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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tctaatgatttcacaagtatcgaagttgctttttagtccttgggtgctattacaatagttagatttcagttgctcattatcaacctctttgttatgccagTGTTGTACAGCAAATCCTGATGGCCGCAAGAGAGCTTTGGTTGTCGGTGGAGGCATTGCTAACTTCACTGATGTTGCAGCAACTTTCAACGGCATCATTC

Basic information

species Physcomitrella patens
transcript PP1S63_54V6.2
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S63_54V6.2 (Physcomitrella patens), 3'ss of exon 11
lower sequence: GLYMA15G42140.2 (Glycine max), 3'ss of exon 9
tctaatgatttcacaagtat-cgaagttgctttttagtccttgggtgctattacaata-gttagatttcagttgctcattatcaacctctttgttatgccagTGTTGTACAGCAAATCCTGATGGCCGCAAGAGAGCTTTGGTTGTCGGTGGAGGCATTGCTAACTTCACTGATGTTGCAGCAACTTTCAACGGCATCATTC
 | ||  |||  |  ||| |  |||  |   || |     |||  ||||| |   | |  | | ||     ||  | | | || |   |  | |  |  ||||||   ||  |||||||||||||||  ||| ||||  | || || |||||||| || |||||||| ||||||||||| || || |||| |||||| ||||
-ccaaacattctaagagtgtgtgaaaatagcttatgaaa-ttgcatgctactttgaaacatgatatagtgattctttaatctctatgacaatctctttgcagTGTGCAACTTCAAATCCTGATGGCCAAAAGCGAGCCCTTGTGGTAGGTGGAGGAATAGCTAACTTTACTGATGTTGCTGCTACATTCAGCGGCATAATTC

upper sequence: PP1S63_54V6.2 (Physcomitrella patens), 3'ss of exon 11
lower sequence: AT1G09430.1 (Arabidopsis thaliana), 3'ss of exon 9
tctaatgatttcacaagtatcgaagttgctttttagtccttgggtgctattacaatagttagatttcagttgctcattatc--aacctctttgttatgccagTGTTGTACAGCAAATCCTGATGGCCGCAAGAGAGCTTTGGTTGTCGGTGGAGGCATTGCTAACTTCACTGATGTTGCAGCAACTTTCAACGGCATCATTC
     ||| | ||   | |  ||| |||   |||  |||||   || |  ||      | | |||| ||    |||    |  ||| |    | | |  ||||||   ||  |  ||||||| || || ||  ||||| |  |  | || ||||||||||| || ||||||||||| ||||| ||||||||||| |||||||
----gtgagt-catg-gcaaagaacttggccttt--tccttaattgtttctat--ctataaaattttagagattcacagaccaaacgttcgggctttctcagTGTGCCACTACTGATCCTGACGGGCGTAAACGAGCTCTTCTAATTGGAGGAGGCATTGCCAATTTCACTGATGTGGCAGCTACTTTCAACGGTATCATTC

upper sequence: PP1S63_54V6.2 (Physcomitrella patens), 3'ss of exon 11
lower sequence: Vv14s0060g00550.t01 (Vitis vinifera), 3'ss of exon 9
tctaatgatttcacaagtatcgaagttgctttttagtccttgggtgctattacaat----------agttagatttcagttgctcattatcaacctctttgttatgccagTGTTGTACAGCAAATCCTGATGGCCGCAAGAGAGCTTTGGTTGTCGGTGGAGGCATTGCTAACTTCACTGATGTTGCAGCAACTTTCAACGGCATCATTC
  |||  | || |  |   | |   |  |||||  |     |     | ||| |||          |  ||  ||||| ||| |    | |||  |  |  |||   ||||||  ||| ||  | ||||||||||| ||||||||  |  |  | || || || ||||||||||||||||||||||| || |||||||| || ||  | |
-gtaagaaatt-atgaactttggcataccttttgggcttcagctctttgttaaaatttgctgcttaaaataattttcatttgttgtggaacaatatactcttta---cagTGTGCTACTGCTGACCCTGATGGCCGTAAGAGAGCCCTTCTCATTGGAGGGGGTATTGCTAACTTCACTGATGTTGCTGCCACTTTCAATGGGATTGTCC

