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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgccttatcaacatctctagagttcatatgtgagctttgtcaaagtcaacacaattgggcattgcgctgttcatagtctctaattgcagaatctgatgctggattgttgtgtgtatcagGGTTAAGAGCCAGCTGAAGAGGATTGCAAGACCAATGTACTCAAACCCACCTGTTCACGGTGCCCGTATTGTTGCCAACGTTGTTGGCGAGCCAACTATG

Basic information

species Physcomitrella patens
transcript PP1S540_7V6.2
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S540_7V6.3 (Physcomitrella patens), 3'ss of exon 9
lower sequence: GRMZM5G836910_T01 (Zea mays), 3'ss of exon 9
gtatgccttatcaacatctctagagttcatatgtgagctttgtcaaagtcaacacaattgggcattgcgctgttcatagtctctaattgcagaatctgatgctggattgttgtgtgtatcagGGTTAAGAGCCAGCTGAAGAGGATTGCAAGACCAATGTACTCAAACCCACCTGTTCACGGTGCCCGTATTGTTGCCAACGTTGTTGGCGAGCCAACTATG
       ||  ||| |  |      |||||||      |  |    || ||| |   ||     | | ||  |  |   | |||  || | | ||   | |     |  ||       ||||||| ||||||||||||||  |  | ||| | || |||||||| ||||| ||| |||||||||||   || ||||||||||||||||| || ||||| |||
-------tttccaatagttgc----ttcatatacagaatcggc---aggcaatagtcttccttttggtgcaatagact-tgtctccttacggcattccacgtcacttcctt-------tcagGGTAAAGAGCCAGCTGAAACGATTGGCACGTCCCATGTACTCGAACCCCCCTATTCACGGTGCCAAGATAGTTGCCAACGTTGTTGGTGATCCAACCATG

upper sequence: PP1S540_7V6.3 (Physcomitrella patens), 3'ss of exon 9
lower sequence: GLYMA17G33050.4 (Glycine max), 3'ss of exon 9
gtatgccttatcaacatctctagagttcatatgtgagctttgtcaaagtcaacacaattgggcattgcgctgttcatagtctctaattgcagaatctgatgctggattgttgtgtgtatcagGGTTAAGAGCCAGCTGAAGAGGATTGCAAGACCAATGTACTCAAACCCACCTGTTCACGGTGCCCGTATTGTTGCCAACGTTGTTGGCGAGCCAACTATG
               | ||  | || | | || | || ||   |    |     ||||   | ||  | | ||  |   ||| |  |     |     |||  | |  |   || || ||||||| |||||||| ||||| ||||||||  ||||||||||||| || ||||| || ||||| ||  | || |||||| | ||||||||  | |||  | | 
--------------taactagaaagatgacatcttagattcaacttgattgtggcaat---gtatgcctcagtagaagttctgtgttgatcaa---caatgtggtaacg--atgcgtttcagGGTAAAGAGCCAACTGAAAAGGATTGCCCGACCAATGTACTCTAATCCACCGGTACACGGGGCTAGGATAGTTGCCGATGTTGTTGGAAACCCAGTTCTC

upper sequence: PP1S540_7V6.3 (Physcomitrella patens), 3'ss of exon 9
lower sequence: Vv04s0008g06040.t01 (Vitis vinifera), 3'ss of exon 11
gtatgccttatcaacatctctagagttcat-atgtgagctttgtc-aaagtcaacacaattgggcattgcgctgttcatagtctctaattgcagaatctgatgct----ggattgttgtgtgtatcagGGTTAAGAGCCAGCTGAAGAGGATTGCAAGACCAATGTACTCAAACCCACCTGTTCACGGTGCCCGTATTGTTGCCAACGTTGTTGGCGAGCCAACTATG
                       |  |||| |||   | ||| || |||||  |  ||  ||     || |  |        || |   || |  | ||| |  |      ||| || |   | ||||||| ||||| ||| |||| ||||||||  |||||||||||||||| || ||| |||| || ||  | ||||||||||| |||||||| || ||| || | 
-----------------------atatcatgatgaatggtttatctaaagttgatccaggtgattcctgagtggc-----aactttgggtggatgacctgctaatttgcatatttttattcttttcagGGTAAAGAGTCAGTTGAAAAGGATTGCTCGACCAATGTACTCAAATCCTCCTATTCATGGAGCTAGGATTGTTGCCAATGTTGTTGGTGATCCAGCTCTC

