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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gttttcgcttggttattggccatgtcaattcatattatgagatgttcaatgccttatggctgttccttggaggtaacagttgtgatcttgtgacttgcagCTCATTAATGAAAAGCCACAAATTGTTCAAGAGTATGAGTCGGGAAAAGCAATTCCCAACCAGCAAATTATCGCGAAGTTGGAACGTGTTCTTGGCGTGA

Basic information

species Physcomitrella patens
transcript PP1S96_94V6.2
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S96_94V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: AT2G42680.1 (Arabidopsis thaliana), 3'ss of exon 3
gttttcgcttggttattggccatgtcaattcatattatgagatgtt-caatgccttatggctgttccttggaggtaacagttgtgatcttgtgacttgcagCTCATTAATGAAAAGCCACAAATTGTTCAAGAGTATGAGTCGGGAAAAGCAATTCCCAACCAGCAAATTATCGCGAAGTTGGAACGTGTTCTTGGCGTGA
          |  ||||  || | ||  |  || |       | || |  |   || |  ||        ||   |    ||||    || ||   || || |||| ||||| ||||||||| |  |||||||||||||||| || ||||| || ||||||||||||||  |  | ||| ||||  | |  ||||| |  |
----------gtatattatccttctctctatatgtcccttattattaccctattttgtaactcggttcatgacaaagtgtttgtttctttttg---tgtagATCATCAATGAGAAGCCACAAGTGATTCAAGAGTATGAGTCTGGCAAAGCTATACCCAACCAGCAAATCCTTTCTAAGCTGGAGAGAGCGCTTGGAGCTA

upper sequence: PP1S96_94V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: EFJ33541 (Selaginella moellendorffii), 3'ss of exon 3
gttttcgcttggttattggccatgtcaattcatattatgagatgttcaatgccttatggctgttccttggaggtaacagttgtgatcttgtgacttgcagCTCATTAATGAAAAGCCACAAATTGTTCAAGAGTATGAGTCGGGAAAAGCAATTCCCAACCAGCAAATTATCGCGAAGTTGGAACGTGTTCTTGGCGTGA
                            ||   || ||    | ||   |   || |   ||   ||     ||     ||||    |||     | ||||| || || || ||||| ||  |  | ||||||||||| ||||||||||| || ||||||||||| || ||| | ||| | || || |  || || |  |
---------------------------gtttggatgattgattctttggttttttctttttgg--ctgatttgttttccttgttggtttgcttggtccagCTGATCAACGAGAAGCCTCAGGTCATCCAAGAGTATGAATCGGGAAAAGCCATCCCCAACCAGCAGATCATCTCCAAGCTCGAGCGCGCGCTGGGAGCCA
