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|208365149|gb|DC946778.1|DC946778
EST:     GAGCTCCAAATGAAGAAGAGACTTTGCAGTATGCCCGTGCTTTGATTGAC                         TGTTGTACAGCAAATCCTGATGGCCGCAAGAGAGCTTTGGTTGTCGGTGGA
genomic: GAGCTCCAAATGAAGAAGAGACTTTGCAGTATGCCCGTGCTTTGATTGACgtaagtccgt ... gttatgccagTGTTGTACAGCAAATCCTGATGGCCGCAAGAGAGCTTTGGTTGTCGGTGGA
EST: gi|18339126|gb|BJ171152.1|BJ171152
EST:     GAGCTCCAAATGAAGAAGAGACTTTGCAGTATGCCCGTGCTTTGATTGAC                         TGTTGTACAGCAAATCCTGATGGCCGCAAGAGAGCTTTGGTTGTCGGTGGA
genomic: GAGCTCCAAATGAAGAAGAGACTTTGCAGTATGCCCGTGCTTTGATTGACgtaagtccgt ... gttatgccagTGTTGTACAGCAAATCCTGATGGCCGCAAGAGAGCTTTGGTTGTCGGTGGA
EST: gi|162235867|gb|FC412418.1|FC412418
EST:     GAGCTCCAAATGAAGAAGAGACTTTGCAGTATGCCCGTGCTTTGATTGAC                         TGTTGTACAGCAAATCCTGATGGCCGCAAGAGAGCTTTGGTTGTCGGTGGA
genomic: GAGCTCCAAATGAAGAAGAGACTTTGCAGTATGCCCGTGCTTTGATTGACgtaagtccgt ... gttatgccagTGTTGTACAGCAAATCCTGATGGCCGCAAGAGAGCTTTGGTTGTCGGTGGA
EST: gi|18336575|gb|BJ168597.1|BJ168597
EST:     GAGCTCCAAATGAAGAAGAGACTTTGCAGTATGCCCGTGCTTTGATTGAC                         TGTTGTACAGCAAATCCTGATGGCCGCAAGAGAGCTTTGGTTGTCGGTGGA
genomic: GAGCTCCAAATGAAGAAGAGACTTTGCAGTATGCCCGTGCTTTGATTGACgtaagtccgt ... gttatgccagTGTTGTACAGCAAATCCTGATGGCCGCAAGAGAGCTTTGGTTGTCGGTGGA
EST: gi|208364467|gb|DC958036.1|DC958036
EST:     GAGCTCCAAATGAAGAAGAGACTTTGCAGTATGCCCGTGCTTTGATTGAC                         TGTTGTACAGCAAATCCTGATGGCCGCAAGAGAGCTTTGGTTGTCGGTGGA
genomic: GAGCTCCAAATGAAGAAGAGACTTTGCAGTATGCCCGTGCTTTGATTGACgtaagtccgt ... gttatgccagTGTTGTACAGCAAATCCTGATGGCCGCAAGAGAGCTTTGGTTGTCGGTGGA
EST: gi|37846736|gb|BJ604744.1|BJ604744
EST:     GAGCTCCAAATGAAGAAGAGACTTTGCAGTATGCCCGTGCTTTGATTGAC                         TGTTGTACAGCAAATCCTGATGGCCGCAAGAGAGCTTTGGTTGTCGGTGGA
genomic: GAGCTCCAAATGAAGAAGAGACTTTGCAGTATGCCCGTGCTTTGATTGACgtaagtccgt ... gttatgccagTGTTGTACAGCAAATCCTGATGGCCGCAAGAGAGCTTTGGTTGTCGGTGGA
EST: gi|22492495|gb|BU052418.1|BU052418
EST:     GAGCTCCAAATGAAGAAGAGACTTTGCAGTATGCCCGTGCTTTGATTGAC                         TGTTGTACAGCAAATCCTGATGGTCGCAAGAGAGCTTTGGTTGTCGGTGGA
genomic: GAGCTCCAAATGAAGAAGAGACTTTGCAGTATGCCCGTGCTTTGATTGACgtaagtccgt ... gttatgccagTGTTGTACAGCAAATCCTGATGGCCGCAAGAGAGCTTTGGTTGTCGGTGGA
EST: gi|37849163|gb|BJ607171.1|BJ607171
EST:     GAGCTCCAAATGAAGAAGAGACTTTGCAGTATGCCCGTGCTTTGATTGAC                         TGTTGTACAGCAAATCCTGATGGCCGCAAGAGAGCTTTGGTTGTCGGTGGA
genomic: GAGCTCCAAATGAAGAAGAGACTTTGCAGTATGCCCGTGCTTTGATTGACgtaagtccgt ... gttatgccagTGTTGTACAGCAAATCCTGATGGCCGCAAGAGAGCTTTGGTTGTCGGTGGA
