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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atcggttaattcttgaccggtcctatagtcgtcttcaagaggagtgtctggtttgtgctgacagaagtctgatgtttgtctgtgatgggcggggttctagGAAGGGAGACTACTACCGGTACCTGGCGGAGTTCAAAACTGGGGCTGAGAGAAAAGAAGCTGCTGACCAATCTTTGAAGGCCTACCAG

Basic information

species Physcomitrella patens
transcript PP1S201_25V6.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S201_25V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: LOC_Os01g11110.2 (Oryza sativa), 3'ss of exon 2
atcggttaattcttgaccggtcctatagtcgtcttcaagaggagtgtctggtttgtgctgacagaagtctgatgtttgtctgtgatgggcggggttctagGAAGGGAGACTACTACCGGTACCTGGCGGAGTTCAAAACTGGGGCTGAGAGAAAAGAAGCTGCTGACCAATCTTTGAAGGCCTACCAG
      | |  || |      ||| |  |  |  |    |   |||| ||| || |  || | ||      |||  |  |||            || |||||||||||| |||||||||||||| || |||||||| |||||| ||||||  |  ||||   |||| |  ||  | || || ||  ||
-----gtgacgct-gctttaccctttgttaattcttgttaaatgtgtttggattat--tgtctga---tcaatgcattcctg-----------attttagGAAGGGAGATTACTACCGGTACCTTGCAGAGTTCAAGACTGGGACTGAGAAGATTGAAGTGTCTGAACTGTCACTCAATGCTTATGAG

upper sequence: PP1S201_25V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GLYMA08G12220.5 (Glycine max), 3'ss of exon 2
atcggttaattcttgaccggtcctatagtcgtcttcaagaggagtgtctgg---tttgtgctg---acagaagtctgatgtttgtctgtgatgggcgg--ggttctagGAAGGGAGACTACTACCGGTACCTGGCGGAGTTCAAAACTGGGGCTGAGAGAAAAGAAGCTGCTGACCAATCTTTGAAGGCCTACCAG
    || | | ||   | | ||  ||  | ||  |  || || |  | | |   || ||  ||          | | |  |  | || || |||  ||  ||||  |||||||| ||||| ||||||||||| |||||||||||  | || | |||||||||||| |||||||| || ||  ||||||| || |||
----gtgagtgctgctcagttctcatttttgttcttcagtggggaatttagactttcgttttgtgtgtgttgatttaaattaagcctttgttggttggttggttgcagGAAGGGGGACTATTACCGGTACCTCGCGGAGTTCAAGTCCGGTGATGAGAGAAAAGAGGCTGCTGATCATTCCATGAAGGCGTATCAG

upper sequence: PP1S201_25V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GLYMA05G29080.2 (Glycine max), 3'ss of exon 2
atcggttaattcttgaccggtcctatagtcgtcttcaagaggagtgtctggtttgtgctgacagaagtctgatgtttgtctgtgatgggcggggttctagGAAGGGAGACTACTACCGGTACCTGGCGGAGTTCAAAACTGGGGCTGAGAGAAAAGAAGCTGCTGACCAATCTTTGAAGGCCTACCAG
    || | | ||     |    | |  |  ||||||   ||| | |   |||| ||            ||||    | || || |||      ||  |||||||| ||||| ||||||||||| || ||||||||  | || | |||||||||||| |||||||| || ||  |||| || || |||
----gtgagtgctgagttgtcatttttttgttcttcagtgggaatttagagtttttgtgtgt-------tgattaaagcctttgttgg------ttgcagGAAGGGGGACTATTACCGGTACCTCGCAGAGTTCAAGTCCGGTGATGAGAGAAAAGAGGCTGCTGATCATTCCATGAAAGCGTATCAG