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|67578500|gb|BJ950667.1|BJ950667
EST:     TTATGCAGGCGCGGTTGGATAAGAAGATGACACAAGCTCAACTTGCACAG                         CTCATTAATGAAAAGCCACAAATTGTTCAAGAGTATGAGTCGGGAAAAGCA
genomic: TTATGCAGGCGCGGTTGGATAAGAAGATGACACAAGCTCAACTTGCACAGgtttgtcctg ... tgacttgcagCTCATTAATGAAAAGCCACAAATTGTTCAAGAGTATGAGTCGGGAAAAGCA
EST: gi|162261021|gb|FC437428.1|FC437428
EST:     TTATGCAGGCGCGGTTGGATAAGAAGATGACACAAGCTCAACTTGCACAG                         CTCATTAATGAAAAGCCACAAATTGTTCAAGAGTATGAGTCGGGAAAAGCA
genomic: TTATGCAGGCGCGGTTGGATAAGAAGATGACACAAGCTCAACTTGCACAGgtttgtcctg ... tgacttgcagCTCATTAATGAAAAGCCACAAATTGTTCAAGAGTATGAGTCGGGAAAAGCA
EST: gi|162225111|gb|FC401735.1|FC401735
EST:     TTATGCAGGCGCGGTTGGATAAGAAGATGACACAAGCTCAACTTGCACAG                         CTCATTAATGAAAAGCCACAAATTGTTCAAGAGTTTGAGTCGGGAAAAGCA
genomic: TTATGCAGGCGCGGTTGGATAAGAAGATGACACAAGCTCAACTTGCACAGgtttgtcctg ... tgacttgcagCTCATTAATGAAAAGCCACAAATTGTTCAAGAGTATGAGTCGGGAAAAGCA
EST: gi|37826092|gb|BJ584104.1|BJ584104
EST:     TTATGCAGGCGCGGTTGGATAAGAAGATGACACAAGCTCAACTTGCACAG                         CTCATTAATGAAAAGCCACAAATTGTTCAAGAGTATGAGTCGGGAAAAGCA
genomic: TTATGCAGGCGCGGTTGGATAAGAAGATGACACAAGCTCAACTTGCACAGgtttgtcctg ... tgacttgcagCTCATTAATGAAAAGCCACAAATTGTTCAAGAGTATGAGTCGGGAAAAGCA
EST: gi|67578369|gb|BJ950536.1|BJ950536
EST:     TTATGCAGGCGCGGTTGGATAAGAAGATGACACAAGCTCAACTTGCACAG                         CTCATTAATGAAAAGCCACAAATTGTTCAAGAGTATGAGTCGGGAAAAGCA
genomic: TTATGCAGGCGCGGTTGGATAAGAAGATGACACAAGCTCAACTTGCACAGgtttgtcctg ... tgacttgcagCTCATTAATGAAAAGCCACAAATTGTTCAAGAGTATGAGTCGGGAAAAGCA
EST: gi|67695053|gb|BJ955286.1|BJ955286
EST:     TTATGCAGGCGCGGTTGGATAAGAAGATGACACAAGCTCAACTTGCACAG                         CTCATTAATGAAAAGCCACAAATTGTTCAAGAGTATGAGTCGGGAAAAGCA
genomic: TTATGCAGGCGCGGTTGGATAAGAAGATGACACAAGCTCAACTTGCACAGgtttgtcctg ... tgacttgcagCTCATTAATGAAAAGCCACAAATTGTTCAAGAGTATGAGTCGGGAAAAGCA
EST: gi|67574919|gb|BJ947743.1|BJ947743
EST:     TTATGCAGGCGCGGTTGGATAAGAAGATGACACAAGCTCAACTTGCACAG                         CTCATTAATGAAAAGCCACAAATTGTTCAAGAGTATGAGTCGGGAAAAGCA
genomic: TTATGCAGGCGCGGTTGGATAAGAAGATGACACAAGCTCAACTTGCACAGgtttgtcctg ... tgacttgcagCTCATTAATGAAAAGCCACAAATTGTTCAAGAGTATGAGTCGGGAAAAGCA
EST: gi|67701255|gb|BJ961488.1|BJ961488
EST:     TTATGCAGGCGCGGTTGGATAAGAAGATGACACAAGCTCAACTTGCACAG                         CTCATTAATGAAAAGCCACAAATTGTTCAAGAGTATGAGTCGGGAAAAGCA
genomic: TTATGCAGGCGCGGTTGGATAAGAAGATGACACAAGCTCAACTTGCACAGgtttgtcctg ... tgacttgcagCTCATTAATGAAAAGCCACAAATTGTTCAAGAGTATGAGTCGGGAAAAGCA
EST: gi|67698680|gb|BJ958913.1|BJ958913
EST:     TTATGCAGGCGCGGTTGGATAAGAAGATGACACAAGCTCAACTTGCACAG                         CTCATTAATGAAAAGCCACAAATTGTTCAAGAGTATGAGTCGGGAAAAGCA
genomic: TTATGCAGGCGCGGTTGGATAAGAAGATGACACAAGCTCAACTTGCACAGgtttgtcctg ... tgacttgcagCTCATTAATGAAAAGCCACAAATTGTTCAAGAGTATGAGTCGGGAAAAGCA
EST: gi|162222413|gb|FC397173.1|FC397173
EST:     AACTTGCACAG                         CTCATTAATGAAAAGCCACAAATTGTTCAAGAGTATGAGTCGGGAAAAGCA
genomic: AACTTGCACAGgtttgtcctg ... tgacttgcagCTCATTAATGAAAAGCCACAAATTGTTCAAGAGTATGAGTCGGGAAAAGCA
EST: gi|67574035|gb|BJ946859.1|BJ946859
EST:     TTATGCAGGCGCGGTTGGATAAGAAGATGACACAAGCTCAACTTGCACAG                         CTCATTAATGAAAAGCCACAAATTGTTCAAGAGTATGAGTCGGGAAAAGCA