EST: gi|37841322|gb|BJ599330.1|BJ599330
EST:     GAGCTCCAAATGAAGAAGAGACTTTGCAGTATGCCCGTGCTTTGATTGAC                         TGTTGTACAGCAAATCCTGATGGCCGCAAGAGAGCTTTGGTTGTCGGTGGA
genomic: GAGCTCCAAATGAAGAAGAGACTTTGCAGTATGCCCGTGCTTTGATTGACgtaagtccgt ... gttatgccagTGTTGTACAGCAAATCCTGATGGCCGCAAGAGAGCTTTGGTTGTCGGTGGA
EST: gi|67697641|gb|BJ957874.1|BJ957874
EST:     GAGCTCCAAATGAAGAAGAGACTTTGCAGTATGCCCGTGCTTTGATTGAC                         TGTTGTACAGCAAATCCTGATGGCCGCAAGAGAGCTTTGGTTGTCGGTGGA
genomic: GAGCTCCAAATGAAGAAGAGACTTTGCAGTATGCCCGTGCTTTGATTGACgtaagtccgt ... gttatgccagTGTTGTACAGCAAATCCTGATGGCCGCAAGAGAGCTTTGGTTGTCGGTGGA
EST: gi|22132424|gb|BQ827155.1|BQ827155
EST:     GAGCTCCAAATGAAGAAGAGACTTTGCAGTATGCCCGTGCTTTGATTGAC                         TGTTGTACAGCAAATCCTGATGGCCGCAAGAGAGCTTTGGTTGTCGGTGGA
genomic: GAGCTCCAAATGAAGAAGAGACTTTGCAGTATGCCCGTGCTTTGATTGACgtaagtccgt ... gttatgccagTGTTGTACAGCAAATCCTGATGGCCGCAAGAGAGCTTTGGTTGTCGGTGGA
EST: gi|208385420|gb|DC956632.1|DC956632
EST:     GAGCTCCAAATGAAGAAGAGACTTTGCAGTGTGCCCGTGCTTTGATTGAC                         TGTTGTACAGCAAATCCTGATGGCCGCAAGAGAGCTTTGGTTGTCGGTGGA
genomic: GAGCTCCAAATGAAGAAGAGACTTTGCAGTATGCCCGTGCTTTGATTGACgtaagtccgt ... gttatgccagTGTTGTACAGCAAATCCTGATGGCCGCAAGAGAGCTTTGGTTGTCGGTGGA
EST: gi|37845681|gb|BJ603689.1|BJ603689
EST:     GAGCTCCAAATGAAGAAGAGACTTTGCAGTATGCCCGTGCTTTGATTGAC                         TGTTGTACAGCAAATCCTGATGGCCGCAAGAGAGCTTTGGTTGTCGGTGGA
genomic: GAGCTCCAAATGAAGAAGAGACTTTGCAGTATGCCCGTGCTTTGATTGACgtaagtccgt ... gttatgccagTGTTGTACAGCAAATCCTGATGGCCGCAAGAGAGCTTTGGTTGTCGGTGGA
EST: gi|162162206|gb|FC337988.1|FC337988
EST:     GAGCTCCAAATGAAGAAGAGACTTTGCAGTATGCCCGTGCTTTGATTGAC                         TGTTGTACAGCAAATCCTGATGGCCGCAAGAGAGCTTTGGTTGTCGGTGGA
genomic: GAGCTCCAAATGAAGAAGAGACTTTGCAGTATGCCCGTGCTTTGATTGACgtaagtccgt ... gttatgccagTGTTGTACAGCAAATCCTGATGGCCGCAAGAGAGCTTTGGTTGTCGGTGGA

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), 34 (downstream exon)
Score: 13

CGGGGATCTTGGTTATGCACACGAGCTTGGCAATTATGCTGAGTACAGTGGAGCTCCAAATGAAGAAGAGACTTTGCAGTATGCCCGTGCTTTGATTGACgtaagtccgt ... gttatgccagTGTTGTACAGCAAATCCTGATGGCCGCAAGAGAGCTTTGGTTGTCGGTGGAGGCATTGCTAACTTCACTGATGTTGCAGCAACTTTCAACGGCATCATTC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gctattacaatagttagatttcagttgctcattatcaacctctttgttatgccagTGTTGTACAGCAAATCCTGATGGCCGCAAGAGAGCTTTGGTTGTCGGTGGAGGCATTGCTAACTTCACTGATGTTGCAGCAACTTTCAACGGCATCATTC
                                      cctctttgtt  CT-rich tract
        aatagtta  TA-rich tract