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|162205866|gb|FC381104.1|FC381104
EST:     TTGATTCCTTCGTCCAGCACGGGAGAGTCCACCGTGTTCTACTACAAAAT                         GAAGGGAGACTACTACCGGTACCTGGCGGAGTTCAAAACTGGGGCTGAGAG
genomic: TTGATTCCTTCGTCCAGCACGGGAGAGTCCACCGTGTTCTACTACAAAATgtacggcatg ... ggggttctagGAAGGGAGACTACTACCGGTACCTGGCGGAGTTCAAAACTGGGGCTGAGAG
EST: gi|208397825|gb|DC916160.1|DC916160
EST:     TTGATTCCTTCGTCCAGCACGGGAGAGTCCACCGTGTTCTACTACAAAAT                         GAAGGGAGACTACTACCGGTACCTGGCGGAGTTCAAAACTGGGGCTGAGAG
genomic: TTGATTCCTTCGTCCAGCACGGGAGAGTCCACCGTGTTCTACTACAAAATgtacggcatg ... ggggttctagGAAGGGAGACTACTACCGGTACCTGGCGGAGTTCAAAACTGGGGCTGAGAG
EST: gi|162276326|gb|FC452628.1|FC452628
EST:     TTGATTCCTTCGTCCAGCACGGGAGAGTCCACCGTGTTCTACTACAAAAT                         GAAGGGAGACTACTACCGGTACCTGGCGGAGTTCAAAACTGGGGCTGAGAG
genomic: TTGATTCCTTCGTCCAGCACGGGAGAGTCCACCGTGTTCTACTACAAAATgtacggcatg ... ggggttctagGAAGGGAGACTACTACCGGTACCTGGCGGAGTTCAAAACTGGGGCTGAGAG
EST: gi|208352969|gb|DC913853.1|DC913853
EST:     TTGATTCCTTCGTCCAGCACGGGAGAGTCCACCGTGTTCTACTACAAAAT                         GAAGGGAGACTACTACTGGTACCTGGCGGAGTTCAAAACTGGGGCTGAGAG
genomic: TTGATTCCTTCGTCCAGCACGGGAGAGTCCACCGTGTTCTACTACAAAATgtacggcatg ... ggggttctagGAAGGGAGACTACTACCGGTACCTGGCGGAGTTCAAAACTGGGGCTGAGAG
EST: gi|162228076|gb|FC404644.1|FC404644
EST:     TTGATTCCTTCGTCCAGCACGGGAGAGTCCACCGTGTTCTACTACAAAAT                         GAAGGGAGACTACTACCGGTACCTGGCGGAGTTCAAAACTGGGGCTGAGAG
genomic: TTGATTCCTTCGTCCAGCACGGGAGAGTCCACCGTGTTCTACTACAAAATgtacggcatg ... ggggttctagGAAGGGAGACTACTACCGGTACCTGGCGGAGTTCAAAACTGGGGCTGAGAG
EST: gi|208379881|gb|DC927607.1|DC927607
EST:     TTGATTCCTTCGTCCAGCACGGGAGAGTCCACCGTGTTCTACTACAAAAT                         GAAGGGAGACTACTACTGGTACCTGGCGGAGTTCAAAACTGGGGCTGAGAG
genomic: TTGATTCCTTCGTCCAGCACGGGAGAGTCCACCGTGTTCTACTACAAAATgtacggcatg ... ggggttctagGAAGGGAGACTACTACCGGTACCTGGCGGAGTTCAAAACTGGGGCTGAGAG
EST: gi|208396625|gb|DC924293.1|DC924293
EST:     TTGATTCCNTCGTCCAGCACGGGAGAGTCCACCGTGTTATANTACAAAAT                         GAAGGGAGACTACTACCGGTACCTGGCGGAGTTCAAAACTGGGGCTGAGAG
genomic: TTGATTCCTTCGTCCAGCACGGGAGAGTCCACCGTGTTCTACTACAAAATgtacggcatg ... ggggttctagGAAGGGAGACTACTACCGGTACCTGGCGGAGTTCAAAACTGGGGCTGAGAG
EST: gi|162252871|gb|FC429244.1|FC429244
EST:     TTGATTCCTTCGTCCAGCACGGGAGAGTCCACCGTGTTCTACTACAAAAT                         GAAGGGAGACTACTACCGGTACCTGGCGGAGTTCAAAACTGGGGCTGAGAG
genomic: TTGATTCCTTCGTCCAGCACGGGAGAGTCCACCGTGTTCTACTACAAAATgtacggcatg ... ggggttctagGAAGGGAGACTACTACCGGTACCTGGCGGAGTTCAAAACTGGGGCTGAGAG
EST: gi|67694367|gb|BJ954600.1|BJ954600
EST:     TTGATTCCTTCGTCCAGCACGGGAGAGTCCACCGTGTTCTACTACAAAAT                         GAAGGGAGACTACTACCGGTACCTGGCGGAGTTCAAAACTGGGGCTGAGAG