genomic: TTATGCAGGCGCGGTTGGATAAGAAGATGACACAAGCTCAACTTGCACAGgtttgtcctg ... tgacttgcagCTCATTAATGAAAAGCCACAAATTGTTCAAGAGTATGAGTCGGGAAAAGCA
EST: gi|67698346|gb|BJ958579.1|BJ958579
EST:     TTATGCAGGCGCGGTTGGATAAGAAGATGACACAAGCTCAACTTGCACAG                         CTCATTAATGAAAAGCCACAAATTGTTCAAGAGTATGAGTCGGGAAAAGCA
genomic: TTATGCAGGCGCGGTTGGATAAGAAGATGACACAAGCTCAACTTGCACAGgtttgtcctg ... tgacttgcagCTCATTAATGAAAAGCCACAAATTGTTCAAGAGTATGAGTCGGGAAAAGCA
EST: gi|67697424|gb|BJ957657.1|BJ957657
EST:     TTATGCAGGCGCGGTTGGATAAGAAGATGACACAAGCTCAACTTGCACAG                         CTCATTAATGAAAAGCCACAAATTGTTCAAGAGTATGAGTCGGGAAAAGCA
genomic: TTATGCAGGCGCGGTTGGATAAGAAGATGACACAAGCTCAACTTGCACAGgtttgtcctg ... tgacttgcagCTCATTAATGAAAAGCCACAAATTGTTCAAGAGTATGAGTCGGGAAAAGCA
EST: gi|67697361|gb|BJ957594.1|BJ957594
EST:     TTATGCAGGCGCGGTTGGATAAGAAGATGACACAAGCTCAACTTGCACAG                         CTCATTAATGAAAAGCCACAAATTGTTCAAGAGTATGAGTCGGGAAAAGCA
genomic: TTATGCAGGCGCGGTTGGATAAGAAGATGACACAAGCTCAACTTGCACAGgtttgtcctg ... tgacttgcagCTCATTAATGAAAAGCCACAAATTGTTCAAGAGTATGAGTCGGGAAAAGCA
EST: gi|37828988|gb|BJ587000.1|BJ587000
EST:     TTATGCAGGCGCGGTTGGATAAGAAGATGACACAAGCTCAACTTGCACAG                         CTCATTAATGAAAAGCCACAAATTGTTCAAGAGTATGAGTCGGGAAAAGCA
genomic: TTATGCAGGCGCGGTTGGATAAGAAGATGACACAAGCTCAACTTGCACAGgtttgtcctg ... tgacttgcagCTCATTAATGAAAAGCCACAAATTGTTCAAGAGTATGAGTCGGGAAAAGCA
EST: gi|22491864|gb|BU051787.1|BU051787
EST:     TTATGCAGGCGCGGTTGGATAAGAAGATGACACAAGCTCAACTTGCACAG                         CTCATTAATGAAAAGCCACAAATTGTTCAAGAGTATGAGTCGGGAAAAGCA
genomic: TTATGCAGGCGCGGTTGGATAAGAAGATGACACAAGCTCAACTTGCACAGgtttgtcctg ... tgacttgcagCTCATTAATGAAAAGCCACAAATTGTTCAAGAGTATGAGTCGGGAAAAGCA
EST: gi|37830434|gb|BJ588446.1|BJ588446
EST:     TTATGCAGGCGCGGTTGGATAAGAAGATGACACAAGCTCAACTTGCACAG                         CTCATTAATGAAAAGCCACAAATTGTTCAAGAGTATGAGTCGGGAAAAGCA
genomic: TTATGCAGGCGCGGTTGGATAAGAAGATGACACAAGCTCAACTTGCACAGgtttgtcctg ... tgacttgcagCTCATTAATGAAAAGCCACAAATTGTTCAAGAGTATGAGTCGGGAAAAGCA
EST: gi|67575221|gb|BJ948045.1|BJ948045
EST:     TTATGCAGGCGCGGTTGGATAAGAAGATGACACAAGCTCAACTTGCACAG                         CTCATTAATGAAAAGCCACAAATTGTTCAAGAGTATGAGTCGGGAAAAGCA
genomic: TTATGCAGGCGCGGTTGGATAAGAAGATGACACAAGCTCAACTTGCACAGgtttgtcctg ... tgacttgcagCTCATTAATGAAAAGCCACAAATTGTTCAAGAGTATGAGTCGGGAAAAGCA
EST: gi|162225112|gb|FC401736.1|FC401736
EST:     TTATGCAGGCGCGGTTGGATAAGAAGATGACACAAGCTCAACTTGCACAG                         CTCATTAATGAAAAGCCACAAATTGTTCAAGAGTATGAGTCGGGAAAAGCA
genomic: TTATGCAGGCGCGGTTGGATAAGAAGATGACACAAGCTCAACTTGCACAGgtttgtcctg ... tgacttgcagCTCATTAATGAAAAGCCACAAATTGTTCAAGAGTATGAGTCGGGAAAAGCA

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: 34 (upstream exon), 33 (downstream exon)
Score: 17

ACGAGAAAGTGCCTTCTGAACTCAAGAAGAACATTATGCAGGCGCGGTTGGATAAGAAGATGACACAAGCTCAACTTGCACAGgtttgtcctg ... tgacttgcagCTCATTAATGAAAAGCCACAAATTGTTCAAGAGTATGAGTCGGGAAAAGCAATTCCCAACCAGCAAATTATCGCGAAGTTGGAACGTGTTCTTGGCGTGA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcaatgccttatggctgttccttggaggtaacagttgtgatcttgtgacttgcagCTCATTAATGAAAAGCCACAAATTGTTCAAGAGTATGAGTCGGGAAAAGCAATTCCCAACCAGCAAATTATCGCGAAGTTGGAACGTGTTCTTGGCGTGA
                         aggtaac  putative branch site (score: 17)