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|18339711|gb|BJ171738.1|BJ171738
EST:     TGTGGGTGCTATCAATGCGATTGTATCCTCTGCAGATGTTGCTGCTAG                         GGTTAAGAGCCAGCTGAAGAGGATTGCAAGACCAATGTACTCAAACCCACC
genomic: TGTGGGTGCTATCAATGCGATTGTATCCTCTGCAGATGTTGCTGCTAGgtatgcctta ... tgtgtatcagGGTTAAGAGCCAGCTGAAGAGGATTGCAAGACCAATGTACTCAAACCCACC
EST: gi|208386964|gb|DC956933.1|DC956933
EST:     CGTGTGGGTGCTATCAATGCGATTGTATCCTCTGCAGATGTTGCTGNTAG                         GGTTAAGAGCCAGCTGAAGAGGATTGCAAGACCAATGTACTCAAACCCACC
genomic: CGTGTGGGTGCTATCAATGCGATTGTATCCTCTGCAGATGTTGCTGCTAGgtatgcctta ... tgtgtatcagGGTTAAGAGCCAGCTGAAGAGGATTGCAAGACCAATGTACTCAAACCCACC
EST: gi|37838764|gb|BJ596772.1|BJ596772
EST:     CGTGTGGGTGCTATCAATGCGATTGTATCCTCTGCAGATG-TGCTGCTAG                         GGTTAAGAGCCAGCTGAAGAGGATTGCAAGACCAATGTACTCCAAANNNNN
genomic: CGTGTGGGTGCTATCAATGCGATTGTATCCTCTGCAGATGTTGCTGCTAGgtatgcctta ... tgtgtatcagGGTTAAGAGCCAGCTGAAGAGGATTGCAAGACCAATGTACT-CAAA-CCCA
EST: gi|162158558|gb|FC334561.1|FC334561
EST:     TCTGCAGATGTTGCTGCTAG                         GGTTAAGAGCCAGCTGAAGAGGATTGCAAGACCAATGTACTCAAACCCACC
genomic: TCTGCAGATGTTGCTGCTAGgtatgcctta ... tgtgtatcagGGTTAAGAGCCAGCTGAAGAGGATTGCAAGACCAATGTACTCAAACCCACC
EST: gi|208382292|gb|DC919280.1|DC919280
EST:     ATCAATGCGATTGTATCCTNTGCAGATGNTGCTGCTAG                         GGTTAAGAGCCAGCTGAAGAGGATTGCAAGACCAATGTACTCAAACCCACC
genomic: ATCAATGCGATTGTATCCTCTGCAGATGTTGCTGCTAGgtatgcctta ... tgtgtatcagGGTTAAGAGCCAGCTGAAGAGGATTGCAAGACCAATGTACTCAAACCCACC
EST: gi|67698272|gb|BJ958505.1|BJ958505
EST:     CGTGTGGGTGCTATCAATGCGATTGTATCCTCTGCAGATGTTGCTGCTAG                         GGTTAAGAGCCAGCTGAAGAGGATTGCAAGACCAATGTACTCAAACCCACC
genomic: CGTGTGGGTGCTATCAATGCGATTGTATCCTCTGCAGATGTTGCTGCTAGgtatgcctta ... tgtgtatcagGGTTAAGAGCCAGCTGAAGAGGATTGCAAGACCAATGTACTCAAACCCACC
EST: gi|162196656|gb|FC373802.1|FC373802
EST:     CGTGTGGGTGCTATCAATGCGATTGTATCCTCTGCAGATGTTGCTGCTAG                         GGTTAAGAGCCAGCTGAAGAGGATTGCAAGACCAATGTACTCAAACCCACC
genomic: CGTGTGGGTGCTATCAATGCGATTGTATCCTCTGCAGATGTTGCTGCTAGgtatgcctta ... tgtgtatcagGGTTAAGAGCCAGCTGAAGAGGATTGCAAGACCAATGTACTCAAACCCACC
EST: gi|208386221|gb|DC952934.1|DC952934
EST:     CGTGTGGGTGCTATCAATGCGATTGTATCCTCTGCAGATGTTGCTGCTAG                         GGTTAAGAGCCAGCTGAAGAGGATTGCAAGACCAATGTACTCAAACCCACC
genomic: CGTGTGGGTGCTATCAATGCGATTGTATCCTCTGCAGATGTTGCTGCTAGgtatgcctta ... tgtgtatcagGGTTAAGAGCCAGCTGAAGAGGATTGCAAGACCAATGTACTCAAACCCACC