genomic: TTGATTCCTTCGTCCAGCACGGGAGAGTCCACCGTGTTCTACTACAAAATgtacggcatg ... ggggttctagGAAGGGAGACTACTACCGGTACCTGGCGGAGTTCAAAACTGGGGCTGAGAG
EST: gi|208365604|gb|DC944102.1|DC944102
EST:     TTGATTCCTTCGTCCAGCACGGGAGAGTCCACCGTGTTCTACTACAAAAT                         GAAGGGAGACTACTACCGGTACCTGGCGGAGTTCAAAACTGGGGCTGAGAG
genomic: TTGATTCCTTCGTCCAGCACGGGAGAGTCCACCGTGTTCTACTACAAAATgtacggcatg ... ggggttctagGAAGGGAGACTACTACCGGTACCTGGCGGAGTTCAAAACTGGGGCTGAGAG
EST: gi|208348120|gb|DC916930.1|DC916930
EST:     TTGATTCCTTCGTCCAGCACGGGAGAGTCCACCGTGTTCTACTACAAAAT                         GAAGGGAGACTACTACCGGTACCTGGCGGAGTTCAAAACTGGGGCTGAGAG
genomic: TTGATTCCTTCGTCCAGCACGGGAGAGTCCACCGTGTTCTACTACAAAATgtacggcatg ... ggggttctagGAAGGGAGACTACTACCGGTACCTGGCGGAGTTCAAAACTGGGGCTGAGAG
EST: gi|162228075|gb|FC404643.1|FC404643
EST:     TTGATTCCTTCGTCCAGCACGGGAGAGTCCACCGTGTTCTACTACAAAAT                         GAAGGGAGACTACTACCGGTACCTGGCGGAGTTCAAAACTGGGGCTGAGAG
genomic: TTGATTCCTTCGTCCAGCACGGGAGAGTCCACCGTGTTCTACTACAAAATgtacggcatg ... ggggttctagGAAGGGAGACTACTACCGGTACCTGGCGGAGTTCAAAACTGGGGCTGAGAG
EST: gi|208376281|gb|DC940979.1|DC940979
EST:     TTGATTCCTTCGTCCAGCACGGGAGAGTCCACCGTGTTCTACTACAAAAT                         GAAGGGAGACTACTACCGGTACCTGGCGGAGTTCAAAACTGGGGCTGAGAG
genomic: TTGATTCCTTCGTCCAGCACGGGAGAGTCCACCGTGTTCTACTACAAAATgtacggcatg ... ggggttctagGAAGGGAGACTACTACCGGTACCTGGCGGAGTTCAAAACTGGGGCTGAGAG
EST: gi|100376622|gb|BY986255.1|BY986255
EST:     TTGATTCCTTCGTCCAGCACGGGAGAGTCCACCGTGTTCTACTACAAAAT                         GAAGGGAGACTACTACCGGTACCTGGCGGAGTTCAAAACTGGGGCTGAGAG
genomic: TTGATTCCTTCGTCCAGCACGGGAGAGTCCACCGTGTTCTACTACAAAATgtacggcatg ... ggggttctagGAAGGGAGACTACTACCGGTACCTGGCGGAGTTCAAAACTGGGGCTGAGAG
EST: gi|67694695|gb|BJ954928.1|BJ954928
EST:     TTGATTCCTTCGTCCAGCACGGGAGAGTCCACCGTGTTCTACTACAAAAT                         GAAGGGAGACTACTACCGGTACCTGGCGGAGTTCAAAACTGGGGCTGAGAG
genomic: TTGATTCCTTCGTCCAGCACGGGAGAGTCCACCGTGTTCTACTACAAAATgtacggcatg ... ggggttctagGAAGGGAGACTACTACCGGTACCTGGCGGAGTTCAAAACTGGGGCTGAGAG

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: 45

AGGAGCTGTCGAAGATCTGCAATGACATACTGTCGATCATTGATGGGCATTTGATTCCTTCGTCCAGCACGGGAGAGTCCACCGTGTTCTACTACAAAATgtacggcatg ... ggggttctagGAAGGGAGACTACTACCGGTACCTGGCGGAGTTCAAAACTGGGGCTGAGAGAAAAGAAGCTGCTGACCAATCTTTGAAGGCCTACCAG




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Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atcggttaattcttgaccggtcctatagtcgtcttcaagaggagtgtctggtttgtgctgacagaagtctgatgtttgtctgtgatgggcggggttctagGAAGGGAGACTACTACCGGTACCTGGCGGAGTTCAAAACTGGGGCTGAGAGAAAAGAAGCTGCTGACCAATCTTTGAAGGCCTACCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG