACCATCTGCAAG                         ATTTCGAAGGGGGATATTGTGCCTCCAGTCGGACTCAAAGATGAGGAAGGC
genomic: CCTCGTTCCATGTCAAGTCCCGCCACACCTCACCCCTCACCATCTGCAAGgtatgtattg ... tccaatgcagATTTCGAAGGGGGATATTGTGCCTCCAGTCGGACTCAAAGATGAGGAAGGC
EST: gi|162213415|gb|FC389092.1|FC389092
EST:     CCTCGTTCCATGTCAAGTCCCGCCACACCTCACCCCTCACCATCTGCAAG                         ATTTCGAAGGGGGATATTGTGCCTCCAGTCGGACTCAAAGATGAGGAAGGC
genomic: CCTCGTTCCATGTCAAGTCCCGCCACACCTCACCCCTCACCATCTGCAAGgtatgtattg ... tccaatgcagATTTCGAAGGGGGATATTGTGCCTCCAGTCGGACTCAAAGATGAGGAAGGC
EST: gi|208364380|gb|DC950681.1|DC950681
EST:     CCTCGTTCCATGTCAAGTCCCGCCACACCTCACCCCTCACCATNTGCAAG                         ATTTCGAAGGGGGATATTGTGCCTCCAGTCGGACTCAAAGATGAGGAAGGC
genomic: CCTCGTTCCATGTCAAGTCCCGCCACACCTCACCCCTCACCATCTGCAAGgtatgtattg ... tccaatgcagATTTCGAAGGGGGATATTGTGCCTCCAGTCGGACTCAAAGATGAGGAAGGC
EST: gi|19790520|gb|BQ041917.1|BQ041917
EST:     CCTCGTTCCATGTCAAGTCCCGCCACACCTCACCCCTCACCATCTGCAAG                         ATTTCGAAGGGGGATATTGTGCCTCCAGTCGGACTCAAAGATGAGGAAGGC
genomic: CCTCGTTCCATGTCAAGTCCCGCCACACCTCACCCCTCACCATCTGCAAGgtatgtattg ... tccaatgcagATTTCGAAGGGGGATATTGTGCCTCCAGTCGGACTCAAAGATGAGGAAGGC
EST: gi|208382790|gb|DC903834.1|DC903834
EST:     CCTCGTTCCATGTCAAGTCCCGCCACACCTCACCCCTCACCATCTGCAAG                         ATTTCGAAGGGGGATATTGTGCCTCCAGTCGGACTCAAAGATGAGGAAGGC
genomic: CCTCGTTCCATGTCAAGTCCCGCCACACCTCACCCCTCACCATCTGCAAGgtatgtattg ... tccaatgcagATTTCGAAGGGGGATATTGTGCCTCCAGTCGGACTCAAAGATGAGGAAGGC
EST: gi|208351001|gb|DC917732.1|DC917732
EST:     CCTCGTTCCATGTCAAGT-CCGCCACACNTCACCCNTCACCATNTGCAAG                         ATTTCGAAGGGGGATATTGTGCCTCCAGTCGGACTCAAAGATGAGGAAGGC
genomic: CCTCGTTCCATGTCAAGTCCCGCCACACCTCACCCCTCACCATCTGCAAGgtatgtattg ... tccaatgcagATTTCGAAGGGGGATATTGTGCCTCCAGTCGGACTCAAAGATGAGGAAGGC
EST: gi|208363733|gb|DC954704.1|DC954704
EST:     NCTCGTTCCATGTCAAGTCCCGCCACACCTCACCCCTCACCATNTGCAAG                         ATTTCGAAGGGGGATATTGTGCCTCCAGTCGGACTCAAAGATGAGGAAGGC
genomic: CCTCGTTCCATGTCAAGTCCCGCCACACCTCACCCCTCACCATCTGCAAGgtatgtattg ... tccaatgcagATTTCGAAGGGGGATATTGTGCCTCCAGTCGGACTCAAAGATGAGGAAGGC
EST: gi|162173048|gb|FC348660.1|FC348660