EST: gi|162217709|gb|FC393801.1|FC393801
EST:     CGTGTGGGTGCTATCAATGCGATTGTATCCTCTGCAGATGTTGCTGCTAG                         GGTTAAGAGCCAGCTGAAGAGGATTGCAAGACCAATGTACTCAAACCCACC
genomic: CGTGTGGGTGCTATCAATGCGATTGTATCCTCTGCAGATGTTGCTGCTAGgtatgcctta ... tgtgtatcagGGTTAAGAGCCAGCTGAAGAGGATTGCAAGACCAATGTACTCAAACCCACC
EST: gi|162217708|gb|FC393800.1|FC393800
EST:     CTGCAGATGTTGCTGCTAG                         GGTTAAGAGCCAGCTGAAGAGGATTGCAAGACCAATGTACTCAAACCCACC
genomic: CTGCAGATGTTGCTGCTAGgtatgcctta ... tgtgtatcagGGTTAAGAGCCAGCTGAAGAGGATTGCAAGACCAATGTACTCAAACCCACC
EST: gi|208366815|gb|DC940129.1|DC940129
EST:     CGTGTGGGTGCTATCAATGCGATTGTATCCTCTGCAGATGTTGCTGCTAG                         GGTTAAGAGCCAGCTGAAGAGGATTGCAAGACCAATGTACTCAAACCCACC
genomic: CGTGTGGGTGCTATCAATGCGATTGTATCCTCTGCAGATGTTGCTGCTAGgtatgcctta ... tgtgtatcagGGTTAAGAGCCAGCTGAAGAGGATTGCAAGACCAATGTACTCAAACCCACC
EST: gi|162158559|gb|FC334562.1|FC334562
EST:     CGTGTGGGTGCTATCAATGCGATTGTATCCTCTGCAGATGTTGCTGCTAG                         GGTTAAGAGCCAGCTGAAGAGGATTGCAAGACCAATGTACTCAAACCCACC
genomic: CGTGTGGGTGCTATCAATGCGATTGTATCCTCTGCAGATGTTGCTGCTAGgtatgcctta ... tgtgtatcagGGTTAAGAGCCAGCTGAAGAGGATTGCAAGACCAATGTACTCAAACCCACC
EST: gi|162196657|gb|FC373803.1|FC373803
EST:     CGTGTGGGTGCTATCAATGCGATTGTATCCTCTGCAGATGTTGCTGCTAG                         GGTTAAGAGCCAGCTGAAGAGGATTGCAAGACCAATGTACTCAAACCCACC
genomic: CGTGTGGGTGCTATCAATGCGATTGTATCCTCTGCAGATGTTGCTGCTAGgtatgcctta ... tgtgtatcagGGTTAAGAGCCAGCTGAAGAGGATTGCAAGACCAATGTACTCAAACCCACC
EST: gi|162167594|gb|FC343739.1|FC343739
EST:     GCAGATGTTGCTGCTAG                         GGTTAAGAGCCAGCTGAAGAGGATTGCAAGACCAATGTACTCAAACCCACC
genomic: GCAGATGTTGCTGCTAGgtatgcctta ... tgtgtatcagGGTTAAGAGCCAGCTGAAGAGGATTGCAAGACCAATGTACTCAAACCCACC

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: 33 (upstream exon), 31 (downstream exon)
Score: 28

AGGTTTTCGTGGCACAATCCTACAGCAAGAATCTCGGTCTCTATGCCGAGCGTGTGGGTGCTATCAATGCGATTGTATCCTCTGCAGATGTTGCTGCTAGgtatgcctta ... tgtgtatcagGGTTAAGAGCCAGCTGAAGAGGATTGCAAGACCAATGTACTCAAACCCACCTGTTCACGGTGCCCGTATTGTTGCCAACGTTGTTGGCGAGCCAACTATG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cgctgttcatagtctctaattgcagaatctgatgctggattgttgtgtgtatcagGGTTAAGAGCCAGCTGAAGAGGATTGCAAGACCAATGTACTCAAACCCACCTGTTCACGGTGCCCGTATTGTTGCCAACGTTGTTGGCGAGCCAACTATG
              tctaatt  TA-rich tract