EST:     CCTCGTTCCATGTCAAGTCCCGCCACACCTCACCCCTCACCATCTGTAAG                         ATTTCGAAGGGGGATATTGTGCCTCCAGTCGGACTCAAAGATGAGGAAGGC
genomic: CCTCGTTCCATGTCAAGTCCCGCCACACCTCACCCCTCACCATCTGCAAGgtatgtattg ... tccaatgcagATTTCGAAGGGGGATATTGTGCCTCCAGTCGGACTCAAAGATGAGGAAGGC
EST: gi|162238382|gb|FC415898.1|FC415898
EST:     CCTCGTTCCATGTCAAGTCCCGCCACACCTCACCCCTCACCATCTGCAAG                         ATTTCGAAGGGGGATATTGTGCCTCCAGTCGGACTCAAAGATGAGGAAGGC
genomic: CCTCGTTCCATGTCAAGTCCCGCCACACCTCACCCCTCACCATCTGCAAGgtatgtattg ... tccaatgcagATTTCGAAGGGGGATATTGTGCCTCCAGTCGGACTCAAAGATGAGGAAGGC
EST: gi|208361271|gb|DC930324.1|DC930324
EST:     CCTCGTTCCATGTCAAGTCCCGCCACACCTCACCCCTCACCATCTGCAAG                         ATTTCGAAGGGGGATATTGTGCCTCCAGTCGGACTCAAAGATGAGGAAGGC
genomic: CCTCGTTCCATGTCAAGTCCCGCCACACCTCACCCCTCACCATCTGCAAGgtatgtattg ... tccaatgcagATTTCGAAGGGGGATATTGTGCCTCCAGTCGGACTCAAAGATGAGGAAGGC
EST: gi|162269654|gb|FC445587.1|FC445587
EST:     CCTCGTTCCATGTCAAGTCCCGCCACACCTCACCCCTCACCATTTGCAAG                         ATTTCGAAGGGGGATATTGTGCCTCCAGTCGGACTCAAAGATGAGGAAGGC
genomic: CCTCGTTCCATGTCAAGTCCCGCCACACCTCACCCCTCACCATCTGCAAGgtatgtattg ... tccaatgcagATTTCGAAGGGGGATATTGTGCCTCCAGTCGGACTCAAAGATGAGGAAGGC
EST: gi|208345604|gb|DC909288.1|DC909288
EST:     CCTCGTTCCATGTCAAGTCCCGCCACACCTCACCCCTCACCATCTGCAAG                         ATTTCGAAGGGGGATATTGTGCCTCCAGTCGGACTCAAAGATGAGGAAGGC
genomic: CCTCGTTCCATGTCAAGTCCCGCCACACCTCACCCCTCACCATCTGCAAGgtatgtattg ... tccaatgcagATTTCGAAGGGGGATATTGTGCCTCCAGTCGGACTCAAAGATGAGGAAGGC
EST: gi|18364209|gb|BJ196282.1|BJ196282
EST:     CCTCGTTCCATGTCAAGTCCCGCCACACCTCACCCCTCACCATCTGCAAG                         ATTTCGAAGGGGGATATTGTGCCTCCAGTCGGACTCAAAGATGAGGAAGGC
genomic: CCTCGTTCCATGTCAAGTCCCGCCACACCTCACCCCTCACCATCTGCAAGgtatgtattg ... tccaatgcagATTTCGAAGGGGGATATTGTGCCTCCAGTCGGACTCAAAGATGAGGAAGGC
EST: gi|100430029|gb|BY978211.1|BY978211
EST:     CCTCGTTCCATGTCAAGTCCCGCCACACCTCACCCCTCACCATCTGCAAG                         ATTTCGAAGGGGGATATTGTGCCTCCAGTCGGACTCAAAGATGAGGAAGGC
genomic: CCTCGTTCCATGTCAAGTCCCGCCACACCTCACCCCTCACCATCTGCAAGgtatgtattg ... tccaatgcagATTTCGAAGGGGGATATTGTGCCTCCAGTCGGACTCAAAGATGAGGAAGGC
EST: gi|208351999|gb|DC925808.1|DC925808
EST:     CTCGTTCCATGTCAAGTCCCGCCACACCTCAACCCCTCACCATNTGCAAG                         ATTTCGAAGGGGGATATTGTGCCTCCAGTCGGACTCAAAGATGAGGAAGGC
genomic: CTCGTTCCATGTCAAGTCCCGCCACACCTC-ACCCCTCACCATCTGCAAGgtatgtattg ... tccaatgcagATTTCGAAGGGGGATATTGTGCCTCCAGTCGGACTCAAAGATGAGGAAGGC
EST: gi|67692676|gb|BJ952909.1|BJ952909
EST:     CCTCGTTCCATGTCAAGTCCCGCCACACCTCACCCCTCACCATCTGCAAG                         ATTTCGAAGGGGGATATTGTGCCTCCAGTCGGACTCAAAGATGAGGAAGGC
genomic: CCTCGTTCCATGTCAAGTCCCGCCACACCTCACCCCTCACCATCTGCAAGgtatgtattg ... tccaatgcagATTTCGAAGGGGGATATTGTGCCTCCAGTCGGACTCAAAGATGAGGAAGGC
EST: gi|208381565|gb|DC923151.1|DC923151
EST:     TCACCCCTCACCATTTGCAAG                         ATTTCGAAGGGGGATATTGTGCCTCCAGTCGGACTCAAAGATGAGGAAGGC
genomic: TCACCCCTCACCATCTGCAAGgtatgtattg ... tccaatgcagATTTCGAAGGGGGATATTGTGCCTCCAGTCGGACTCAAAGATGAGGAAGGC
EST: gi|208391468|gb|DC937616.1|DC937616
EST:     CCTCGTTCCATGTCAAGTCCCGCCACACCTCACCCCTCACCATCTGCAAG                         ATTTCGAAGGGGGATATTGTGCCTCCAGTCGGACTCAAAGATGAGGAAGGC
genomic: CCTCGTTCCATGTCAAGTCCCGCCACACCTCACCCCTCACCATCTGCAAGgtatgtattg ... tccaatgcagATTTCGAAGGGGGATATTGTGCCTCCAGTCGGACTCAAAGATGAGGAAGGC
EST: gi|208387358|gb|DC933109.1|DC933109
EST:     CCTCGTTCCATGTCAAGTCCCGCCACACCTCACCCCTCACCATCTGCAAG                         ATTTCGAAGGGGGATATTGTGCCTCCAGTCGGACTCAAAGATGAGGAAGGC
genomic: CCTCGTTCCATGTCAAGTCCCGCCACACCTCACCCCTCACCATCTGCAAGgtatgtattg ... tccaatgcagATTTCGAAGGGGGATATTGTGCCTCCAGTCGGACTCAAAGATGAGGAAGGC

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: 14

CTCCGAGCTCTTTTCTTCCAAGGCTGGTTTAAGCGCACGCGTGGCTGGAGCCTCGTTCCATGTCAAGTCCCGCCACACCTCACCCCTCACCATCTGCAAGgtatgtattg ... tccaatgcagATTTCGAAGGGGGATATTGTGCCTCCAGTCGGACTCAAAGATGAGGAAGGCAAATTGGTGAATCTAGACAAGTTCAGGGGCAAGCCCCTGGTGCTGTACT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgaagctgtgcaaatagggttattctcagtgaaactgaattaatgtccaatgcagATTTCGAAGGGGGATATTGTGCCTCCAGTCGGACTCAAAGATGAGGAAGGCAAATTGGTGAATCTAGACAAGTTCAGGGGCAAGCCCCTGGTGCTGTACT
                                     aattaat  putative branch site (score: 14)
                                   tgaattaat  TA-rich tract